ecocyc_rxns_and_comments_of_gene = {'B0173' : {'ecocyc-rxns': {"""DXPREDISOM-RXN""": """2-C-methyl-D-erythritol-4-phosphate + NADP+ = 1-deoxy-D-xylulose 5-phosphate + NADPH""",},'ucsd-rxns' : ['DXPRIi',], 'protein-comments' : ["""(DXP reductoisomerase is a Dxr homodimer |CITS: [11872159], [12621040]|; it is a class B dehydrogenase
|CITS: [10631325]| that catalyzes the conversion of 1-deoxy-D-xylulose
5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate (MEP), and this reaction is found to be NADPH
dependent and divalent cation (Mn2+, Co2+, or Mg2+) dependent
|CITS: [9707569]|. The enzyme does not efficiently utilize NADH in place of NADPH |CITS: [9707569]|.
Dxr is an essential protein that acts in the mevalonate-independent pathway of isopentenyl diphosphate biosynthesis
|CITS: [9707569], [10361694]|. As DXP is an intermediate in the biosynthesis of isopentenyl diphosphate (IPP),
thiamine and pyridoxal, synthesis of MEP is the committed step in IPP formation. Overproduction affects flux through
the pathway under some circumstances |CITS: [11180061]|.
The reaction stereospecificity is examined |CITS: [10631325]|.
The reaction occurs in two steps. The first step is an NADPH-dependent rearrangement (without reduction) that
generates 2-C-methyl-d-erythrose 4-phosphate, and the second step is an NADPH-dependent, divalent
cation-dependent reduction of this intermediate |CITS: [12230556]|. The reaction is reversible in vitro, but in vivo
the reaction is driven unidirectionally by equilibrium |CITS: [12230556]|.
A crystal structure of the enzyme bound to a sulfate ion and NADPH is presented at 2.2 angstroms resolution
|CITS: [11872159]|. The implications of the structure are discussed with respect to substrate binding, substrate
specificity, and catalysis |CITS: [11872159]|. A crystal structure of the enzyme bound to a manganese ion and to the
inhibitor fosmidomycin, which is an antimalarial drug, is presented at 2.5 angstroms resolution |CITS: [12621040]|.
The implications of this structure are discussed with respect to catalytic mechanism |CITS: [12621040]|. Residues
involved in 1-deoxy-d-xylulose 5-phosphate (DXP) binding and catalysis have been mutated and a kinetic
characterization of these mutant proteins is presented |CITS: [10787409]|.
Mutants lacking dxr exhibit 2-C-methylerythritol auxotrophy |CITS: [9707569], [10361694]|. Production of
Arabidopsis thaliana DXR functionally complements phenotypes of an E. coli mutant |CITS: [12177470]|. A dxr mutant shows a defect in activation of human Vgamma9/Vdelta2 T lymphocytes |CITS: [11238603]|. Residues involved in 1-deoxy-d-xylulose 5-phosphate (DXP) binding and catalysis have been mutated and a kinetic characterization of these mutant proteins is presented |CITS: [10787409]|.
Overproduction and purification of Dxr is described |CITS: [9707569]|. A tagged Dxr protein has been generated and
purified |CITS: [10787409], [11701035]|.)""","""NIL""",]},
'B3610' : {'ecocyc-rxns': {},'ucsd-rxns' : ['RNDR2b','RNDR3b','RNDR1b','GRXR','PAPSR2','RNDR4b',], 'protein-comments' : ["""(There at least three glutaredoxins in E. coli. Glutaredoxin
3 is able to function as a disulfide reductase, but not as well as
glutaredoxin 1. Coupled with cellular glutathione it may be the third
hydrogen donor system in the absence of thioredoxin and glutaredoxin
1. Under normal conditions it is likely that glutaredoxin has other
functions. |CITS: [95024051] [96215095]|)""","""NIL""",]},
'B1469' : {'ecocyc-rxns': {"""TRANS-RXN-26""": """H+[periplasmic space] + nitrite[cytosol] =H+[cytosol] + nitrite[periplasmic space] """,},'ucsd-rxns' : ['NO3t7pp',], 'protein-comments' : ["""(NarU is a probable nitrite extrusion protein. NarU is a member of
the major facilitator superfamily (MFS) of transporters |CITS: [93040298]|,
and is highly similar to the nitrite extrusion protein, NarK, which is
involved in anaerobic nitrate respiration |CITS: [95020592]|. The cloned
narU gene was shown to be able to complement a narK mutation
based on assays of nitrite concentrations in the external medium
|CITS: [97189586]|. NarU probably functions as a nitrite/proton antiporter.
Membrane topology predictions using experimentally determined C terminus
locations indicate that NarU has 12 transmembrane helices and the C-terminus is
located in the cytoplasm |CITS:[15044727]|.)""",]},
'B3958' : {'ecocyc-rxns': {"""N-ACETYLGLUTPREDUCT-RXN""": """N-acetyl-L-glutamate 5-semialdehyde + NADP+ + phosphate = N-acetylglutamyl-phosphate + NADPH""",},'ucsd-rxns' : ['AGPR',], 'protein-comments' : ["""NIL""",]},
'B3617' : {'ecocyc-rxns': {"""AKBLIG-RXN""": """glycine + acetyl-CoA = 2-amino-3-oxobutanoate + coenzyme A""",},'ucsd-rxns' : ['GLYAT',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B3946' : {'ecocyc-rxns': {"""RXN0-313""": """D-fructose-6-phosphate = dihydroxy-acetone + D-glyceraldehyde-3-phosphate""",},'ucsd-rxns' : ['F6PA',], 'protein-comments' : ["""NIL""",]},
'B1896' : {'ecocyc-rxns': {"""TREHALOSE6PSYN-RXN""": """UDP-D-glucose + α-D-glucose-6-phosphate = UDP + trehalose 6-phosphate""",},'ucsd-rxns' : ['TRE6PS',], 'protein-comments' : ["""(Under conditions of high osmolarity, E. coli synthesizes high concentrations of internal trehalose.
Trehalose-6-phosphate synthase catalyzes the first step in that biosynthetic pathway.
|CITS: [93302496][91334986][88227872]|
otsA mutants are viable, but osmotically sensitive in minimal media |CITS: [3131312]| and sensitive to cold
shock |CITS: [12105274]|. Stability of otsBA mRNA is increased approximately 10-fold at 16 degrees C
compared to 37 degrees C |CITS: [12105274]|. Accumulation of trehalose at low temperatures enhances cell viability
|CITS: [12105274]|.
Crystal structures of OtsA have been solved |CITS: [12498887][14570926]|.
otsA: "osmoregulatory trehalose synthesis" |CITS: [3131312]|
Review: |CITS: [12626396]|)""",]},
'B0509' : {'ecocyc-rxns': {"""TSA-REDUCT-RXN""": """glycerate + NAD(P)+ = tartronate semialdehyde + NAD(P)H + H+""",},'ucsd-rxns' : ['TRSARr',], 'protein-comments' : ["""NIL""",]},
'B1622' : {'ecocyc-rxns': {"""CYSTATHIONINE-BETA-LYASE-RXN""": """cystathionine + H2O = pyruvate + ammonia + L-homocysteine""",},'ucsd-rxns' : ['CYSTL',], 'protein-comments' : ["""(MalY is a bifunctional protein with a regulatory |CITS: [1856179]| as well as an enzymatic |CITS: [7665481]| function.
MalY acts as a negative regulator of the maltose regulon. MalY interacts directly with the MalT transcriptional
activator, competing with the inducer maltotriose |CITS: [10698925][10692154]|.)""",]},
'B1623' : {'ecocyc-rxns': {"""ADDALT-RXN""": """ammonia + deoxyinosine = H2O + deoxyadenosine""","""ADENODEAMIN-RXN""": """H2O + adenosine = ammonia + inosine""",},'ucsd-rxns' : ['ADA','DADA',], 'protein-comments' : ["""NIL""",]},
'B0505' : {'ecocyc-rxns': {"""UREIDOGLYCOLATE-HYDROLASE-RXN""": """H2O + (S)-ureidoglycolate = CO2 + 2 ammonia + glyoxylate""",},'ucsd-rxns' : ['UGLYCH',], 'protein-comments' : ["""NIL""",]},
'B1781' : {'ecocyc-rxns': {"""RXN0-4281""": """methylglyoxal + NADPH -> acetol + NADP+""",},'ucsd-rxns' : ['ALR2',], 'protein-comments' : ["""(YeaE has been shown to have methylglyoxal reductase activity. Growth of a yeaE gloA double mutant is
inhibited by 0.3 mM methylglyoxal |CITS: [16077126]|.
Expression of yeaE is not increased in response to methylglyoxal |CITS: [16077126]|.
)""",]},
'B2277' : {'ecocyc-rxns': {"""NADH-DEHYDROG-A-RXN""": """ubiquinone-8 + NADH = ubiquinol-8 + NAD+""",},'ucsd-rxns' : ['NADH17pp','NADH18pp','NADH16pp',], 'protein-comments' : ["""(This subunit may function in proton translocation.
|CITS: [98256007]|
NuoM is part of the inner membrane component of NADH dehydrogenase I |CITS: [7607227]| and
contains the ubiquinone binding site |CITS: [12730198]|.)""","""(There is a cluster of 13 genes that code for NADH dehydrogenase I. Six of the subunits are peripheral proteins and
the other seven are very hydrophobic |CITS: [94178656] [98256007]|. Three-dimensional reconstruction of the
complex based on cryo-electron microscopy showed an L-shaped form with an integral membrane and a peripheral
arm |CITS: [9514725]|. A model of the spatial arrangement of the subunits and the possible functional mechanism of
proton pumping has been proposed |CITS: [12923180]|.)""",]},
'B2200' : {'ecocyc-rxns': {"""TRANS-RXN0-162""": """protoheme IX[cytosol] + ATP + H2O =phosphate + ADP + protoheme IX[periplasmic space] """,},'ucsd-rxns' : ['PHEMEabcpp',], 'protein-comments' : ["""(ccmA is a member of an operon whose gene products (CcmA-H) have been shown to be cytoplasmic membrane proteins required for cytochrome c maturation |CITS:[7635817]|. Sequence similarity and the presence of an ATP-binding motif indicate that CcmA is an ATP-binding member of the ATP-binding cassette (ABC) transporter family |CITS:[10339610]| and is thought to form an ABC transporter CcmAB. The substrate for the putative ABC transporter, CcmAB, is unknown. Heme transport across the cytoplasmic membrane has been shown to occur in the absence of ATP |CITS:[10708391]| and deletion mutation studies suggest that heme transport into the periplasm occurs independently of the putative CcmAB transporter |CITS:[10339610]|.)""","""(The CcmABC (Cytochrome C Maturation proteins) putative transporter is a member of the ATP-Binding
Cassette (ABC) transporter superfamily |CITS: [98254124]|. Sequence analysis suggest that CcmA is the
ATP binding subunit and occurs as a homodimer and CcmB and CcmC are transmembrane domains.
CcmABC has been proposed to function as a heme exporter, which exports heme to the periplasm where it
is incorporated into cytochrome c apoproteins |CITS: [97438699]|. However, CcmC has been shown
to function independently and is essential for heme attachment to CcmE, a periplasmic heme chaperone,
that binds heme covalently in the periplasm and then acts as a heme donor for ligation to apocytochrome
c |CITS:[99272716]|. Analysis of a ccmA deletion mutant has suggested that CcmAB is not
essential for heme export |CITS: [20170685]|.)""","""(Type c cytochrome in Escherichia coli is only synthesized during anaerobic growth conditions |CITS:[8039676]|. CcmA-H in E. coli are cytoplasmic membrane proteins which together make up a type 1 cytochrome c biogenesis system |CITS:[7635817]|. All eight proteins have been shown to be required for cytochrome c maturation |CITS:[8830238]|, |CITS:[7635817]|. In cytochrome c biogenesis, apocytochrome c, is translocated across the cytoplasmic membrane into the periplasm through the sec secretion system |CITS:[9720859]| where it complexes with heme, also transported across the cytoplasmic membrane. While CcmA and CcmB have been shown to constitute an ABC transporter, and are required for proper cytochrome c maturation, they have not been shown to be required for heme transport |CITS:[10708391]|. An intramolecular disulfide bond in the apocyctochrome c must be reduced in order for the covalent attachment of heme cofactor to occur. CcmG and CcmH have been identified as having the characteristic C-X-X-C motif of oxidoreductases and to function in the redox pathway of cytochrome c maturation |CITS:[10841975]|, |CITS:[9914305]|. CcmE acts as a periplasmic heme chaperone, binding heme covalently and transferring it to apocytochrome c |CITS:[10339610]|. Heme binding to CcmE is dependent on the presence of CcmC while the small integral membrane protein CcmD has been shown to play a role in CcmE stabilization |CITS:[10339610]|. Results of mutation deletion studies suggest that a periplasmically-situated hydrophobic surface of CcmC binds heme and presents it to CcmE in the periplasm |CITS:[10998170]|. Studies of ccmD deletion mutants have shown that CcmD affects the level of CcmE in the cytoplasmic membrane and is critical for CcmE function |CITS:[10998170]|. Deletion mutation and immunoprecipitation studies suggest that CcmE shuttles between CcmC and CcmF for heme transfer to apocytochrome c |CITS:[14532274]|.)""",]},
'B2232' : {'ecocyc-rxns': {"""2-OCTAPRENYL-6-OHPHENOL-METHY-RXN""": """2-octaprenyl-6-hydroxyphenol + S-adenosyl-L-methionine = 2-octaprenyl-6-methoxyphenol + S-adenosyl-L-homocysteine""","""DHHB-METHYLTRANSFER-RXN""": """3-demethylubiquinone-8 + S-adenosyl-L-methionine = ubiquinone-8 + S-adenosyl-L-homocysteine""",},'ucsd-rxns' : ['OHPHM','DMQMT',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B3945' : {'ecocyc-rxns': {"""AMINOPROPDEHYDROG-RXN""": """1-amino-propan-2-ol + NAD+ = aminoacetone + NADH""","""GLYCDEH-RXN""": """NAD+ + glycerol = NADH + dihydroxy-acetone""",},'ucsd-rxns' : ['GLYCDx','LALDO2x','ALR4x',], 'protein-comments' : ["""NIL""","""(The enzyme is found in two catalytically active forms, a
large form of eight subunits and a small form of two subunits. The
large form appears to be the major species. |CITS: [80049495][84090261][84135662]|)""",]},
'B4311' : {'ecocyc-rxns': {"""RXN0-0""": """N-acetylneuraminate[extracellular space] =N-acetylneuraminate[periplasmic space] """,},'ucsd-rxns' : ['ACNAMtex',], 'protein-comments' : ["""(Sequence similarity suggests that NanC is a member of the OmpG Porin (OmpG)
family. |CITS: [12192075]| nanC (yjhA) is the first gene in the yjhATS operon. Transporter
assays using purified NanC reconstituted into liposomes show NanC is
a volatage-dependent outer membrane-specific channel of the KdgM family that transports
N-acetylneuraminic acid (Neu5Ac). Mutations studies show that NanC is necessary for growth on
Neu5Ac as a carbon source when OmpF and OmpC are absent. Expression of nanC is induced by
Neu5Ac and is modulated by N-acetylglucosamine. Regulators of nanC expression include NanR,
NagC, cAMP/CAP, OmpR, and CpxR. |CITS:[15743943]|.)""",]},
'B4227' : {'ecocyc-rxns': {},'ucsd-rxns' : ['RIBabcpp',], 'protein-comments' : ["""(periplasmic binding component of ABC transporter
YtfQ is upregulated under glucose-limited fed-batch conditions |CITS: [16180237]|.)""","""(YtfR, YtfS, YjfF, YtfT, and YtfQ are uncharacterized members
of the ABC superfamily of transporters |CITS: [99091701]|.
YtfR and YtfS are the putative ATP-binding components.
YjfF and YtfT are the putative membrane components.
YtfQ is the putative binding protein. Based on sequence
similarity they probably function together as an ATP-dependant
sugar transporter. The genes ytfR, ytfS, yjfF,
ytfT, and ytfQ probably constitute a single operon.)""",]},
'B1262' : {'ecocyc-rxns': {"""IGPSYN-RXN""": """1-(o-carboxyphenylamino)-1'-deoxyribulose-5'-phosphate -> indole-3-glycerol-phosphate + CO2 + H2O""","""PRAISOM-RXN""": """N-(5'-phosphoribosyl)-anthranilate -> 1-(o-carboxyphenylamino)-1'-deoxyribulose-5'-phosphate""",},'ucsd-rxns' : ['PRAIi','IGPS',], 'protein-comments' : ["""(The trpC gene encodes a monomeric bifunctional enzyme which catalyzes two sequential reactions in the tryptophan
biosynthesis pathway: the Amadori rearrangement of phosphoribosylanthranilate (PRA) to
carboxyphenylaminodeoxyribulosephosphate (CdRP) is catalyzed by the phosphoribosylanthranilate isomerase
domain, and the ring closure of CdRP to indole-3-glycerol phosphate (InGP) by the indole-3-glycerol phosphate
synthase domain |CITS:[Febslett14887-90]|.
Genetic and biochemical evidence indicates that the InGP synthase reaction is catalyzed by the amino terminal
portion of the bifunctional polypeptide, while the carboxyl terminal region is primarily responsible for the PRA
isomerase reaction |CITS:[89171311]|. The crystal structure of the enzyme shows that the two activities reside on
two well-separated domains. Each domain has the folding pattern of an 8-fold parallel beta-alpha barrel |CITS:[89171311]|.
The two active sites face away from each other, which seems to rule out direct transfer of CdRP.
The N-terminal IGP synthase domain alone is quite unstable; the advantage of gene fusion may be mutually
stabilizing interactions between the two functional domains |CITS:[7014916][87289670]|.
In other organisms, for example Acinetobacter calcoaceticus, two distinct proteins catalyze these two
activities. In those organisms, the gene encoding the
phosphoribosylanthranilate isomerase enzyme is designated trpF |CITS: [2299982]|.
TrpC is unique among the five enzymes in the tryptophan biosynthesis pathway in E. coli in that
it is not part of a multisubunit enzyme complex |CITS:[81119811]|.
)""",]},
'B2587' : {'ecocyc-rxns': {"""TRANS-RXN-23""": """H+[periplasmic space] + α-ketoglutarate[periplasmic space] =H+[cytosol] + α-ketoglutarate[cytosol] """,},'ucsd-rxns' : ['AKGt2rpp',], 'protein-comments' : ["""(KgtP is a proton-driven transporter for α-ketoglutarate. kgtP
mutants show greatly impaired growth on α-ketoglutarate which
can be complemented by the cloned kgtP gene |CITS: [91219460]|.
KgtP-dependent α-ketogluterate/proton symport activity has been
demonstrated in membrane vesicles |CITS: [92210624]|.
KgtP displays a Km for α-ketoglutarate of 13-46 μM. KgtP-mediated
α-ketoglutarate transport could be partially inhibited by fumarate,
malate and succinate |CITS: [92210624]|.
Consistent with its function as an α-ketoglutarate/proton symport,
KgtP is a member of the major facilitator superfamily |CITS: [93040298]|.
Alkaline phosphatase fusions have demonstrated that KgtP consists
of twelve transmembrane spanning segments |CITS: [93123179]|.
Arg-92 and Asp-88 have been shown to be essential residues in the
KgtP transporter |CITS: [92207981]|.
kgtP appears to be constitutively expressed |CITS: [92210624]|.)""",]},
'B1991' : {'ecocyc-rxns': {"""DMBPPRIBOSYLTRANS-RXN""": """nicotinate nucleotide + dimethylbenzimidazole = nicotinate + α-ribazole-5'-P""",},'ucsd-rxns' : ['NNDMBRT',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B3918' : {'ecocyc-rxns': {"""CDPDIGLYPYPHOSPHA-RXN""": """a CDP-diacylglycerol + H2O = CMP + an L-phosphatidate""",},'ucsd-rxns' : ['CDAPPA120','CDAPPA141','CDAPPA140','CDAPPA161','CDAPPA160','CDAPPA181','CDAPPA180',], 'protein-comments' : ["""NIL""",]},
'B2204' : {'ecocyc-rxns': {"""RXN0-2081""": """ubiquinol-10 + NO3- = ubiquinone-10 + nitrite + H2O""",},'ucsd-rxns' : ['NO3R1bpp',], 'protein-comments' : ["""(The napH gene encodes a non-haem iron-sulfur protein. |CITS: [96439840] [96228696] [97078524]|
NapH together with NapG is required for electron transfer from ubiquinol, but not menaquinol, via NapC to the NapAB
complex |CITS: [11967083][14674886]|. NapH is an integral membrane protein with four membrane-spanning
domains; the C-terminal domain with its two predicted [4Fe-4S] clusters is located in the cytoplasm
|CITS: [14674886]|. Using two-hybrid assays, it has been shown that NapH interacts strongly with NapC
|CITS: [14674886]|.)""","""(Both NapG and NapH are required for efficient electron transfer from ubiquinol, but not menaquinol, via NapC to the
NapAB complex. NapGH acts as an alternative quinol dehydrogenase to NapC, which can utilize menaquinol directly
|CITS: [11967083][14674886]|.
No direct evidence for the formation of a NapGH complex has been obtained yet, but the available experimental data
is consistent with its existence |CITS: [14674886]|.)""","""(E. coli contains three nitrate reductases. Two of them, nitrate reductase A (NRA) and nitrate reductase Z
(NRZ), are membrane bound and biochemically similar. The third nitrate reductase, Nap, is located in the periplasm.
It is induced by anaerobiosis through the mediation of the transcription factor Fnr and low concentrations of nitrate
through the mediation of NarP |CITS: [12029041]|. Nap is not itself a coupling site for generating proton motive force;
acting as a terminal electron acceptor, it does support anaerobic respiration of various carbon sources
|CITS: [11844760]|.
The physiological role of Nap is that of mediating anaerobic respiration at the expense of low concentrations of nitrate.
Owing to the periplasmic location of Nap, the cost of pumping nitrate into the cell is avoided. In addition, Nap has a
significantly higher affinity for nitrate than NRA and is thus able to exploit the low concentrations of nitrate occuring in
the natural environment of E. coli |CITS: [10548536]|. Notably, several pathogenic bacterial species, such as
Haemophilus influenzae, only contain orthologs of the periplasmic nitrate reductase |CITS: [10548536]|. During
glucose fermentation in the absence of menaquinone, a very low level of Nap activity appears to substitute for the
redox-balancing role of fumarate reductase, which is dependent on menaquinone |CITS: [14674886]|.
The nap operon encodes seven proteins. The catalytic portion of the protein, consisting of the periplasmic NapA and
NapB polypeptides, receives electrons via the membrane-bound cytochrome NapC from NapGH or directly from the
quinone pool. The NapD polypeptide is required for enzyme activity and is thought to be involved in the
post-translational assembly of the molybdoprotein NapA. NapF, NapG and NapH are predicted to encode
iron-sulfur proteins and are not required for Nap activity; they do, however, contribute to the maximum rate of nitrate
reduction. NapG and NapH facilitate electron transfer from ubiquinol via NapC to NapAB.
|CITS: [14674886] [11967083] [20018017] [97078524] [96228696] [96439840] [94314186]|)""",]},
'B4460' : {'ecocyc-rxns': {"""ABC-2-RXN""": """H2O + α-L-arabinose[periplasmic space] + ATP =α-L-arabinose[cytosol] + phosphate + ADP """,},'ucsd-rxns' : ['ARBabcpp',], 'protein-comments' : ["""NIL""","""(The AraFGH arabinose transporter is a member of the ATP Binding Cassette (ABC) transporter superfamily.
Expression of all three components was necessary to complement high-affinity arabinose transport in an
araFGH knockout strain |CITS: [89255061]| Membrane vesicle studies have shown that there are
two main arabinose uptake systems in E. coli: the low affinity proton-driven AraE transporter and a
high affinity ATP-driven system utilizing AraF as a binding protein |CITS:[82205973]|. The AraF binding
protein has been purified, crystallized and its high resolution structure shown to bind arabinose
|CITS:[78070158]|. Based on sequence similarity, AraH is the membrane component and AraG is the
ATP-binding component of this ABC transporter |CITS: [88062740]|.)""",]},
'B0997' : {'ecocyc-rxns': {"""1.7.2.3-RXN""": """trimethylamine + 2 oxidized cytochrome c + H2O -> trimethylamine-N-oxide + 2 reduced cytochrome c + 2 H+""",},'ucsd-rxns' : ['TMAOR1pp','TMAOR2pp',], 'protein-comments' : ["""(The TorA protein is exported to the periplasm via the twin-arginine transport (TAT) system. A 39 amino acid signal
peptide is cleaved |CITS: [8022286]|.)""","""(There are three to four forms of trimethylamine N-oxide
(TMAO) reductase in E. coli, one is a constitutive form and the
others inducible. TorA and TorC constitute the inducible TMAO reductase I which
can accept electrons from various physiological donors via several
carriers. It acts as a terminal electron acceptor for the respiratory
electron flow under anaerobic conditions. The enzyme contains
molybdenum, iron, zinc and acid-labile sulfur. Ubiquinones may
substitute for menaquinones in TMAO respiration. |CITS: [86304244]
[86049288] [88193091] [90089471]|
There is evidence that the catalytic TorA subunit can exist as both a dimer
and a monomer. |CITS: [88193091] [90089471]|)""",]},
'B3850' : {'ecocyc-rxns': {"""PROTOPORGENOXI-RXN""": """1.5 O2 + protoporphyrinogen IX = 3 H2O + protoporphyrin IX""",},'ucsd-rxns' : ['PPPGO3','PPPGO',], 'protein-comments' : ["""NIL""",]},
'B0854' : {'ecocyc-rxns': {"""ABC-25-RXN""": """ATP + putrescine[periplasmic space] + H2O =ADP + phosphate + putrescine[cytosol] """,},'ucsd-rxns' : ['PTRCabcpp',], 'protein-comments' : ["""NIL""","""(The PotFGHI ATP-dependent putrescine transporter is a member of the ATP Binding Cassette (ABC)
Superfamily of transporters |CITS: [96381453]|. PotFGHI is similar in sequence and subunit composition to
the PotABCD putrescine/spermidine uptake system. Based on sequence similarity, PotG is the ATP-
binding component, PotH and Pot I are the membrane components, and PotF is the periplasmic binding
component of the ABC transporter. The PotF protein possesses a high binding affinity to putrescine
(Kd=2.0 μM) |CITS: [98316327]|. Site-directed mutagenesis have shown that PotF is the
putrescine-binding protein |CITS: [98316327]|, and gel filtration studies have show that in the presence of
1mM magnesium ion and 100mM potassium ion, PotF bound putrescine, but not spermidine, in a 1:1 ratio
|CITS: [93106992]|. A high resolution structure of PotF has been determined by x-ray crystallography
|CITS: [98316327]|. Knockout and complementation studies showed that the expression of all four proteins
was necessary for maximal putrescine transport activity |CITS: [93106992]|.)""",]},
'B2801' : {'ecocyc-rxns': {"""TRANS-RXN-20""": """H+[periplasmic space] + L-fucose[periplasmic space] =H+[cytosol] + L-fucose[cytosol] """,},'ucsd-rxns' : ['FUCtpp',], 'protein-comments' : ["""(FucP is an L-fucose/proton symporter, responsible for the uptake of
L-fucose. L-fucose transport in membrane vesicles is inhibited
by protonophores and ionophores |CITS: [88133900]|. FucP has
been overexpressed to a high level and shown in whole cells
to mediate L-fucose/proton symport |CITS: [94328931]|.
L-galactose and D-arabinose have also been shown to be substrates,
but unlike L-fucose, they do not act as inducers
|CITS: [88133900] [94328931]|.
FucP is a member of the major facilitator superfamily (MFS) of
transporters |CITS: [98190790]|, and analysis of alkaline
phosphatase fusions has indicated that FucP contains twelve
transmembrane segments |CITS:[95302988]|. The fucP gene
forms part of a fucose-inducible operon containing fucI
and fucK, encoding L-fucose isomerase and fuculose
kinase, respectively. Expression of the fucPIK operon is
controlled by the FucR regulator |CITS: [88142551] [90036697]|.
Imported fucose is metabolised to dihydroxyacetone phosphate and
L-lactaldehyde by the action of FucI, FucK and FucA.)""",]},
'B0856' : {'ecocyc-rxns': {"""ABC-25-RXN""": """ATP + putrescine[periplasmic space] + H2O =ADP + phosphate + putrescine[cytosol] """,},'ucsd-rxns' : ['PTRCabcpp',], 'protein-comments' : ["""NIL""","""(The PotFGHI ATP-dependent putrescine transporter is a member of the ATP Binding Cassette (ABC)
Superfamily of transporters |CITS: [96381453]|. PotFGHI is similar in sequence and subunit composition to
the PotABCD putrescine/spermidine uptake system. Based on sequence similarity, PotG is the ATP-
binding component, PotH and Pot I are the membrane components, and PotF is the periplasmic binding
component of the ABC transporter. The PotF protein possesses a high binding affinity to putrescine
(Kd=2.0 μM) |CITS: [98316327]|. Site-directed mutagenesis have shown that PotF is the
putrescine-binding protein |CITS: [98316327]|, and gel filtration studies have show that in the presence of
1mM magnesium ion and 100mM potassium ion, PotF bound putrescine, but not spermidine, in a 1:1 ratio
|CITS: [93106992]|. A high resolution structure of PotF has been determined by x-ray crystallography
|CITS: [98316327]|. Knockout and complementation studies showed that the expression of all four proteins
was necessary for maximal putrescine transport activity |CITS: [93106992]|.)""",]},
'B0996' : {'ecocyc-rxns': {"""1.7.2.3-RXN""": """trimethylamine + 2 oxidized cytochrome c + H2O -> trimethylamine-N-oxide + 2 reduced cytochrome c + 2 H+""",},'ucsd-rxns' : ['TMAOR1pp','TMAOR2pp',], 'protein-comments' : ["""(TorC is a pentahemic c-type cytochrome that is anchored to the inner membrane. |CITS: [20461225] [94293785] [11056172]|
The C-terminal domain of the TorC apoprotein is involved in autoregulation of the tor operon |CITS: [11562502]|.)""","""(There are three to four forms of trimethylamine N-oxide
(TMAO) reductase in E. coli, one is a constitutive form and the
others inducible. TorA and TorC constitute the inducible TMAO reductase I which
can accept electrons from various physiological donors via several
carriers. It acts as a terminal electron acceptor for the respiratory
electron flow under anaerobic conditions. The enzyme contains
molybdenum, iron, zinc and acid-labile sulfur. Ubiquinones may
substitute for menaquinones in TMAO respiration. |CITS: [86304244]
[86049288] [88193091] [90089471]|
There is evidence that the catalytic TorA subunit can exist as both a dimer
and a monomer. |CITS: [88193091] [90089471]|)""",]},
'B3176' : {'ecocyc-rxns': {"""PHOSGLUCOSAMINEMUT-RXN""": """D-glucosamine-6-phosphate = D-glucosamine 1-phosphate""",},'ucsd-rxns' : ['PGAMT',], 'protein-comments' : ["""NIL""",]},
'B1588' : {'ecocyc-rxns': {"""DIMESULFREDUCT-RXN""": """dimethyl sulfoxide + H+ + menaquinol -> dimethylsulfide + H2O + menaquinone-8""",},'ucsd-rxns' : ['TMAOR1','DMSOR1',], 'protein-comments' : ["""(YnfF is highly similar to DmsA, the catalytic subunit of the dimethyl sulfoxide reductase heterotrimer, and
cross-reacts with an anti-DmsA antibody. The protein is poorly expressed. When expressed together with DmsB
and DmsC in a plasmid expression system, YnfF can form a complex with DmsB and DmsC, but the chimeric enzyme
does not support growth on DMSO |CITS: [14522592]|.
Based on sequence similarity, YnfF was predicted to be a trimethylamine-N-oxide reductase (TMAO reductase II)
|CITS: [12952533]|.)""","""(A strain carrying a deletion of dmsABC and containing ynfFGH on a multicopy plasmid is able to grow
poorly under anaerobic conditions utilizing dimethyl sulfoxide as a terminal oxidant. The physiological substrate for
this enzyme is unknown |CITS: [14522592]|.)""",]},
'B2800' : {'ecocyc-rxns': {"""DARABALDOL-RXN""": """D-ribulose-1-phosphate = glycolaldehyde + dihydroxy-acetone-phosphate""","""FUCPALDOL-RXN""": """fuculose-1-phosphate = lactaldehyde + dihydroxy-acetone-phosphate""",},'ucsd-rxns' : ['FCLPA',], 'protein-comments' : ["""NIL""",]},
'B1301' : {'ecocyc-rxns': {"""RXN0-3921""": """γ-glutamyl-L-putrescine + H2O + O2 = γ-glutamyl-γ-aminobutyraldehyde + H2O2 + NH4+""",},'ucsd-rxns' : ['GGPTRCO',], 'protein-comments' : ["""(PuuB is probably the γ-glutamylputrescine oxidase in a putrescine utilization pathway; together with PuuC,
γ-glutamyl-γ-aminobutyrate is produced from γ-glutamylputrescine |CITS: [15590624]|.
The function of genes in the puu gene cluster was initially inferred by similarity with the ipuABCDEGFH
operon in Pseudomonas sp. |CITS: [15590624]|
The puuC, puuB, and puuE genes may form an operon |CITS: [9150200][1840553]|.)""",]},
'B0142' : {'ecocyc-rxns': {"""H2PTERIDINEPYROPHOSPHOKIN-RXN""": """6-hydroxymethyl-dihydropterin + ATP = 2-amino-4-hydroxy-6-hydroxymethyl-7,8-dihydropteridine diphosphate + AMP""",},'ucsd-rxns' : ['HPPK2',], 'protein-comments' : ["""(Reduced folate cofactors are required for the syntheses of various essential cell nutrients. E. coli and other
microorganisms must synthesize folates de novo as they lack the transport pathway to take up folate cofactors.
6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) catalyzes a reaction in the folate biosynthesis pathway.
|CITS: [69130253] [92394901]|
Various crystal and solution structures of HPPK have been solved and have elucidated the reaction mechanism and
kinetics; selected recent publications are |CITS: [14769023][15016362][15018613]|.
HPPK is essential in microorganisms, and the enzyme is not present in mammals; it is therefore a target for the
development of antimicrobial drugs.
)""",]},
'B1852' : {'ecocyc-rxns': {"""GLU6PDEHYDROG-RXN""": """β-D-glucose-6-phosphate + NADP+ = D-glucono-δ-lactone-6-phosphate + NADPH + H+""",},'ucsd-rxns' : ['G6PDH2r',], 'protein-comments' : ["""(A null mutation in the zwf gene encoding glucose 6-phosphate-1-dehydrogenase does not affect the growth rate
significantly. However, cellular metabolism and metabolic flux is changed |CITS: [14661115][15113569]|.
Growth rate-dependent regulation has been described |CITS: [1729252]|.)""",]},
'B1851' : {'ecocyc-rxns': {"""PGLUCONDEHYDRAT-RXN""": """6-phospho-D-gluconate = 2-keto-3-deoxy-6-phospho-gluconate + H2O""",},'ucsd-rxns' : ['EDD',], 'protein-comments' : ["""(There has been little work done on this enzyme in E. coli.)""",]},
'B1919' : {'ecocyc-rxns': {"""DCYSDESULF-RXN""": """D-cysteine + H2O = pyruvate + hydrogen sulfide + ammonia""","""ALADEHYDCHLORO-RXN""": """3-chloro-D-alanine + thioglycolate = S-carboxymethyl-D-cysteine + chloride""",},'ucsd-rxns' : ['CYSDDS',], 'protein-comments' : ["""(D-cysteine desulfhydrase is involved in utilization of D-cysteine as a source of sulfur. The enzyme also protects
the cell from growth inhibition caused by D-cysteine, which interferes with isoleucine, leucine, and valine biosynthesis
via inhibition of threonine deaminase |CITS: [11527960]|. D-cysteine desulfhydrase is also involved in utilization of
D-cysteine as a source of sulfur |CITS: [11527960]|.
A dcyD mutant exhibits decreased resistance to D-cysteine, compared to wild type |CITS: [11527960]|.
Overexpression causes increased resistance to D-cysteine, compared to wild type |CITS: [11527960]|.
DcyD has similarity to 1-aminocyclopropane-carboxylate deaminases, but does not exhibit activity toward this
substrate |CITS: [11527960]|.
Transcription of dcyD is induced under low sulfate conditions |CITS: [11527960]|.)""","""NIL""",]},
'B1857' : {'ecocyc-rxns': {"""ABC-63-RXN""": """Zn2+[periplasmic space] + H2O + ATP =Zn2+[cytosol] + ADP + phosphate """,},'ucsd-rxns' : ['ZNabcpp',], 'protein-comments' : ["""(substrate-binding component of ABC transporter)""","""(ZnuABC is a high-affinity zinc uptake system that is a member
of the ATP Binding Cassette (ABC) Superfamily |CITS: [96381453]|.
znuA encodes the periplasmic zinc-binding component
of the transporter, while znuB encodes the membrane
component, and znuC encodes the ATPase subunit.
Complementation analysis of znu mutants showed that
transport of zinc (II) ion was restored in the presence of
znuABC cloned on a low-copy-number vector |CITS: [98343803]|.
The three components of ZnuABC also show high nucleotide
sequence similarity to the corresponding components of the
AdcABC zinc transporter of S. pneumoniae as well as
subunits of other ABC metal ion transporters. The high-affinity
transport of zinc ion by ZnuABC is inhibited by arsenate,
suggesting that ZnuABC-mediated transport is energized by
ATP hydrolysis |CITS: [98343803]|. Analysis of LacZ fusions indicated that
expression of znuA and znuB was regulated by
the protein Zur, which has amino acid sequence similarity to
the iron regulator Fur |CITS: [98343803]|. znuA and znuBC
are transcribed divergently |CITS: [98343803]|.)""",]},
'B3744' : {'ecocyc-rxns': {"""ASNSYNA-RXN""": """ammonia + L-aspartate + ATP -> L-asparagine + diphosphate + AMP""",},'ucsd-rxns' : ['ASNS2',], 'protein-comments' : ["""(The crystal structure of AsnA has been solved at 2.5 A resolution |CITS: [9437423]|.
Mutational studies in Klebsiella aerogenes show that in the absence of the
glutamine-hydrolyzing asparagine synthetase B enzyme, asparagine synthetase A is not sufficient for growth on poor
nitrogen sources. The asnA asnB double mutant is an asparagine auxotroph |CITS: [6125499]|.
Regulation has been described |CITS: [11814655]|.)""","""NIL""",]},
'B3747' : {'ecocyc-rxns': {"""TRANS-RXN-143""": """K+[periplasmic space] =K+[cytosol] """,},'ucsd-rxns' : ['Kt2pp',], 'protein-comments' : ["""(Kup (TrkD) is involved in potassium ion uptake under hyper-osmotic
stress at a low pH |CITS:[99229748]|. The Kup protein is composed of two
domains--an integral membrane domain that has 12 putative trans-membrane
spanners and a hydrophilic C-terminal domain. Both N and C termini of the
protein are located at the cytoplasmic side of the cell membrane and deletion of
most of the hydrophilic domain reduced, but did not abolish Kup transport activity
|CITS:[94042856]|. Kup has been shown to also transport cations such as Cs+
and Rb+ |CITS:[89197799]|. While it is assumed to be a secondary transporter,
and its uptake is blocked by protonophores such as CCCP, the energy coupling
mechanism has not been defined. Other possible transporters for potassium ion
uptake in E. coli include Kdp and TrkA |CITS:[99229748]|.)""",]},
'B2585' : {'ecocyc-rxns': {"""PHOSPHASERSYN-RXN""": """a CDP-diacylglycerol + L-serine = CMP + an L-1-phosphatidylserine""",},'ucsd-rxns' : ['PSSA120','PSSA181','PSSA180','PSSA141','PSSA140','PSSA161','PSSA160',], 'protein-comments' : ["""NIL""","""(The enzyme is a multimer of unknown subunits. |CITS:
[92356873]|)""",]},
'B1912' : {'ecocyc-rxns': {"""PHOSPHAGLYPSYN-RXN""": """a CDP-diacylglycerol + sn-glycerol-3-phosphate = CMP + an L-1-phosphatidylglycerol-phosphate""",},'ucsd-rxns' : ['PGSA161','PGSA181','PGSA180','PGSA160','PGSA120','PGSA141','PGSA140',], 'protein-comments' : ["""NIL""",]},
'B3748' : {'ecocyc-rxns': {},'ucsd-rxns' : ['RIBabcpp',], 'protein-comments' : ["""(The RbsD protein is required for efficient utilization of ribose when ribose is transported into the cell via a mutated form
of PtsG, the glucose transporter |CITS: [10318813]|. A mutation in rbsD does not abolish ribose transport
|CITS: [10318813]|.
Utilizing NMR techniques, RbsD was shown to catalyze the conversion of the pyran to the furan form of ribose
|CITS: [15060078]|.
)""",]},
'B1859' : {'ecocyc-rxns': {"""ABC-63-RXN""": """Zn2+[periplasmic space] + H2O + ATP =Zn2+[cytosol] + ADP + phosphate """,},'ucsd-rxns' : ['ZNabcpp',], 'protein-comments' : ["""(membrane component of ABC transporter)""","""(ZnuABC is a high-affinity zinc uptake system that is a member
of the ATP Binding Cassette (ABC) Superfamily |CITS: [96381453]|.
znuA encodes the periplasmic zinc-binding component
of the transporter, while znuB encodes the membrane
component, and znuC encodes the ATPase subunit.
Complementation analysis of znu mutants showed that
transport of zinc (II) ion was restored in the presence of
znuABC cloned on a low-copy-number vector |CITS: [98343803]|.
The three components of ZnuABC also show high nucleotide
sequence similarity to the corresponding components of the
AdcABC zinc transporter of S. pneumoniae as well as
subunits of other ABC metal ion transporters. The high-affinity
transport of zinc ion by ZnuABC is inhibited by arsenate,
suggesting that ZnuABC-mediated transport is energized by
ATP hydrolysis |CITS: [98343803]|. Analysis of LacZ fusions indicated that
expression of znuA and znuB was regulated by
the protein Zur, which has amino acid sequence similarity to
the iron regulator Fur |CITS: [98343803]|. znuA and znuBC
are transcribed divergently |CITS: [98343803]|.)""",]},
'B0149' : {'ecocyc-rxns': {"""RXN0-3461""": """EC# 3.4.99.-""","""PEPTIDOGLYCAN-GLYCOSYLTRANSFERASE-RXN""": """N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminoheptane-D-alanyl-D-alanine-diphosphoundecaprenyl-N-acetylglucosamine + [GlcNAc-(14)-Mur2Ac(oyl-L-Ala-g-D-Glu-L-Lys-D-Ala-D-Ala)]n-diphosphoundecaprenol = [GlcNAc-(14)-Mur2Ac(oyl-L-Ala-g-D-Glu-L-Lys-D-Ala-D-Ala)]n+1-diphosphoundecaprenol + undecaprenyl diphosphate""",},'ucsd-rxns' : ['MCTP2App','MCTP1App','MCTP1Bpp','MPTG','MPTG2',], 'protein-comments' : ["""NIL""","""(PBP1B is a
bifunctional, inner membrane enzyme catalyzing the transglycosylation and
transpeptidation of murein (peptidoglycan) precursors in the formation of the
murein sacculus |CITS:[9529891]|.
There are three distinct proteins encoded by
mrcB |CITS:[341159]|. These are α, β, and γ, and each
has both transglycosylation and transpeptidation activities |CITS:[7049165]|.
The major products α and γ are predicted to have a Mr of 94,100 and
88,800 respectively. The γ component is produced by initiation of
translation at the second initiation codon for methionine at amino acid 46 of
the α component |CITS:[3882429][6094972]|. The β component
is the product of the removal of the amino-terminal 24 amino acids from the α
component |CITS:[3542976]|. The α form is required for growth when PBP1A
and PBP3 are inhibited by antibiotics. It has been shown that residues 2-7 and
11-13 are required for proper functioning of the α form, though the
β and γ forms are active without these residues |CITS:[11114917]|.
The transglycosylase domain of PBP1B is located upstream of the transpeptidase
domain. It has been suggested that the protein is the product of a fusion
between a transglycosylase gene and a downstream transpeptidase gene
|CITS:[6389538]|. It has been shown that the region between the transmembrane
segment and the transglycosylase domain has an effect on the activity of the
protein. The conserved SXXK box at ser-510, the SXN box at ser-572, and
the KTG box at lys-698 are necessary for transpeptidase and
penicillin-binding activity. The junction between the transglycosylase and
transpeptidase domains allows for some insertions of amino acids without
affecting activity |CITS:[9244263]|. The carboxy-terminal portion of PBP1B beyond
residue 780 is not necessary for activity |CITS:[2993822]|.
PBP1B has been found to be localized primarily to the inner membrane, but also
to adhesion sites where the inner and outer membranes contact |CITS:[2403537]|.
PBP1B is anchored in the inner membrane by a single hydrophobic segment from
residues 64 to 87 |CITS:[3330753]|. PBP1B has an additional membrane association site
due to hydrophobicity within the region of residues 88 to 250 |CITS:[8645198]|.
When it is cleaved directly c-terminal to the transmembrane segment, the protein
continues to associate with the membrane |CITS:[8449926]|.
PBP1B has been shown to exist as a homodimer, not linked by disulfide bonds,
which is more strongly associated with the peptidoglycan or the outer membrane
than the monomer. The dimer is able to bind penicillin G. The part of the
PBP1B protein necessary for formation of dimer lies in the amino-terminal
portion that contains fewer than 405 amino acids. PBP1B forms homodimers with
respect to the form of the protein (α-α, β-β, or
γ-γ) |CITS:[1885547][10037771]|. PBP1B is more active as a dimer
than when it is measured in its monomeric state |CITS:[16154998]|.
The cytoplasmic domain of
PBP1B is not necessary for dimer formation |CITS:[11114917]|.
Either PBP1B or PBP1A (the other major bifunctional enzyme in murein synthesis
with a different penicillin-binding affinity) is required for cell elongation
because a PBP1B-PBP1A double mutation is lethal |CITS:[1103132][345275][2993822]|.
PBP1B does not form a complex with PBP1A
|CITS:[12057973]|. PBP1B has been found to bind specifically to MipA. It has
also been shown to form a trimeric complex with MipA and MltA (membrane-bound
lytic transglycosylase) though PBP1B doesn't bind MltA alone |CITS:[10037771]|.
Overproduction of inactive forms of PBP1B results in lysis of the cell due
mainly to the action of lytic transglycosylases. It is suggested that this may
be due to the replacement within a murein synthesizing enzyme complex of an
active transglycosylase-transpeptidase with an inactive one, resulting in the
lytic hydrolases making cuts in the murein sacculus without replacement by the
transglycosylase-transpeptidase |CITS:[12949085]|.
Experiments have been performed involving inhibition or mutation of PBP1B alone
or coupled with inhibition or mutation of other proteins involved in cell
division and murein metabolism |CITS:[341159][7007327][2211517][2066344][10383966][12714684]|.)""",]},
'B2615' : {'ecocyc-rxns': {"""NAD-KIN-RXN""": """NAD+ + ATP = NADP+ + ADP""",},'ucsd-rxns' : ['NADK',], 'protein-comments' : ["""(Purifications of native NAD kinase |CITS: [11488932], [3025169]| and overproduced YfjB |CITS: [11488932]| are
described. Two isoforms have been observed |CITS: [10779996]|.
The protein has similarity to the inorganic polyphosphate/ATP-NAD kinase from
Mycobacterium tuberculosis |CITS: [11488932]|. Other, uncharacterized
proteins are identified as likely NAD kinases that show conserved motifs |CITS: [11488932]|.
)""","""NIL""",]},
'B1711' : {'ecocyc-rxns': {"""RXN0-2121""": """cob(I)alamin[extracellular space] =cob(I)alamin[cytosol] ""","""ABC-5-RXN""": """ATP + cob(I)alamin[periplasmic space] + H2O =ADP + phosphate + cob(I)alamin[cytosol] """,},'ucsd-rxns' : ['CBL1abcpp','CBIuabcpp','ADOCBLabcpp',], 'protein-comments' : ["""(BtuC is the integral membrane component of BtuCD, an ABC type vitamin B12 uptake system.
Membrane topology predictions using experimentally determined C terminus
locations indicate that BtuC has 8 transmembrane helices and the C-terminus is
located in the cytoplasm |CITS:[15044727]|.)""","""(BtuCDF is a vitamin B12 transport system that is a member of the ATP-Binding Cassette
(ABC) Superfamily of transporters |CITS: [96381453]|. Based on sequence similarity, BtuD is the ATP-binding
component, BtuC is the integral membrane component, and BtuF is the periplasmic substrate-binding
component of the ABC transporter |CITS: [12475936]| . Transposon insertions in the btuCand regions
conferred a deficiency in vitamin B12 utilization and transport |CITS: [86304183]|. However, there are
indications that BtuE (residing within the operon) is not required for transport. Transposon insertions in btuE were not
complemented by plasmids carrying btuE alone, whereas insertions in btuC and
btuD were effectively complemented by plasmids carrying the corresponding functional gene |CITS: [86304183] [89364713]|.
btuE mutants were also shown to have little effect on vitamin B12 binding and
transport and did not affect the utilization of vitamin B12 or other cobalamins for
methionine biosynthesis |CITS: [89364713]|.
The crystal structure of the Escherichia coli BtuCD protein has been resolved to 3.2 angstrom resolution |CITS:[12004122]|.)""","""NIL""",]},
'B3917' : {'ecocyc-rxns': {"""ABC-7-RXN""": """ATP + thiosulfate[periplasmic space] + H2O =ADP + phosphate + thiosulfate[cytosol] ""","""ABC-70-RXN""": """sulfate[periplasmic space] + H2O + ATP =sulfate[cytosol] + phosphate + ADP """,},'ucsd-rxns' : ['TSULabcpp','SULabcpp',], 'protein-comments' : ["""NIL""","""(CysATWP-Sbp is a sulfate transporter that is a member of the ATP-Binding Cassette (ABC) Superfamily
of transporters |CITS: [96381453]|. Based on sequence similarity, CysA is the ATP-binding component;
CysT and CysW are the membrane components, CysP is the periplasmic thiosulfate-binding component,
and Sbp is the periplasmic sulfate-binding component of the ABC transporter |CITS: [90264334] [95332222]|.
Single cysP and spb insertional mutants are able to utilized both sulfate and thiosulfate as a
sole sulfur source; however, both mutants have impaired growth compared with the wild-type strain,
suggesting that both proteins are required for the normal transport of these ions |CITS: [95332222]|. The
inactivation of both cysP and spb genes blocks the transport of both sulfate and thiosulfate,
and the transport activity is restored by the presence of intact copies of either the cysP or sbp
gene |CITS:[95332222]|. These results indicate that the two binding proteins have partially overlapping
activities, and that a single mutation, inactivating only one of them does not completely inactivate
thiosulfate and sulfate uptake. CysP and Sbp are therefore an example of periplasmic binding proteins
having overlapping activities and interacting with the common membrane proteins, CysATW.)""",]},
'B3583' : {'ecocyc-rxns': {"""RIBULPEPIM-RXN""": """L-ribulose-5-phosphate = D-xylulose-5-phosphate""",},'ucsd-rxns' : ['RBP4E',], 'protein-comments' : ["""NIL""",]},
'B3941' : {'ecocyc-rxns': {"""1.5.1.20-RXN""": """5-methyl-THF + NAD(P)+ = 5,10-methylene-THF + NAD(P)H + H+""",},'ucsd-rxns' : ['MTHFR2',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B3628' : {'ecocyc-rxns': {"""RXN0-5124""": """glucosyl-heptosyl3-KDO2-lipid A-bisphosphate + UDP-galactose = galactosyl-glucosyl-heptosyl3-KDO2-lipid A-bisphosphate + UDP""",},'ucsd-rxns' : ['GALT1',], 'protein-comments' : ["""(The lipopolysaccharide of E. coli K-12 consists of two major components:
the hydrophobic lipid A moiety inserted into the outer membrane and the
phosphorylated core oligosaccharide |CITS:[12045108]|. E. coli K-12
does not produce O antigen to attach to the LPS core due to a defect in the
rfb gene cluster which can be complemented with genes from a second,
independent rfb mutant to produce an O16 type O antigen |CITS:[7517391]|.
E. coli K-12 may have two major pathways for LPS biosynthesis. One
generates LPS cores suitable for O antigen attachment, and a second generates
lipooligosaccharides (LOS) with modifications to the core structure which prevent
O antigen attachment |CITS:[1385388]|.
WaaB attaches galactose to the first glucose (GlcI) of the outer core of LPS |CITS:[1624461]|.
Mutation experiments show WaaB activity is essential for completion of the outer core |CITS:[1624461]|.
Reviews: |CITS:[12045108],[9791168],[7504166]|)""",]},
'B3629' : {'ecocyc-rxns': {"""RXN0-5129""": """a lipopolysaccharide + TDP-rhamnose = rhamnosyl-lipopolysaccharide + dTDP""",},'ucsd-rxns' : ['RHAT1',], 'protein-comments' : ["""(The lipopolysaccharide of E. coli K-12 consists of two major components:
the hydrophobic lipid A moiety inserted into the outer membrane and the
phosphorylated core oligosaccharide |CITS:[12045108]|. E. coli K-12
does not produce O antigen to attach to the LPS core due to a defect in the
rfb gene cluster which can be complemented with genes from a second,
independent rfb mutant to produce an O16 type O antigen |CITS:[7517391]|.
E. coli K-12 may have two major pathways for LPS biosynthesis. One
generates LPS cores suitable for O antigen attachment, and a second generates
lipooligosaccharides (LOS) with modifications to the core structure which prevent
O antigen attachment |CITS:[1385388]|.
waaS encodes a protein necessary for the attachment of Rha to the
LPS core by a linkage to the KDOII residue |CITS:[7504166]|. WaaS could play
a role in an LOS biosynthesis pathway, because waaS mutants do
not produce certain unsubstituted core bands |CITS:[1385388]|. A truncated
waaS gene was shown to prevent LPS outer core completion |CITS:[1624461]|.
Reviews: |CITS:[12045108],[9791168],[7504166]|)""",]},
'B3626' : {'ecocyc-rxns': {"""RXN0-5126""": """galactosyl-glucosyl2-heptosyl3-KDO2-lipid A-bisphosphate + UDP-D-glucose = galactosyl-glucosyl3-heptosyl3-KDO2-lipid A-bisphosphate + UDP""","""2.4.1.58-RXN""": """a lipopolysaccharide + UDP-D-glucose = D-GLUCOSYL-LIPOPOLYSACCHARIDE + UDP""",},'ucsd-rxns' : ['GLCTR3',], 'protein-comments' : ["""(The lipopolysaccharide of E. coli K-12 consists of two major components:
the hydrophobic lipid A moiety inserted into the outer membrane and the
phosphorylated core oligosaccharide |CITS:[12045108]|. E. coli K-12
does not produce O antigen to attach to the LPS core due to a defect in the
rfb gene cluster which can be complemented with genes from a second,
independent rfb mutant to produce an O16 type O antigen |CITS:[7517391]|.
E. coli K-12 may have two major pathways for LPS biosynthesis. One
generates LPS cores suitable for O antigen attachment, and a second generates
lipooligosaccharides (LOS) with modifications to the core structure which prevent
O antigen attachment |CITS:[1385388]|.
WaaR adds the third glucose (GlcIII) to the second glucose (GlcII) of the outer core of LPS |CITS:[1624461]|.
Activity of WaaR requires a functional waaB gene |CITS:[1624461]|.
Reviews: |CITS:[12045108],[9791168],[7504166]|)""",]},
'B0662' : {'ecocyc-rxns': {"""OCTAPRENYL-METHYL-METHOXY-BENZOQ-OH-RXN""": """2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinone + O2 = 3-demethylubiquinone-8 + H2O""",},'ucsd-rxns' : ['OMMBLHX',], 'protein-comments' : ["""NIL""",]},
'B3624' : {'ecocyc-rxns': {"""RXN0-5128""": """a lipopolysaccharide + CMP-3-deoxy-D-manno-octulosonate = KDOIII-lipopolysaccharide + CMP""",},'ucsd-rxns' : ['MOAT3C',], 'protein-comments' : ["""(The lipopolysaccharide of E. coli K-12 consists of two major components:
the hydrophobic lipid A moiety inserted into the outer membrane and the
phosphorylated core oligosaccharide |CITS:[12045108]|. E. coli K-12
does not produce O antigen to attach to the LPS core due to a defect in the
rfb gene cluster which can be complemented with genes from a second,
independent rfb mutant to produce an O16 type O antigen |CITS:[7517391]|.
E. coli K-12 may have two major pathways for LPS biosynthesis. One
generates LPS cores suitable for O antigen attachment, and a second generates
lipooligosaccharides (LOS) with modifications to the core structure which prevent
O antigen attachment |CITS:[1385388]|.
WaaZ is involved in the nonstoichiometric addition of 3-deoxy-D-manno-oct-2-ulosonic
acid III (KDOIII) to the KDOII residue of the inner lipopolysaccharide core |CITS: [12591884]|.
WaaZ could play a role in an LOS biosynthesis pathway, because
waaZ mutants do not produce certain unsubstituted core bands |CITS: [1385388]|.
A waaZ mutant exhibits a defect in formation of LOS
compared to wild type |CITS: [1385388]|. Overproduction of WaaZ
causes defects in lipopolysaccharide biosynthesis, including
underextended outer core structures and less abundant O antigen,
compared to wild type |CITS: [12591884]|. An waaZ mutation does not
cause an O antigen attachment defect |CITS: [1385388]|.
WaaZ has 72% identity to Salmonella typhimurium WaaZ |CITS: [1624462]|.
Reviews: |CITS:[12045108],[9791168],[7504166]|)""",]},
'B3625' : {'ecocyc-rxns': {"""RXN0-5123""": """glucosyl-heptosyl3-KDO2-lipid A-phosphate + ATP = glucosyl-heptosyl3-KDO2-lipid A-bisphosphate + ADP""",},'ucsd-rxns' : ['HEPK2',], 'protein-comments' : ["""(The lipopolysaccharide of E. coli K-12 consists of two major components:
the hydrophobic lipid A moiety inserted into the outer membrane and the
phosphorylated core oligosaccharide |CITS:[12045108]|. E. coli K-12
does not produce O antigen to attach to the LPS core due to a defect in the
rfb gene cluster which can be complemented with genes from a second,
independent rfb mutant to produce an O16 type O antigen |CITS:[7517391]|.
E. coli K-12 may have two major pathways for LPS biosynthesis. One
generates LPS cores suitable for O antigen attachment, and a second generates
lipooligosaccharides (LOS) with modifications to the core structure which prevent
O antigen attachment |CITS:[1385388]|.
WaaY is a kinase responsible for phosphorylation of the heptose II residue in
the inner core of LPS |CITS:[9756860],[9791168]|. WaaY requires an intact
waaG and waaP in order to phosphorylate the HepII residue in
E. coli strain F470 |CITS:[9756860],[10986272]|.
Reviews: |CITS:[12045108],[9791168],[7504166]|)""",]},
'B3622' : {'ecocyc-rxns': {},'ucsd-rxns' : ['ECA4OALpp','O16A4Lpp',], 'protein-comments' : ["""(The lipopolysaccharide of E. coli K-12 consists of two major components:
the hydrophobic lipid A moiety inserted into the outer membrane and the
phosphorylated core oligosaccharide |CITS:[12045108]|. E. coli K-12
does not produce O antigen to attach to the LPS core due to a defect in the
rfb gene cluster which can be complemented with genes from a second,
independent rfb mutant to produce an O16 type O antigen |CITS:[7517391]|.
E. coli K-12 may have two major pathways for LPS biosynthesis. One
generates LPS cores suitable for O antigen attachment, and a second generates
lipooligosaccharides (LOS) with modifications to the core structure which prevent
O antigen attachment |CITS:[1385388]|.
WaaL is thought to be the O-antigen ligase in the lipopolysaccharide synthesis pathway.
Unlike most LPS core
biosynthesis genes, waaL has little sequence similarity to the counterpart gene in Salmonella
enterica
|CITS: [1624462]|. This diversity is thought to play a role in generating core specificity and
species-specific
attachment of O antigen |CITS: [1385388]|. WaaL may function together with WaaU |CITS: [9535865]|.
Both WaaU and WaaL are required for the complementation of a waaK mutation in
S. typhimurium LT2, suggesting an interaction between the two proteins |CITS:[1385388]|.
WaaL is an inner membrane protein with 12 predicted membrane-spanning regions. Its C terminus is located in the
cytoplasm |CITS: [15919996]|.
Inactivation of waaL does not cause a detectable
morphological phenotype; this is not surprising, because the
K-12 strain lacks the O antigen |CITS: [1577693]|.
However, waaL appears to be required for core completion
|CITS: [1385388]|. A waaL mutant prevents core completion
by rfp of Shigella dysenteriae 1, suggesting its own
role in core completion |CITS:[1385388]|.
Reviews: |CITS:[12045108],[9157235],[9791168],[7504166]|)""",]},
'B3623' : {'ecocyc-rxns': {"""RXN0-5127""": """galactosyl-glucosyl3-heptosyl3-KDO2-lipid A-bisphosphate + ADP-L-glycero-D-manno-heptose = Lipid A-core + ADP""",},'ucsd-rxns' : ['HEPT4',], 'protein-comments' : ["""(The lipopolysaccharide of E. coli K-12 consists of two major components:
the hydrophobic lipid A moiety inserted into the outer membrane and the
phosphorylated core oligosaccharide |CITS:[12045108]|. E. coli K-12
does not produce O antigen to attach to the LPS core due to a defect in the
rfb gene cluster which can be complemented with genes from a second,
independent rfb mutant to produce an O16 type O antigen |CITS:[7517391]|.
E. coli K-12 may have two major pathways for LPS biosynthesis. One
generates LPS cores suitable for O antigen attachment, and a second generates
lipooligosaccharides (LOS) with modifications to the core structure which prevent
O antigen attachment |CITS:[1385388]|.
WaaU is responsible for the attachment of HepIV to the GlcIII residue of the outer core |CITS:[9791168]|.
A waaU mutant is unable to add O antigen when a rfb cluster is supplied on a plasmid
|CITS:[1385388]|.
It is also suggested that WaaU may attach GlcNAc to an inner core heptose since a waaU
mutant becomes sensitive to phage Br2 |CITS:[1385388]|.
Reviews: |CITS:[12045108],[9791168],[7504166]|
)""",]},
'B3620' : {'ecocyc-rxns': {"""RXN0-5061""": """heptosyl-KDO2-lipid A + ADP-L-glycero-D-manno-heptose = heptosyl2-KDO2-lipid A + ADP""",},'ucsd-rxns' : ['HEPT2',], 'protein-comments' : ["""(The lipopolysaccharide of E. coli K-12 consists of two major components:
the hydrophobic lipid A moiety inserted into the outer membrane and the
phosphorylated core oligosaccharide |CITS:[12045108]|. E. coli K-12
does not produce O antigen to attach to the LPS core due to a defect in the
rfb gene cluster which can be complemented with genes from a second,
independent rfb mutant to produce an O16 type O antigen |CITS:[7517391]|.
E. coli K-12 may have two major pathways for LPS biosynthesis. One
generates LPS cores suitable for O antigen attachment, and a second generates
lipooligosaccharides (LOS) with modifications to the core structure which prevent
O antigen attachment |CITS:[1385388]|.
RfaF is the enzyme responsible for transfer of the second heptose sugar onto the heptosyl-KDO2 moiety of the
lipopolysaccharide inner core |CITS: [11054112]|.
Review: |CITS: [12045108],[9791168],[7504166]|)""",]},
'B3621' : {'ecocyc-rxns': {"""RXN0-5118""": """KDO2-lipid A + ADP-L-glycero-D-manno-heptose = heptosyl-KDO2-lipid A + ADP""","""RXN0-5057""": """KDO2-lipid IVA + ADP-L-glycero-D-manno-heptose = heptosyl-KDO2-lipid IVA + ADP""",},'ucsd-rxns' : ['HEPT1',], 'protein-comments' : ["""(The lipopolysaccharide of E. coli K-12 consists of two major components:
the hydrophobic lipid A moiety inserted into the outer membrane and the
phosphorylated core oligosaccharide |CITS:[12045108]|. E. coli K-12
does not produce O antigen to attach to the LPS core due to a defect in the
rfb gene cluster which can be complemented with genes from a second,
independent rfb mutant to produce an O16 type O antigen |CITS:[7517391]|.
E. coli K-12 may have two major pathways for LPS biosynthesis. One
generates LPS cores suitable for O antigen attachment, and a second generates
lipooligosaccharides (LOS) with modifications to the core structure which prevent
O antigen attachment |CITS:[1385388]|.
WaaC is the enzyme responsible for transfer of the first heptose sugar
onto the KDO2 moiety of the lipopolysaccharide
inner core |CITS: [9446588][11054112]|.
A mutation in waaC causes a deep-rough phenotype;
the lipopolysaccharide of the mutant strain is heptoseless
and contains 2-keto-3-deoxyoctulosonic acid (KDO) as its
only core sugar |CITS: [3882666]|. waaC is able to
complement the phenotype of a Salmonella typhimurium
waaC mutant |CITS: [8478319]|. Cell extracts
made from an waaC mutant strain are unable to catalyze
ADP-mannose-dependent glycosylation of
KDO2-lipid IVA, and introduction of a plasmid carrying
waaC leads to overexpression of that activity
|CITS: [8943265]|. (The non-physiological substrate
ADP-mannose was used to substitute for ADP-heptose.)
Overexpression of waaC leads to formation of biofilms
with abnormal architecture |CITS: [12900028]|.
Reviews: |CITS: [12045108],[9791168],[7504166]|)""",]},
'B1981' : {'ecocyc-rxns': {"""TRANS-RXN-27""": """H+[periplasmic space] + shikimate[periplasmic space] =H+[cytosol] + shikimate[cytosol] """,},'ucsd-rxns' : ['SKMt2pp',], 'protein-comments' : ["""(ShiA has been implicated in the high affinity transport of shikimate, an intermediate in the
aromatic amino acid biosynthetic pathway |CITS: [98192527] [76206090]|.
Chromosomal mutants in shiA are unable to transport shikimate, and introduction
of the cloned shiA gene restores shikimate transport |CITS: [98192527]|. The ShiA protein
has twelve predicted 12 TMS and is a member of the major facilitator superfamily of transporters (MFS)
|CITS: [98190790]| and hence is likely to function as a
proton/shikimate symporter. Analysis of a shiA-lacZ fusion has suggested
that shiA expression is constitutive and is not regulated by the TyrR represso
r |CITS: [98192527]|.
The shiA gene probably constitutes a monocistronic operon. Imported shikimate presumably
serves as a substrate for biosynthesis of aromatic compounds.)""",]},
'B2724' : {'ecocyc-rxns': {"""FHLMULTI-RXN""": """formate = CO2 + H2""","""RXN0-3283""": """2 H+ + 2 e- -> H2""",},'ucsd-rxns' : ['FHL','HYD1pp',], 'protein-comments' : ["""(HycB is thought to code for a subunit of hydrogenase 3, a peptide of the [4Fe-4S] ferredoxin type, which
functions as an intermediate electron carrier protein between hydrogenase 3 and formate dehydrogenase
|CITS: [92255260][92326636][10926369]|.
A hycB deletion mutant loses molecular hydrogen production and 2H+/K+ echange abilities under anaerobic
glucose-fermenting conditions. It is suggested that HycB is part of the formate-hydrogen lyase complex that
interacts directly with the F0F1 ATPase complex and the TrkA system |CITS: [10926369]|.)""","""NIL""","""(A report has described that formate oxidation in anaerobically grown E. coli is coupled to proton translocation
|CITS: [15848284]|.)""",]},
'B4382' : {'ecocyc-rxns': {"""THYM-PHOSPH-RXN""": """thymidine + phosphate = deoxyribose-1-phosphate + thymine""","""URA-PHOSPH-RXN""": """deoxyuridine + phosphate = deoxyribose-1-phosphate + uracil""",},'ucsd-rxns' : ['TMDPP','DURIPP',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B1982' : {'ecocyc-rxns': {"""AMP-NUCLEOSID-RXN""": """H2O + AMP = D-ribose-5-phosphate + adenine""",},'ucsd-rxns' : ['AMPN',], 'protein-comments' : ["""(AMP nucleosidase is the primary intracellular mechanism for AMP degradation in E. coli. The adenine which
is produced in the nucleosidase reaction can be reincorporated into the purine pool |CITS: [81046949] [90105402]|.
An amp mutant carrying a small deletion has been studied |CITS: [8473316]|.
Expression of amp is induced under limiting phosphate conditions |CITS: [2690948]|.
Crystal structures of AMP nucleosidase in the unliganded form and in complex with formycin 5'-monophosphate or
inorganic phosphate have been determined |CITS: [2670945][15296732]|. The enzyme is a homohexamer
|CITS: [2670945][15296732]|, and each monomer consists of a catalytic and a proposed regulatory domain. The
catalytic domain resembles nucleoside phosphorylases |CITS: [15296732][7920254]|.)""","""NIL""",]},
'B4384' : {'ecocyc-rxns': {"""PNP-RXN""": """phosphate + a purine ribonucleoside = ribose-1-phosphate + a purine base""","""GUANPHOSPHOR-RXN""": """phosphate + guanosine = ribose-1-phosphate + guanine""","""DEOXYGUANPHOSPHOR-RXN""": """guanine + deoxyribose-1-phosphate = deoxyguanosine + phosphate""","""INOPHOSPHOR-RXN""": """inosine + phosphate = ribose-1-phosphate + hypoxanthine""","""DEOXYINOPHOSPHOR-RXN""": """hypoxanthine + deoxyribose-1-phosphate = deoxyinosine + phosphate""","""ADENPHOSPHOR-RXN""": """ribose-1-phosphate + adenine = adenosine + phosphate""","""DEOXYADENPHOSPHOR-RXN""": """deoxyadenosine + phosphate = adenine + deoxyribose-1-phosphate""",},'ucsd-rxns' : ['PUNP1','PUNP5','PUNP4','PUNP6','PUNP2','PUNP3','DURIPP',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B2582' : {'ecocyc-rxns': {},'ucsd-rxns' : ['TRDR','DSBDR','RNDR4','RNDR3','RNDR2','RNDR1','PAPSR','THIORDXi','METSOXR2','METSOXR1',], 'protein-comments' : ["""(The trxC gene encodes a second thioredoxin in E. coli. Thioredoxin 2 can perform many of
thioredoxin 1's roles in vivo; it is able to reduce some essential cytoplasmic enzymes.
Along with thioredoxin 1 and glutaredoxin 1, thioredoxin 2 is one of E. coli's most
effective cytoplasmic disulfide-reducing proteins. Any one of these three is sufficient
to support aerobic growth. |CITS: [98429478] [98049550]|)""","""NIL""",]},
'B0349' : {'ecocyc-rxns': {"""MHPCHYDROL-RXN""": """2-hydroxy-6-oxonona-2,4-diene-1,9-dioate + H2O = 2-oxopent-4-enoate + succinate""",},'ucsd-rxns' : ['HKNTDH','HKNDDH',], 'protein-comments' : ["""NIL""",]},
'B4388' : {'ecocyc-rxns': {"""RXN0-5114""": """3-phospho-serine + H2O -> L-serine + phosphate""",},'ucsd-rxns' : ['PSP_L',], 'protein-comments' : ["""(Phosphoserine phosphatase, which catalyzes the last step in serine biosynthesis, has not been studied extensively.
Enzymatic studies were performed using partially purified enzyme from E. coli strain W |CITS: [PizerJBC2383934]|.)""",]},
'B3632' : {'ecocyc-rxns': {"""RXN0-5122""": """glucosyl-heptosyl2-KDO2-lipid A-phosphate + ADP-L-glycero-D-manno-heptose = glucosyl-heptosyl3-KDO2-lipid A-phosphate + ADP""",},'ucsd-rxns' : ['HEPT3',], 'protein-comments' : ["""(The lipopolysaccharide of E. coli K-12 consists of two major components:
the hydrophobic lipid A moiety inserted into the outer membrane and the
phosphorylated core oligosaccharide |CITS:[12045108]|. E. coli K-12
does not produce O antigen to attach to the LPS core due to a defect in the
rfb gene cluster which can be complemented with genes from a second,
independent rfb mutant to produce an O16 type O antigen |CITS:[7517391]|.
E. coli K-12 may have two major pathways for LPS biosynthesis. One
generates LPS cores suitable for O antigen attachment, and a second generates
lipooligosaccharides (LOS) with modifications to the core structure which prevent
O antigen attachment |CITS:[1385388]|.
WaaQ is a transferase responsible for addition of the side-branch heptose
of the inner core of LPS |CITS:[9756860],[9791168]|. Studies of waaQ
mutants suggest different roles for WaaQ in the O antigen-substituted LPS
and unsubstituted LOS pathways |CITS:[1385388]|. WaaQ requires an intact
waaP in order to add the HepIII residue to the inner core |CITS:[9756860]|.
Reviews: |CITS:[12045108],[9791168],[7504166]|)""",]},
'B4260' : {'ecocyc-rxns': {"""3.4.11.1-RXN""": """a peptide + H2O = an amino acid + a peptide""",},'ucsd-rxns' : ['AMPTASEPG','AMPTASECG',], 'protein-comments' : ["""NIL""","""NIL""","""NIL""","""(Aminopeptidase A/I is a peptidase which binds DNA and is required for maintenance of plasmid
monomers, which is critical for proper plasmid segregation |CITS: [355237][2670557]|.
Aminopeptidase A/I is part of the site-specific recombination system required to decatenate the
plasmids ColE1 and pSC101, maintaining them as monomers |CITS: [2649493][2670557][8605888]|.
Aminopeptidase A/I is responsible for coordinating DNA strands during
recombination, pairing cer sites in ColE1 plasmids and allowing the formation of
Holliday junctions |CITS: [15049810][7773410][8168483]|.
Aminopeptidase A/I, along with ArgR, may be involved in blocking trans recombination,
thus preventing formation of new catenated plasmids during recombination |CITS: [8736540]|.
This overall role in site-specific recombination is independent of Aminopeptidase A/I's peptidase
activity |CITS: [8057849]|.
Aminopeptidase A/I binds specifically to several DNA regions, including the carAB and carP regulatory
sequences |CITS: [7616564]|. If Aminopeptidase A/I is not present to bind to the carAB control
region, pyrimidine regulation of that promoter is impaired |CITS: [7616563]|. This
transcriptional repression requires additional protein factors beyond Aminipeptidase A/I alone
binding to DNA |CITS: [10970742]|.
Aminopeptidase A/I comprises a hexamer of PepA monomers |CITS: [10449417]|.)""",]},
'B4267' : {'ecocyc-rxns': {"""IDONDEHYD-RXN""": """L-idonate + NAD+ = NADH + 5-ketogluconate""",},'ucsd-rxns' : ['IDOND2','IDOND',], 'protein-comments' : ["""(The subunit structure has not been determined.)""",]},
'B4266' : {'ecocyc-rxns': {"""ACETOINDEHYDROG-A-RXN""": """diacetyl + NADPH -> acetoin + NADP+""","""GLUCONATE-5-DEHYDROGENASE-RXN""": """NAD(P)+ + gluconate = NAD(P)H + 5-ketogluconate""",},'ucsd-rxns' : ['5DGLCNR',], 'protein-comments' : ["""(The subunit structure of 5-keto-D-gluconate 5-reductase has not been determined.)""",]},
'B4265' : {'ecocyc-rxns': {"""TRANS-RXN-81""": """H+[periplasmic space] + fructuronate[periplasmic space] =H+[cytosol] + fructuronate[cytosol] ""","""TRANS-RXN-181""": """H+[periplasmic space] + L-idonate[periplasmic space] =L-idonate[cytosol] + H+[cytosol] """,},'ucsd-rxns' : ['GLCNt2rpp','IDONt2rpp','5DGLCNt2rpp',], 'protein-comments' : ["""(IdnT is a probable L-idonate and D-gluconate transporter. Originally thought to
be a subsidiary gluconate uptake system, the primary role of IdnT appears to
be in L-idonate transport. The idnT gene is located in the idnDOTR
operon involved in metabolising L-idonate to D-gluconate |CITS: [98324983]|.
Expression of this operon is induced by idonate or by 5-ketogluterate
|CITS: [98324983]|. The cloned idnT gene was shown to confer gluconate
transport in a gluconate transport negative mutant in whole cell experiments
with IdnT displaying a Km of 60 μM for gluconate |CITS: [97212001]|. While
direct transport of L-idonate has not been shown experimentally, IdnT-mediated
gluconate transport is strongly inhibited by idonate |CITS: [98324983]|.
IdnT is a member of the Gnt family of gluconate transporters |CITS: [97212001]|
and is homologous to the E. coli GntT and GntU gluconate transporters.
Gluconate uptake has been reported to occur via a proton-symport mechanism in
E. coli |CITS: [74033664]|. It seems likely that IdnT mediates
L-idonate/proton and D-gluconate/proton symport.)""",]},
'B1621' : {'ecocyc-rxns': {},'ucsd-rxns' : ['GLCptspp','MALTptspp',], 'protein-comments' : ["""(contains PTS Enzyme IIB and IIC domains)""","""(MalX, the maltose-glucose PTS permease, belongs to the functional
superfamily of the phosphoenolpyruvate (PEP)-dependent, sugar
transporting phosphotransferase system (PTS). The PTS transports
and simultaneously phosphorylates its sugar substrates in a process
called group translocation. MalX presumably takes up exogenous
sugar, releasing the phosphate ester into the cell cytoplasm in
preparation for metabolism |CITS: [8246840]|. The overall PTS-mediated phosphoryl
transfer reaction, requiring the two general energy coupling proteins
of the PTS, Enzyme I and HPr, as well as the three domains of
the Enzyme II complex is:
PEP --> Enzyme I(his~~P)
--> HPr(his~~P)
--> IIA(his~~P) -->
IIB(cys~~P) -(IIC)-> sugar-P.
The MalX (Enzyme IICBMal) can use glucose
and maltose as substrates. It may catalyze facilitated diffusion
as well as group translocation |CITS: [1856179]| . The protein presumably functions
with the glucose Enzyme IIA and is homologous to the glucose-
and N-acetylglucosamine-specific Enzyme IICBs. The physiological
function of MalX is not known |CITS: [1856179]|.
)""",]},
'B2311' : {'ecocyc-rxns': {"""3-OCTAPRENYL-4-OHBENZOATE-DECARBOX-RXN""": """3-octaprenyl-4-hydroxybenzoate = 2-octaprenylphenol + CO2""",},'ucsd-rxns' : ['OPHBDC',], 'protein-comments' : ["""(E. coli contains a second 3-octaprenyl-4-hydroxybenzoate decarboxylase encoded by the ubiX gene.
UbiX is present in much lower levels than the ubiD-encoded decarboxylase. The ubiX-encoded
enzyme has not been characterized |CITS: [ColiSalII] [76253689]|.
Regulation of ubiX expression has been described |CITS: [12799002]|.
A ubiX null mutant grows more slowly than wild type and is more resistant to heat shock than wild type
|CITS: [16030245]|.
)""",]},
'B2310' : {'ecocyc-rxns': {"""ABC-37-RXN""": """ATP + L-ornithine[periplasmic space] + H2O =ADP + phosphate + L-ornithine[cytosol] ""","""ABC-4-RXN""": """ATP + L-arginine[periplasmic space] + H2O =ADP + phosphate + L-arginine[cytosol] ""","""ABC-3-RXN""": """L-lysine[periplasmic space] + ATP + H2O =L-lysine[cytosol] + ADP + phosphate """,},'ucsd-rxns' : ['ORNabcpp','LYSabcpp','ARGabcpp',], 'protein-comments' : ["""NIL""","""(Functions with HisMQP.)""",]},
'B2312' : {'ecocyc-rxns': {"""PRPPAMIDOTRANS-RXN""": """5-phospho-β-D-ribosyl-amine + diphosphate + L-glutamate -> 5-phosphoribosyl 1-pyrophosphate + L-glutamine + H2O""",},'ucsd-rxns' : ['GLUPRT',], 'protein-comments' : ["""(The glutamine amide transfer domain has been identified near the
N-terminal end |CITS:[90264358]|.
purF is a component of a polycistronic mRNA |CITS:[79151096]|.
Expression of the pur genes is repressed when purines are added to the
growth medium and derepressed when purine auxotrophs are starved for
purines. |CITS:[89066794]|
)""","""NIL""",]},
'B3385' : {'ecocyc-rxns': {"""GPH-RXN""": """H2O + 2-phosphoglycolate = glycolate + phosphate""",},'ucsd-rxns' : ['PGLYCP',], 'protein-comments' : ["""(The gph gene encodes an enzyme with 2-phosphoglycolate phosphatase activity
|CITS: [7603433][10572959]|. 2-phosphoglycolate phosphatase is an enzyme of the Calvin Cycle, and it was thus
not clear why it would be found in E. coli. However, 2-phosphoglycolate is formed during repair of DNA strand
breaks with 3'-phosphoglycolate ends; such breaks can be caused by radiomimetic drugs like bleomycin. Gph was
shown to be involved in the removal of 2-phosphoglycolate after bleomycin treatment |CITS: [13129953]|.
Expression of gph appears to be constitutive |CITS: [13129953]|. A gph deletion mutation has no
apparent physiological effect |CITS: [10572959]|.)""",]},
'B3384' : {'ecocyc-rxns': {"""TRYPTOPHAN--TRNA-LIGASE-RXN""": """L-tryptophan + tRNAtrp + ATP -> L-tryptophanyl-tRNAtrp + diphosphate + AMP""",},'ucsd-rxns' : ['TRPTRS',], 'protein-comments' : ["""(Tryptophanyl-tRNA synthetase (TrpRS) is a member of the family of aminoacyl-tRNA synthetases, which interpret the
genetic code by covalently linking amino acids to their specific tRNA molecules. The reaction is driven by ATP
hydrolysis. TrpRS belongs to the Class I aminoacyl tRNA synthetases |CITS: [2203971][7647112]|.
The enzyme purified from E. coli B is a homodimer in solution |CITS: [4332555][4944315]|. The dimer has two
binding sites for both tryptophan and tRNATrp |CITS: [783157]|.
Specificity determinants within tRNATrp that are important for recognition by TrpRS have been
identified. The anticodon and the G73 discriminator base are the major identity determinants |CITS: [1721699]|, and
C35 is recognized as well |CITS: [1565639]|. The apparent affinity of TrpRS for tryptophan appears to be dependent
on the tRNA |CITS: [8692925]|. The identity of tRNATrp predominantly affects the rate of transfer of
tryptophan from the TrpRS-tryptophanyl adenylate to the tRNA |CITS: [10471730]|. TrpRS also aminoacylates
tRNATrp with D-tryptophan; the resulting D-Trp-tRNATrp can be hydrolyzed by
D-Tyr-tRNATyr deacylase |CITS: [10918062]|. A strain that can incorporate 4-fluorotryptophan in
place of tryptophan into proteins has been isolated and contains, among others, mutations in TrpRS
|CITS: [11514527]|.
The sequential processes involved in the tRNA charging reaction have been studied
|CITS: [3881255][3516215][7659511]|. Mutagenesis of the Thr17 residue in the TIGN motif indicates that Thr17 is
important for binding of substrate in the transition state |CITS: [8155701]|, and mutagenesis of Lys195 in the
conserved KMSKS motif indicates that Lys195 may interact with ATP in the transition state |CITS: [7729548]|.
Mutants that are auxotrophic for tryptophan and map within trpS have been identified; the mutations are located
within the conserved KMSKS motif, near the active site, or lining a proposed dimerization interface, supporting a role
for dimerization of the enzyme in catalysis |CITS: [8555191]|.
TrpRS activity increases with the growth rate; the regulation is at the level of trpS transcription
|CITS: [7047500]|.
Review: |CITS: [10966471]|
)""","""NIL""",]},
'B0584' : {'ecocyc-rxns': {"""RXN0-2181""": """ferric enterobactin[extracellular space] =ferric enterobactin[cytosol] ""","""RXN0-1682""": """ferric enterobactin[extracellular space] =ferric enterobactin[periplasmic space] """,},'ucsd-rxns' : ['FEENTERtonex',], 'protein-comments' : ["""(FepA is a protein involved with transport of enterobactin-iron across the outer membrane. |CITS: [10209114]| Its
structure consists of a 22-strand antiparallel β-barrel and an N-terminal globular domain which folds into the
barrel. |CITS: [9886293]| FepA interacts with a TonB, ExbB, ExbD complex, linking the movement of ferric enterobactin
from the environment into the periplasm with the proton gradient of the inner membrane, making this translocation an
active process. |CITS: [9886293]| FepA is also involved with the passage of colicins B and D through the outer membrane. |CITS: [22310698]|)""","""NIL""","""(FepA is a 22-stranded membrane-spanning beta barrel protein in the outer membrane. FepA is a TonB dependent active transporter
that recognizes ferric enterobactin and translocates the molecule across the outer membrane into the periplasm. FepB is a
periplasmic binding protein that binds ferric enterobactin for transport across the inner membrane by the FepCDG ABC transporter.)""",]},
'B0585' : {'ecocyc-rxns': {"""RXN0-1661""": """enterobactin + 3 H2O -> 3 2,3-dihydroxybenzoylserine""",},'ucsd-rxns' : ['ENTERES','ENTERES2',], 'protein-comments' : ["""(The activity of the enzyme has been characterized |CITS: [150859], [1534808]|. Fes catalyzes hydrolysis of the 2,3-dihydroxy-N-benzoyl-L-serine trimer, enterochelin, forming 2,3-dihydroxybenzoylserine |CITS: [150859]|. Fes catalyzes hydrolysis of free enterobactin and ferric enterobactin |CITS: [1534808]|. Upon hydrolysis of ferric enterobactin by Fes, released iron is probably reduced by a second enzyme |CITS: [1534808]|.
Regulation has been described |CITS: [6260580], [3040679], [2974033], [8021177], [9573216]|.
Fes has similarity to proteins from Yersinia enterocolitica |CITS: [10515929]|, Erwinia chrysanthemi |CITS: [11694506]|, and Acinetobacter baumannii |CITS: [12724384]|.
)""",]},
'B3389' : {'ecocyc-rxns': {"""3-DEHYDROQUINATE-SYNTHASE-RXN""": """3-deoxy-D-arabino-heptulosonate-7-phosphate = phosphate + 3-dehydroquinate""",},'ucsd-rxns' : ['DHQS',], 'protein-comments' : ["""NIL""",]},
'B2251' : {'ecocyc-rxns': {"""DCTP-PYROPHOSPHATASE-RXN""": """dCTP + H2O -> dCMP + diphosphate""","""DUTP-PYROP-RXN""": """dUTP + H2O -> dUMP + diphosphate""","""RXN0-5107""": """dTTP + H2O -> dTMP + diphosphate""",},'ucsd-rxns' : ['NTPP7','NTPP3','DUTPDP',], 'protein-comments' : ["""(The yfaO gene product is a member of the Nudix hydrolase superfamily of nucleoside diphosphatases. The
preferred substrate of the purified enzyme is dUTP, but it also shows 67 and 58% of activity with dTTP and dCTP,
respectively. The enzyme is a monomer in solution |CITS: [16766526]|.
Review: |CITS: [16378245]|
)""",]},
'B0588' : {'ecocyc-rxns': {"""RXN0-2181""": """ferric enterobactin[extracellular space] =ferric enterobactin[cytosol] ""","""ABC-10-RXN""": """ATP + ferric enterobactin[periplasmic space] + H2O =ADP + phosphate + ferric enterobactin[cytosol] """,},'ucsd-rxns' : ['FEENTERabcpp','FE3DHBZSabcpp',], 'protein-comments' : ["""NIL""","""(FepBCDG are components of a ferric enterobactin transport complex that is a member of the ATP-binding
cassette (ABC) family of transporters. E. coli and several other species of Enterobacteriaceae
secrete the catecholate siderophore enterobactin. The enterobactin siderophore is a small organic
molecule with a high affinity for Fe 3+. FepA has been shown |CITS:[21424666]|, to be
involved in transport of ferric enterobactin across the outer membrane into the periplasm in a TonB-
dependent process which requires the transduction of energy derived from the cytoplasmic membrane
across the periplasm to FepA. Deletion studies |CITS: [92157868]| indicate that fepD and
fepG are essential for transport and sequence analysis indicates that these two proteins are highly
homologous with other integral membrane proteins involved in iron-chelating ABC uptake systems. Based
on sequence similarity, FepC is the ATP-binding component and provides the energy required for transport
across the inner membrane. FepB is not coded in the same operon but has been shown to bind ferric
enterobactin and probably functions as the periplasmic binding protein of the ferric enterobactin ABC
transporter |CITS: [96004464]|.)""","""(FepA is a 22-stranded membrane-spanning beta barrel protein in the outer membrane. FepA is a TonB dependent active transporter
that recognizes ferric enterobactin and translocates the molecule across the outer membrane into the periplasm. FepB is a
periplasmic binding protein that binds ferric enterobactin for transport across the inner membrane by the FepCDG ABC transporter.)""",]},
'B0589' : {'ecocyc-rxns': {"""RXN0-2181""": """ferric enterobactin[extracellular space] =ferric enterobactin[cytosol] ""","""ABC-10-RXN""": """ATP + ferric enterobactin[periplasmic space] + H2O =ADP + phosphate + ferric enterobactin[cytosol] """,},'ucsd-rxns' : ['FEENTERabcpp','FE3DHBZSabcpp',], 'protein-comments' : ["""NIL""","""(FepBCDG are components of a ferric enterobactin transport complex that is a member of the ATP-binding
cassette (ABC) family of transporters. E. coli and several other species of Enterobacteriaceae
secrete the catecholate siderophore enterobactin. The enterobactin siderophore is a small organic
molecule with a high affinity for Fe 3+. FepA has been shown |CITS:[21424666]|, to be
involved in transport of ferric enterobactin across the outer membrane into the periplasm in a TonB-
dependent process which requires the transduction of energy derived from the cytoplasmic membrane
across the periplasm to FepA. Deletion studies |CITS: [92157868]| indicate that fepD and
fepG are essential for transport and sequence analysis indicates that these two proteins are highly
homologous with other integral membrane proteins involved in iron-chelating ABC uptake systems. Based
on sequence similarity, FepC is the ATP-binding component and provides the energy required for transport
across the inner membrane. FepB is not coded in the same operon but has been shown to bind ferric
enterobactin and probably functions as the periplasmic binding protein of the ferric enterobactin ABC
transporter |CITS: [96004464]|.)""","""(FepA is a 22-stranded membrane-spanning beta barrel protein in the outer membrane. FepA is a TonB dependent active transporter
that recognizes ferric enterobactin and translocates the molecule across the outer membrane into the periplasm. FepB is a
periplasmic binding protein that binds ferric enterobactin for transport across the inner membrane by the FepCDG ABC transporter.)""",]},
'B2254' : {'ecocyc-rxns': {"""RXN0-3521""": """UDP-β-L-Ara4FN + undecaprenyl phosphate -> undecaprenyl phosphate-α-L-Ara4FN + UDP""",},'ucsd-rxns' : ['UPLA4FNT',], 'protein-comments' : ["""(ArnC selectively converts uridine 5'-diphospho-β-(4-deoxy-4-formamido-L-arabinose) (UDP-L-Ara4FN),
but not uridine 5'-diphospho-β-(4-amino-4-deoxy-L-arabinose) (UDP-L-Ara4N), to lipid product
|CITS: [15695810]|.
Arn: "L-Ara4N (4-amino-4-deoxy-L-arabinose) biosynthesis" |CITS: [11706007]|.
Pmr: "polymyxin resistance"
Operons similar to the arnC operon of E. coli have been described in Salmonella typhimurium
|CITS: [9570402], [11535603]| and Yersinia pseudotuberculosis |CITS: [12756767]|.)""",]},
'B2255' : {'ecocyc-rxns': {"""RXN0-1862""": """UDP-L-Ara4N + N10-formyl-THF -> UDP-L-Ara4-Formyl-N + tetrahydrofolate""","""RXN0-1861""": """UDP-D-glucuronate + NAD+ -> UDP-L-Ara4O + CO2 + NADH""",},'ucsd-rxns' : ['ULA4NFT','UDPGDC',], 'protein-comments' : ["""(ArnA does not appear to be produced in wild-type strains, but in certain mutant strains ArnA acts within a pathway
(along with Ugd, ArnB, ArnC, and ArnT) that modifies lipid A phosphates with 4-amino-4-deoxy-L-arabinose
(L-Ara4N), which causes increased resistance to polymyxin |CITS: [11706007]|.
ArnA exhibits UDP-glucuronic acid (UDP-GlcA) C-4"-dehydrogenase and UDP-4-amino-4-deoxy-L-arabinose
(UDP-L-Ara4N) formylation activities in vitro |CITS: [11706007]|. The two activities are separable. The
C-terminal domain of 360 amino acids contains the NAD+-dependent decarboxylating activity.
Crystal structures of this domain has been solved at 2.4 and 2.3 A resolution |CITS: [15491143][15809294]|, and
active site residues have been identified |CITS: [15809294]|. The amino terminal domain is similar to
methionyl-tRNAfMet formyltransferase and catalyzes the N-10-formyltetrahydrofolate-dependent formylation
of the 4'' amine of UDP-L-Ara4N |CITS: [15695810]|. Crystal structures of this domain has been solved at 1.7 and
1.2 A resolution |CITS: [15807526][15809294]|. The N-10-formyltetrahydrofolate binding site has been identified and
a reaction mechanism has been proposed; point mutations in the proposed catalytic residues abolish activity
|CITS: [15807526][15809294]|. The activity of both domains is required for polymyxin resistance |CITS: [15695810]|.
Crystal structures of the full-length protein and various point mutants have been solved |CITS: [15939024]|.
ArnA: "L-Ara4N (4-amino-4-deoxy-L-arabinose) biosynthesis" |CITS: [11706007]|.
PmrI: "polymyxin resistance")""",]},
'B3546' : {'ecocyc-rxns': {"""RXN0-4581""": """KDO2-lipid IVA + a phosphatidylethenolamine = a 1,2-diacylglycerol + phosphatidylethanolamine-KDO2-lipidA""",},'ucsd-rxns' : ['PETNT161pp','PETNT181pp',], 'protein-comments' : ["""(The eptB gene encodes the Ca2+-induced phosphoethanolamine transferase |CITS: [15795227]|.
In the presence of Ca2+ in the medium, a phosphoethanolamine (pEtN) group is added to the outer Kdo
residue of lipopolysaccharide, apparently at position 7 |CITS: [9266718][11042192]|. EptB requires Ca2+
and phosphatidylethanolamine (PE) for activity in vitro |CITS: [15795227]|.
Activity of EptB is induced by the presence of Ca2+ in the medium; the highest activity was observed
with 50mM Ca2+ |CITS: [11042192]|.
An in-frame deletion of eptB in a strain lacking waaC and waaF (a heptose-deficient strain)
causes sensitivity to Ca2+, while deletion of eptB in a wild-type background does not
|CITS: [15795227]|.)""",]},
'B3994' : {'ecocyc-rxns': {"""PYRIMSYN1-RXN""": """5-aminoimidazole ribonucleotide = hydroxymethylpyrimidine phosphate""",},'ucsd-rxns' : ['AMPMS2',], 'protein-comments' : ["""(The gene has been sequenced. |CITS: [93163063]|)""",]},
'B2751' : {'ecocyc-rxns': {"""SULFATE-ADENYLYLTRANS-RXN""": """sulfate + ATP = APS + diphosphate""",},'ucsd-rxns' : ['SADT2',], 'protein-comments' : ["""(Believed to be a GTPase that activates the cysD protein.
|CITS: [92268080] [92112707]|)""","""NIL""",]},
'B3997' : {'ecocyc-rxns': {"""UROGENDECARBOX-RXN""": """uroporphyrinogen-III = 4 CO2 + coproporphyrinogen III""",},'ucsd-rxns' : ['UPPDC1',], 'protein-comments' : ["""NIL""",]},
'B2500' : {'ecocyc-rxns': {"""GART-RXN""": """N10-formyl-THF + 5-phospho-ribosyl-glycineamide = tetrahydrofolate + 5'-phosphoribosyl-N-formylglycineamide""",},'ucsd-rxns' : ['GARFT',], 'protein-comments' : ["""(Based on polarity studies, the expression of the purN gene originates from the purM control region and thus forms a purMN operon. The overlapping termination and initiation codons predict that GAR transformylase expression from the purN gene is translationally coupled to AIR synthetase expression from the purM gene |CITS:[87280114]|. The GAR transformylase is an enzyme of fundamental significance in the anabolism of all organisms. Because of its association with DNA synthesis , this enzyme has become the target of antineoplastic agents |CITS:[90373777]|. The 3D structure has been solved |CITS:[92335248]|)""",]},
'B1613' : {'ecocyc-rxns': {"""MANNPISOM-RXN""": """mannose-6-phosphate = D-fructose-6-phosphate""",},'ucsd-rxns' : ['MAN6PI',], 'protein-comments' : ["""NIL""",]},
'B2502' : {'ecocyc-rxns': {"""EXOPOLYPHOSPHATASE-RXN""": """(POLYPHOSPHATE)(N) + H2O -> (polyphosphate)(n-1) + phosphate""",},'ucsd-rxns' : ['PPA2','PPA',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B3993' : {'ecocyc-rxns': {"""THI-P-SYN-RXN""": """4-methyl-5-(β-hydroxyethyl)thiazole phosphate + 4-amino-5-hydroxymethyl-2-methylpyrimidine-pyrophosphate = thiamine-phosphate + diphosphate""",},'ucsd-rxns' : ['TMPPP',], 'protein-comments' : ["""(Thiamine phosphate synthase combines 4-methyl-5-(β-hydroxyethyl)thiazole phosphate and
4-amino-5-hydroxymethyl-2-methylpyrimidine-pyrophosphate to
generate thiamine phosphate |CITS: [JAmChemSoc117-2351]|.)""",]},
'B2467' : {'ecocyc-rxns': {"""RXN0-5108""": """GDP-D-mannose + H2O = GMP + α-D-mannose 1-phosphate""",},'ucsd-rxns' : ['GDPMNP',], 'protein-comments' : ["""(The nudK gene product is a member of the ADP-ribose pyrophosphatase subfamily of the Nudix hydrolases.
The enzyme prefers purine over pyrimidine nucleotide sugars as substrates |CITS: [16766526]|.
NudK is a homotrimer in solution |CITS: [16766526]|. A crystal structure has been solved at 2.4 A resolution
|CITS: [16021622]|.
Review: |CITS: [16378245]|
)""","""NIL""",]},
'B2306' : {'ecocyc-rxns': {"""ABC-14-RXN""": """ATP + L-histidine[periplasmic space] + H2O =ADP + phosphate + L-histidine[cytosol] ""","""ABC-37-RXN""": """ATP + L-ornithine[periplasmic space] + H2O =ADP + phosphate + L-ornithine[cytosol] ""","""ABC-4-RXN""": """ATP + L-arginine[periplasmic space] + H2O =ADP + phosphate + L-arginine[cytosol] ""","""ABC-3-RXN""": """L-lysine[periplasmic space] + ATP + H2O =L-lysine[cytosol] + ADP + phosphate """,},'ucsd-rxns' : ['ORNabcpp','LYSabcpp','HISabcpp','ARGabcpp',], 'protein-comments' : ["""NIL""","""(Functions with HisMQP.)""","""(HisPMQJ is an ATP-dependent histidine transport system that is a member of the ATP-Binding
Cassette (ABC) Superfamily of transporters |CITS: [96381453]|. Based on sequence similarity, HisJ is the
periplasmic histidine-binding protein, HisQ and HisM are the integral membrane components, and HisP is
the ATP-binding component of the ABC transport complex |CITS: [98188231]|. Although the transport
properties of the His complex in E. coli have not yet been characterized, extensive investigations on
the orthologous proteins in Salmonella typhimurium have been reported. The His complex of
Salmonella typhimurium was purified and reconstituted into ATP-encapsulated proteoliposomes,
and histidine transport activity was observed |CITS: [97150838]|. His-mediated transport activity is
completely dependent on the presence of all four protein components and on the internal ATP concentration,
with apparent Km of 8 mM for ATP |CITS: [97150838] [89386658]|. The transport activity is
also affected by pH, temperature, and salt concentration |CITS: [97150838]|. Transport is irreversible and
accumulation reaches a plateau at which point transport ceases |CITS: [97150838]|. The transport complex is
inhibited by ADP and by high concentrations of internal histidine |CITS: [97150838]|.)""",]},
'B2465' : {'ecocyc-rxns': {"""1TRANSKETO-RXN""": """D-ribose-5-phosphate + D-xylulose-5-phosphate = D-sedoheptulose-7-phosphate + D-glyceraldehyde-3-phosphate""","""2TRANSKETO-RXN""": """D-erythrose-4-phosphate + D-xylulose-5-phosphate = D-fructose-6-phosphate + D-glyceraldehyde-3-phosphate""",},'ucsd-rxns' : ['TKT2','TKT1',], 'protein-comments' : ["""(TktB is responsible for the minor transketolase activity in E.
coli, and TktA is responsible for the major transketolase activity
|CITS: [8396116]|.
TktA and/or TktB binds to zinc |CITS: [11985624]|. Superoxide inhibits
transketolase by oxidation of the 1, 2-dihydroxyethyl thiamine
pyrophosphate |CITS: [9933617]|.
Overproduction of TktB causes increased transketolase activity and
suppresses the tktA mutant phenotype |CITS: [8396116]|. A tktA tktB
double mutant exhibits auxotrophy for pyridoxine (or
4-hydroxy-L-threonine or glycolaldehyde), and aromatic amino acids and
vitamins |CITS: [7928977]|.
The subunit structure of transketolase II (TktB) has not been explicitly determined. However, transketolase I (TktA)
is homodimeric |CITS: [7607225]|.
Review: |CITS: [8572885]|.
)""","""NIL""",]},
'B3544' : {'ecocyc-rxns': {"""ABC-8-RXN""": """ATP + a dipeptide[periplasmic space] + H2O =ADP + phosphate + a dipeptide[cytosol] """,},'ucsd-rxns' : ['ALAALAabcpp','CGLYabcpp','PROGLYabcpp',], 'protein-comments' : ["""NIL""","""(The DppABCDF dipeptide transport system is a member of the ATP-Binding Cassette (ABC)
Superfamily of transporters |CITS: [96381453]|. Based on sequence similarity, DppA is the substrate-binding
component, while DppB and DppC are the membrane components, and DppD and DppF are the
ATP-binding components of the ABC transporter. Mutations in dpp displayed resistance to the toxic
dipeptide Lys-aminoxyAla, and the loss of ability to utilize LeuTrp as a source of its required amino acids
|CITS: [85056880]|. Substrate specificity of DppA was studied in a filter binding assay in which column
fractions were monitored for binding activity towards radioactively labeled dipeptides and tripeptides. DppA
was observed to mediate the ATP-driven uptake of dipeptides and, to a lesser extent, tripeptides from the
periplasm |CITS: [20005603]|. DppABCDF is similar in sequence and subunit composition to the oligopeptide
uptake system OppABCDF, suggesting similar subunit functions. DppA?s unbound structure has been
resolved by x-ray crystallography to 2 angstroms, and shows two domains connected by two ?hinge? segments
|CITS: [9618375]|.
)""",]},
'B2463' : {'ecocyc-rxns': {"""MALIC-NADP-RXN""": """NADP+ + malate = NADPH + CO2 + pyruvate""",},'ucsd-rxns' : ['ME2',], 'protein-comments' : ["""NIL""","""(There are two malic enzymes in E. coli, one NAD-linked (encoded by the maeA gene) and the other
NADP-linked (encoded by the maeB gene) |CITS: [90337272]|. The NADP-linked enzyme also
decarboxylates oxaloacetate and various alpha-keto acids. |CITS: [79193995]|
Initial purification studies indicated that the enzyme was composed of 8 subunits, working with E. coli K10
|CITS: [SpinaBiochem193794]|. Further studies, with both E. coli W and K12, have indicated 6 subunits
|CITS: [79193995] [81208122]|.
Deletion of maeB abolishes NADP-dependent malic enzyme activity |CITS: [11092847]|. maeB
expression is upregulated in a pykF (pyruvate kinase) null mutant |CITS: [15158258]|.)""",]},
'B4005' : {'ecocyc-rxns': {"""GLYRIBONUCSYN-RXN""": """ATP + 5-phospho-β-D-ribosyl-amine + glycine = ADP + phosphate + 5-phospho-ribosyl-glycineamide""",},'ucsd-rxns' : ['PRAGSr',], 'protein-comments' : ["""(The purH and purD genes constitute a single operon and are
coregulated in expression by purines as other purine genes are.
E.coli GAR synthetase contains a single activity. However,
in S. cerevisiae and several other organisms GAR synthetase is part of a
bifunctional polypeptide with AIR synthetase.)""",]},
'B3397' : {'ecocyc-rxns': {"""ADPSUGPPHOSPHAT-RXN""": """an ADP-sugar + H2O -> AMP + an α-D-aldose-1-phosphate""",},'ucsd-rxns' : ['ADPRDP',], 'protein-comments' : ["""(NudE belongs to the family of Nudix hydrolases |CITS: [8810257]|. The enzyme is specific for nucleoside
pyrophosphates with an ADP moiety; preferred substrates of NudE include adenosine(5')triphospho(5')adenosine
(Ap3A), ADP-ribose, and NADH |CITS: [9452430]|.
Gel filtration experiments suggest that the enzyme is a dimer in solution |CITS: [9452430]|.
An mrcA nudE yrfF triple mutant exhibits phenotypes including mucoidy, heat sensitivity, growth defects, and
resistance to phage or antibiotic drugs, whereas a single mrcA mutant does not |CITS: [11567017]|.
A crystal structure has been solved at 2.32 A resolution |CITS: [16021622]|.
)""","""NIL""",]},
'B3785' : {'ecocyc-rxns': {},'ucsd-rxns' : ['ECAP3pp','ECAP1pp','ECAP2pp',], 'protein-comments' : ["""(WzzE is responsible for regulating the length of phosphoglyceride-linked
Enterobacterial Common Antigen (ECAPG) polysaccharide
chains formed from polymerization by WzyE utilizing Lipid III in the periplasm.
Typically, ECAPG chain lengths are 1 to 14 repeats long with
a modal value of 6 or 7. wzzE mutants display a random, non-modal
distribution of ECAPG polysaccharide chain lengths |CITS:[10515954]|.
wzzE has been shown to be required for the synthesis of cyclic ECA
which contains 4 trisaccharide repeat units and is located in the periplasm
|CITS:[16199561]|. WzzE is predicted to form a complex with WzyE and WzxE
|CITS:[16816184]|.)""","""(The Enterobacterial Common Antigen biosynthesis protein complex is responsible for synthesizing ECA
polysaccharide chains from Lipid III precursors that have been transferred accross the inner membrane.)""",]},
'B4042' : {'ecocyc-rxns': {"""DIACYLGLYKIN-RXN""": """ATP + a 1,2-diacylglycerol = ADP + an L-phosphatidate""",},'ucsd-rxns' : ['DAGK120','DAGK141','DAGK140','DAGK161','DAGK160','DAGK181','DAGK180',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B2919' : {'ecocyc-rxns': {"""RXN0-310""": """(R)-methylmalonyl-CoA = propionyl-CoA + CO2""",},'ucsd-rxns' : ['MMCD',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B4040' : {'ecocyc-rxns': {"""4OHBENZOATE-OCTAPRENYLTRANSFER-RXN""": """octaprenyl diphosphate + p-hydroxybenzoate = diphosphate + 3-octaprenyl-4-hydroxybenzoate""",},'ucsd-rxns' : ['HBZOPT',], 'protein-comments' : ["""(The sdgG mutation, which suppresses a conditional mutation in dnaG (DNA primase), has been localized to either the ubiC, ubiA or yjbI gene |CITS: [9093842]|.)""",]},
'B2917' : {'ecocyc-rxns': {"""METHYLMALONYL-COA-MUT-RXN""": """(R)-methylmalonyl-CoA = succinyl-CoA""",},'ucsd-rxns' : ['MMM2',], 'protein-comments' : ["""NIL""",]},
'B1210' : {'ecocyc-rxns': {"""GLUTRNAREDUCT-RXN""": """glutamate-1-semialdehyde + NADP+ + tRNAGlu = L-glutamyl-tRNAGlu + NADPH + H+""",},'ucsd-rxns' : ['GLUTRR',], 'protein-comments' : ["""(Glutamyl-tRNA reductase catalyzes the first step of porphyrin biosynthesis. The reaction appears to proceed via a
thioester intermediate |CITS: [12370189]|. Determinants for recognition of Glu-tRNA(Glu) by the enzyme have been
studied |CITS: [15194701]|. HemA can be isolated in multiple multimeric forms, but the dimer may represent the
functional form of the enzyme |CITS: [12370189]|. The HemA dimer forms a tight complex with
glutamate-1-semialdehyde 2,1-aminomutase, the second enzyme in the pathway, suggesting metabolic channeling
of the highly reactive intermediate glutamate-1-semialdehyde |CITS: [15757895]|.
Heme limitation leads to an increase in abundance of HemA protein |CITS: [9139907]|, although only a 3-fold increase
in hemA expression can be detected |CITS: [8997718]|. In Salmonella typhimurium, HemA abundance
appears to be increased by stabilization of the protein |CITS: [9973348]|.)""","""NIL""",]},
'B2914' : {'ecocyc-rxns': {"""RIB5PISOM-RXN""": """D-ribose-5-phosphate = D-ribulose-5-phosphate""",},'ucsd-rxns' : ['RPI',], 'protein-comments' : ["""(RpiA has similarity to an Edwardsiella ictaluri protein that provokes an immune response in catfish |CITS: [12542086]|.)""","""NIL""",]},
'B2913' : {'ecocyc-rxns': {"""KETOGLUTREDUCT-RXN""": """α-ketoglutarate + NADH = (R)-2-hydroxyglutarate + NAD+""","""PGLYCDEHYDROG-RXN""": """3-phosphoglycerate + NAD+ = 3-phospho-hydroxypyruvate + NADH""",},'ucsd-rxns' : ['PGCD',], 'protein-comments' : ["""(SerA has similarity to an Edwardsiella ictaluri protein |CITS: [12542086]|.)""","""NIL""",]},
'B3787' : {'ecocyc-rxns': {"""UDPMANNACADEHYDROG-RXN""": """UDP-N-acetyl-D-mannosamine + 2 NAD+ + H2O = UDP-N-acetyl-β-D-mannosaminouronate + 2 NADH + 2 H+""",},'ucsd-rxns' : ['UACMAMO',], 'protein-comments' : ["""NIL""",]},
'B2663' : {'ecocyc-rxns': {"""TRANS-RXN-57""": """H+[periplasmic space] + 4-aminobutyrate[periplasmic space] =H+[cytosol] + 4-aminobutyrate[cytosol] """,},'ucsd-rxns' : ['ABUTt2pp',], 'protein-comments' : ["""(GabP is a 4-aminobutyrate (GABA) transporter that is a member of the Amino Acid Polyamine
Organocation (APC) Superfamily of transporters |CITS: [20391827]|. Expression of the cloned gabP
on a plasmid vector resulted in a 5-fold increase in GABA uptake. The apparent Km of
GABA uptake was found to be 11.8 μM, and the Vmax was 0.33 nmol/min/g cells
|CITS:[94127927]|. Transport of GABA is dependent upon the presence of phosphatidylethanolamine (PE)
within the membrane. In cells lacking PE, the N-terminal hairpin of GabP is inverted, and there is a hinge
point in transmembrane domain III. Transport of GABA is reduced by over 99% under these conditions
|CITS:[15890647]|. Moreover, the specificity of GabP was investigated by measuring the effects of excess
concentrations of various amino acids on the rate of radioactively labeled GABA uptake. Of the twenty
protein amino acids, only aspartate could compete with GABA for uptake |CITS: [94127927]|. However,
counterflow assays indicate that GabP is able to transport synthetic compounds with little structural
resemblance to GABA, such as 3-piperidinecarboxylic acid and 3-hydroxy-5-aminomethylisoxazole,
while other more structurally similar compounds such as 2-(aminomethyl)-5-hydroxy-4H-pyran-4-one,
and 4-amino-trans-butenoic acid, were not transported |CITS: [96132808]|. The inhibitory action of the
uncoupler 2, 4-dinitrophenol indicated the energy dependence of GABA uptake. On the other hand,
ammonium sulfate, known to increase membrane potential, stimulated GABA uptake significantly
|CITS:[94127927]|. Based on hydropathy analysis, LacZ, and PhoA fusions, GabP is believed to have 12
transmembrane segments |CITS:[99025897]|. C300 of GabP appears to have a large functional
significance, since replacing C300 with A, S, G, K, D, Y or P resulted in a marked loss in transport
activity |CITS: [98352048]|.
The gabT gene was identified in a search for mutants that have lost the ability to utilize 4-aminobutyrate
(GABA) as a nitrogen source |CITS: [374339]|. Regulation of the operon containing gabT has been
studied extensively |CITS: [9512707], [11251833], [11532138], [14731280]|.
)""",]},
'B1216' : {'ecocyc-rxns': {"""TRANS-RXN-101""": """Na+[cytosol] + H+[periplasmic space] =H+[cytosol] + Na+[periplasmic space] ""","""TRANS-RXN-144""": """Ca2+[cytosol] + H+[periplasmic space] =Ca2+[periplasmic space] + H+[cytosol] """,},'ucsd-rxns' : ['Kt3pp','CA2t3pp','NAt3pp',], 'protein-comments' : ["""(ChaA is a calcium ion: proton antiporter that is a member of the Calcium: Cation Antiporter (CaCA) Family
of transporters |CITS: [93266586]|. Studies of calcium ion uptake in everted membrane vesicles
demonstrated that a chaA knockout mutant reduced calcium transport at pH 8.5 but not at pH 7
|CITS: [94292460]|. It was therefore suggested that ChaA plays a role in calcium ion circulation at alkaline
pH |CITS: [94292460]|. ChaA is also found to be responsible for sodium ion: proton antiport in E. coli
A previously isolated E. coli mutant RS1, which had a negligible activity for sodium ion extrusion at
alkaline pH was compensated for by a cloned chaA gene, indicating that ChaA plays a role in
sodium ion extrusion in E. coli at alkaline pH |CITS: [94292460]|. ChaA is thus found to be one of
the three systems in E. coli responsible for sodium ion extrusion, along with NhaA and NhaB
|CITS: [98186658]|. Using cells with intact ChaA and mutated NhaA and NhaB, sodium ion efflux activity
was observed only at pH above 8. In addition, deletion of chaA does not affect the extrusion of
calcium ions at pH 7.0 |CITS: [94292460]|. This also suggests that ChaA extrudes sodium ions mainly at an
alkaline pH |CITS: [98186658]|. Complementation of a strain mutated in both chaA and nhaA
genes using a cloned chaA gene was enough to restored the level of sodium ion extrusion activity
at alkaline pH |CITS: [94292460]|.)""",]},
'B3693' : {'ecocyc-rxns': {"""DEHYDDEOXGALACTKIN-RXN""": """2-dehydro-3-deoxy-D-galactonate + ATP = 2-dehydro-3-deoxy-D-galactonate-6-phosphate + ADP""",},'ucsd-rxns' : ['DDGALK',], 'protein-comments' : ["""(The subunit structure is unknown.)""",]},
'B1764' : {'ecocyc-rxns': {"""2.7.9.3-RXN""": """H2O + selenide + ATP = phosphate + selenophosphate + AMP""",},'ucsd-rxns' : ['SELNPS',], 'protein-comments' : ["""(Selenide, water dikinase, the selD gene product, catalyzes the reaction that produces the selenium
donor compound, selenophosphate. The enzyme contains a cysteine residue that is essential for
catalytic activity. The CsdA, CsdB and IscS proteins can all provide the selenium needed for the reaction.
Selenophosphate reacts with various types of activated receptor molecules involved in selenium
addition or replacement processes. Selenophosphate is required for the synthesis of selenocysteinyl-tRNA.
|CITS: [8144648] [98151486] [10829016] [90138866] [94086510]|
)""",]},
'B3691' : {'ecocyc-rxns': {"""TRANS-RXN-16""": """H+[periplasmic space] + D-galactonate[periplasmic space] =H+[cytosol] + D-galactonate[cytosol] """,},'ucsd-rxns' : ['GALCTNt2pp',], 'protein-comments' : ["""(YidT (DgoT) is a probable galactonate transporter. The yidT gene
is located within a probable 5 gene operon, which includes the dgoD gene,
whose product has been purified and shown to be galactonate dehydratase,
and 3 other genes likely be involved in galactonate utilisation
|CITS: [95158873]|. YidT is a member of the major
facilitator superfamily (MFS) of transporters |CITS: [98190790]|. It is
likely that YidT functions as a galactonate/proton symporter. Imported
galactonate is modified and cleaved by the enzymes of the dgo operon to
yield glyceraldehyde 3-phosphate and pyruvate.)""",]},
'B3786' : {'ecocyc-rxns': {"""UDPGLCNACEPIM-RXN""": """UDP-N-acetyl-D-glucosamine = UDP-N-acetyl-D-mannosamine""",},'ucsd-rxns' : ['UAG2E',], 'protein-comments' : ["""(Isolation of spontaneous N4 bacteriophage-resistant mutants of E. coli K-12 strain SC1100, cloning of the
affected genes, and subsequent complementation experiments revealed that nfrC is important in N4
adsorption |CITS:[2670887]|. Western blots of cellular extracts places the location of NfrC in the cytoplasm.
Also, a mutation in the nfrC gene did not affect transport to the outer membrane of NfrA nor did it
affect NfrB localization and expression in maxicells |CITS:[8226648]|. Both NfrA and NfrB are also important
for N4 adsorption |CITS:[2670887]|.)""",]},
'B1761' : {'ecocyc-rxns': {"""GLUTDEHYD-RXN""": """L-glutamate + H2O + NADP+ = α-ketoglutarate + ammonia + NADPH""",},'ucsd-rxns' : ['GLUDy',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B2779' : {'ecocyc-rxns': {"""2PGADEHYDRAT-RXN""": """2-phosphoglycerate = phosphoenolpyruvate + H2O""",},'ucsd-rxns' : ['ENO',], 'protein-comments' : ["""NIL""","""(Enolase catalyzes the interconversion of 2-phosphoglycerate and phosphoenolpyruvate. It is
also a component of the degradosome, a complex that degrades RNA.
Enolase dimerizes, with two active sites per dimer. It is dependent on Mg ion for
its structure and denatures in the absence of Mg.|CITS:[72060411]| The crystal
structure of enolase was initially determined to a resolution of 2.5 Å, revealing
that its dimer interface is enriched in charged residues relative to typical
protein-protein interfaces |CITS: [11676541]|. A more recent 1.6 Å structure
shows enolase bound to its recognition site on RNase E |CITS: [16516921]|.
Enolase is functionally similar to enolases in other organisms, notably
in its dependence on Mg, inhibition by fluoride ion in the presence of phosphate
and in its catalytic parameters. Its pH optimum is significantly higher
than vertebrate enolases and is somewhat above those of yeast and plant
enolases. |CITS:[72060411]|
Enolase is required for the rapid, degradosome-mediated degradation of ptsG
mRNA in response to high levels of glucose 6-P or fructose 6-P |CITS: [15522087]|.)""","""(The degradosome is a large, multiprotein complex involved in RNA degradation.
It consists of the RNA degradation enzymes RNase E and PNPase, as well
as the ATP-dependent RNA helicase RhlB and the metabolic enzyme enolase |CITS: [7891559][7510217][8610017]|.
Polyphosphate kinase
and the chaperone protein DnaK are also associated with and may be components of
the degradosome |CITS: [9383162][8632981]|. A "minimal" degradosome
composed of only RNase E, PNPase and RhlB degrades malEF REP RNA in an
ATP-dependent manner in vitro, with activity equivalent to purified
whole degradosomes. RNase E enzymatic function is dispensible for this test
case, whereas PNPase must be catalytically active and incorporated into the degradosome
for degradation to occur |CITS: [10521403]|. Based on immunogold
labeling studies, RhlB and RNase E are present in equimolar quantities in
the degradosome, which is tethered to the cytoplasmic membrane via the
amino-terminus of RNase E |CITS: [11134527]|.
RNase E provides the organizational structure for the degradosome. Its
carboxy-terminal half binds PNPase, RhlB and enolase, and the loss of
this portion of the protein prevents degradation of a number of
degradosome substrates, including the ptsG and mukB mRNAs and RNA I |CITS: [8682798][9732274][15522087]|.
This
scaffold region is flexible, with isolated segments of increased structure
that may be involved in binding other degradosome constituents |CITS: [15236960]|.
RNase E binding to partner proteins can
be selectively disrupted. Loss of RhlB and enolase binding results
in reduced degradosome activity. Conversely, disrupted PNPase
binding yields increased activity. Strains any alteration in RNase E
binding do not grow as well as wild type |CITS: [12207692]|.
The amino-terminal half of RNase E contains
sequences involved in oligomerization |CITS: [9732274]|.
In vitro purified degradosome generates 147-nucleotide RNase E
cleavage intermediates from rpsT mRNA. Continuous cycles of polyadenylation
and PNPase cleavage are necessary and sufficient to break down
these intermediates, though RNase II can block this second degradation
step |CITS: [9642084]|. RNAs with 3' REP stabilizers or stem loops
must be polyadenylated to allow breakdown by the degradosome |CITS: [14731278][9933592]|.
Poly(G) and poly(U) tails do not allow degradation, though addition of a stretch
of mixed nucleotides copied from within a coding region has stimulated
degradation of a test substrate |CITS: [9933592]|.
The degradosome copurifies with fragments from its RNA substrates, including
rRNA fragments derived from cleavage of 16S and 23S rRNA by
RNase E, 5S rRNA and ssrA RNA |CITS: [9501232][10535935]|.
The DEAD-box helicases SrmB, RhlE and CsdA bind RNase E in vitro
at a different site than RhlB. RhlE and CsdA can both replace RhlB in
promoting PNPase activity in vitro |CITS: [15554979]|.
CsdA is induced by cold shock, and following a shift to 15 degrees C
it copurifies with the degradosome |CITS: [15554978]|.
At least two poly(A)-binding proteins interact with the degradosome. The
cold-shock protein CspE inhibits internal cleavage and breakdown of
polyadenylated RNA by RNase E and PNPase by blocking digestion through
the poly(A) tail. S1, a component of the 30S ribosome, binds to RNase E
and PNPase without apparent effect on their activities |CITS: [11390393]|.
The global effects of mutations in degradeosome constituents on mRNA levels have
been evaluated using microarrays |CITS: [14981237]|.)""",]},
'B0073' : {'ecocyc-rxns': {"""3-ISOPROPYLMALDEHYDROG-RXN""": """3-isopropylmalate + NAD+ = 2-isopropyl-3-oxosuccinate + NADH + H+""",},'ucsd-rxns' : ['OMCDC','IPMD',], 'protein-comments' : ["""NIL""","""(Work done on S. typhimurium has shown it to be a dimer.
|CITS: [69184144]|)""",]},
'B3781' : {'ecocyc-rxns': {},'ucsd-rxns' : ['TRDR','DSBDR','RNDR4','RNDR3','RNDR2','RNDR1','PAPSR','THIORDXi','METSOXR2','METSOXR1',], 'protein-comments' : ["""(Thioredoxin is a small electron-transfer protein which contains a cysteine
disulfide/dithiol active site. The protein functions in a wide variety of cellular
processes. Thioredoxin is reduced by NADPH in a reaction catalyzed by
thioredoxin reductase. The conversion between the oxidized and reduced
forms results in a change of conformation. The functional properties differ
between the two forms of thioredoxin. The reduced thioredoxin is a powerful
protein disulfide reductase, thioredoxin catalyzes dithiol-disulfide exchange
reactions. The oxidized form of thioredoxin has been crystallized,
the reduced form has been solved by NMR. |CITS: [85277988] [90198521]
[90254096] [90298180] [93264420] [90204538]|)""","""(Thioredoxin is a small electron-transfer protein which contains a cysteine
disulfide/dithiol active site. The protein functions in a wide variety of cellular
processes. Thioredoxin is reduced by NADPH in a reaction catalyzed by
thioredoxin reductase. The conversion between the oxidized and reduced
forms results in a change of conformation. The functional properties differ
between the two forms of thioredoxin. The reduced thioredoxin is a powerful
protein disulfide reductase, thioredoxin catalyzes dithiol-disulfide exchange
reactions. The oxidized form of thioredoxin has been crystallized, the reduced
form has been solved by NMR.
|CITS: [85277988] [90198521] [90254096] [90298180] [93264420] [90204538]|)""",]},
'B4160' : {'ecocyc-rxns': {"""PHOSPHASERDECARB-RXN""": """an L-1-phosphatidylserine = an L-1-phosphatidyl-ethanolamine + CO2""",},'ucsd-rxns' : ['PSD140','PSD141','PSD161','PSD180','PSD181','PSD120','PSD160',], 'protein-comments' : ["""(Phosphatidylserine decarboxylase is composed of two nonidentical subunits,
alpha and beta, derived from a single proenzyme. The proenzyme is processed in
a post-translational event into the heterodimer. |CITS: [88298809] [92356881]|)""","""NIL""","""(This subunit contains the pyruvate prosthetic group.)""","""NIL""","""(Phosphatidylserine decarboxylase is one of a small class of enzymes that use a covalently bound pyruvoyl prosthetic group.
The pyruvoyl group is thought to act analogously to pyridoxal phosphate
cofactor by forming a Schiff base with the amino group of the substrate and then serving as an electron
sink to facilitate the decarboxylation |CITS: [91208149]|.
Four of these enzymes, histidine decarboxylase (E.C. 4.1.1.22), |FRAME: PHOSPHASERDECARB-CPLX|,
|FRAME: CPLX0-2901|, and |FRAME: CPLX-6906| are decarboxylases forming important biological
amines. All of these enzymes are known to have the pyruvoyl prosthetic group attached via an amide
linkage to the amino terminus of the α subunit.
Two other enzymes in this group are are |FRAME: CPLX-782| and glycine reductase
(E.C. 1.21.4.2) |CITS: [10574985]|.
Pyruvoyl-containing enzymes are expressed as a zymogen which is processed post-translationally
by a self-maturation cleavage called serinolysis. In this process the pyruvoul group is formed from a
serine residue, splitting the presursor protein into two parts which become the α and β
subunits. In some cases additional subunits may be involved.
This enzyme differs from other pyruvoyl-dependent decarboxylases composed of nonidentical
subunits in that the pyruvate prosthetic group is associated with the smaller subunit.
The enzyme is a multimer of unknown number of the heterodimer |CITS: [88298809] [92356881]|.)""","""NIL""","""(Phosphatidylserine decarboxylase is one of a small class of enzymes that use a covalently bound pyruvoyl prosthetic group.
The pyruvoyl group is thought to act analogously to pyridoxal phosphate
cofactor by forming a Schiff base with the amino group of the substrate and then serving as an electron
sink to facilitate the decarboxylation |CITS: [91208149]|.
Four of these enzymes, histidine decarboxylase (E.C. 4.1.1.22), |FRAME: PHOSPHASERDECARB-CPLX|,
|FRAME: CPLX0-2901|, and |FRAME: CPLX-6906| are decarboxylases forming important biological
amines. All of these enzymes are known to have the pyruvoyl prosthetic group attached via an amide
linkage to the amino terminus of the α subunit.
Two other enzymes in this group are are |FRAME: CPLX-782| and glycine reductase
(E.C. 1.21.4.2) |CITS: [10574985]|.
Pyruvoyl-containing enzymes are expressed as a zymogen which is processed post-translationally
by a self-maturation cleavage called serinolysis. In this process the pyruvoul group is formed from a
serine residue, splitting the presursor protein into two parts which become the α and β
subunits. In some cases additional subunits may be involved.
This enzyme differs from other pyruvoyl-dependent decarboxylases composed of nonidentical
subunits in that the pyruvate prosthetic group is associated with the smaller subunit.
The enzyme is a multimer of unknown number of the heterodimer |CITS: [88298809] [92356881]|.)""",]},
'B4161' : {'ecocyc-rxns': {"""RXN0-1021""": """GTP + H2O = GDP + phosphate""",},'ucsd-rxns' : ['NTP10','NTP3','NTP1','NTP5',], 'protein-comments' : ["""(The protein is essential for growth |CITS: [9743119]| and may be a novel factor in ribosome function |CITS: [14973029]|.
YjeQ exhibits GTPase activity |CITS: [12220175]|, which is stimulated 160-fold by association of the YjeQ protein with
stochiometric amounts of the 30S subunit of the ribosome |CITS: [14973029]|. Addition of aminoglycosides that bind
to the A site of the 30S ribosomal subunit inhibit that effect |CITS: [15466596]|.
YjeQ is a member of a family of P-loop-containing GTPases with an unusual arrangement of GTPase motifs
|CITS: [12220175]|. The N terminus has an OB-fold RNA-binding domain, the central region comprises the GTPase
motifs, and the C terminus has a potential zinc knuckle domain |CITS: [12220175]|.
The YjeQ protein copurifies with ribosomes at a ratio of 1:200. Recombinant YjeQ interacts most strongly with the
30S subunit in the presence of 5'-guanylylimidodiphosphate (GMP-PNP), a nonhydrolyzable GTP analog
|CITS: [14973029]|.
An S221A mutation within the central GTPase motif causes a catalytic defect |CITS: [12220175]|. N-terminal
truncation mutants showed that the OB-fold region is essential for ribosome interaction and GTPase stimulation; the
N-terminal amino acids 1-20 are essential for GMP-PNP-dependent interaction with the 30S subunit
|CITS: [14973029]|.
The protein has similarity to proteins of Mycoplasma genitalium and Bacillus subtilis |CITS: [9743119]|.
Overproduction and purification is described |CITS: [12220175]|.
RsgA: "ribosome small subunit-dependent GTPase A" |CITS: [15466596]|)""",]},
'B2838' : {'ecocyc-rxns': {"""DIAMINOPIMDECARB-RXN""": """meso-diaminopimelate = L-lysine + CO2""",},'ucsd-rxns' : ['DAPDC',], 'protein-comments' : ["""NIL""","""(Similar to ornithine and arginine decarboxylases.)""",]},
'B0764' : {'ecocyc-rxns': {"""ABC-19-RXN""": """ATP + MoO42-[periplasmic space] + H2O =ADP + phosphate + MoO42-[cytosol] """,},'ucsd-rxns' : ['TUNGSabcpp','MOBDabcpp',], 'protein-comments' : ["""NIL""","""(ModCBA is a high-affinity molybdate transporter that is a member of the ATP-Binding Cassette (ABC)
Superfamily of transporters |CITS: [96381453]|. Based on sequence similarity, modA encodes the
periplasmic binding component, modB encodes the integral membrane component, and modC
encodes the ATP-binding component of the ABC transporter. Complementation of a mod mutant with
the cloned mod genes restored molybdate uptake activities |CITS: [96151473]|. In a mod
mutant, molybdate is not transported by the ModCBA system but by the sulfate transport system or by a
nonspecific anion transporter |CITS: [98004559]|. Transcription of mod genes is regulated by
molybdate and a repressor protein, ModE |CITS: [98004559]|.)""",]},
'B2309' : {'ecocyc-rxns': {"""ABC-14-RXN""": """ATP + L-histidine[periplasmic space] + H2O =ADP + phosphate + L-histidine[cytosol] """,},'ucsd-rxns' : ['HISabcpp',], 'protein-comments' : ["""NIL""","""(HisPMQJ is an ATP-dependent histidine transport system that is a member of the ATP-Binding
Cassette (ABC) Superfamily of transporters |CITS: [96381453]|. Based on sequence similarity, HisJ is the
periplasmic histidine-binding protein, HisQ and HisM are the integral membrane components, and HisP is
the ATP-binding component of the ABC transport complex |CITS: [98188231]|. Although the transport
properties of the His complex in E. coli have not yet been characterized, extensive investigations on
the orthologous proteins in Salmonella typhimurium have been reported. The His complex of
Salmonella typhimurium was purified and reconstituted into ATP-encapsulated proteoliposomes,
and histidine transport activity was observed |CITS: [97150838]|. His-mediated transport activity is
completely dependent on the presence of all four protein components and on the internal ATP concentration,
with apparent Km of 8 mM for ATP |CITS: [97150838] [89386658]|. The transport activity is
also affected by pH, temperature, and salt concentration |CITS: [97150838]|. Transport is irreversible and
accumulation reaches a plateau at which point transport ceases |CITS: [97150838]|. The transport complex is
inhibited by ADP and by high concentrations of internal histidine |CITS: [97150838]|.)""",]},
'B4031' : {'ecocyc-rxns': {"""TRANS-RXN-30""": """H+[periplasmic space] + D-xylose[periplasmic space] =H+[cytosol] + D-xylose[cytosol] """,},'ucsd-rxns' : ['XYLt2pp',], 'protein-comments' : ["""(XylE is a D-xylose/proton symporter, one of two systems in E. coli
responsible for the uptake of D-xylose. The other being the ATP-dependent
ABC transporter XylFGH. The cloned xylE gene has been shown to
complement xylE mutants in vivo |CITS: [88007632]|.
XylE-mediated transport in whole cells is inhibited by protonophores
and elicits an alkaline pH change |CITS: [80249387]|. Experiments
using xylE and xylF mutants have established that
XylE has a Km of 63-169 μM for D-xylose |CITS: [96117780]|. XylE is
a member of the major facilitator superfamily (MFS) of transporters
|CITS: [93040298]| and appears to function as a xylose/proton symporter.
The xylE gene probably constitutes a monocistronic operon whose
expression is inducible by D-xylose. Imported xylose is catabolised to
xylulose-5-phosphate by the action of the XylA and XylB enzymes.)""",]},
'B0928' : {'ecocyc-rxns': {"""ASPAMINOTRANS-RXN""": """L-aspartate + α-ketoglutarate = oxaloacetate + L-glutamate""",},'ucsd-rxns' : ['ASPTA','PHETA1','TYRTA',], 'protein-comments' : ["""NIL""","""(The enzyme is a dimeric form composed of two identical
subunits. Each subunit has two domains, a small and a large one.
In each subunit there exists a PLP molecule
forming a Schiff base with a lysine residue. The crystal structure has
been determined |CITS:[90105323],[91035344]| Aspartate 222 and
tyrosine 70 play important roles at the active site. |CITS: [92304971] [91329396]|)""",]},
'B0929' : {'ecocyc-rxns': {"""RXN0-2481""": """hydrophilic solute or ion < 600 Da[extracellular space] =hydrophilic solute or ion < 600 Da[periplasmic space] """,},'ucsd-rxns' : ['Htex','LEUtex','ALAALAtex','LYStex','ORNtex','O2Stex','UMPtex','GAMAN6Ptex','UDPACGALtex','INDOLEtex','3AMPtex','ACtex','GALBDtex','XTSNtex','THMtex','TRPtex','SERtex','CRNtex','SO4tex','ARGtex','ETHAtex','23CGMPtex','CLtex','ACSERtex','METSOX2tex','ACMANAtex','NOtex','DGSNtex','UDPGtex','23DAPPAtex','GLYCtex','MELIBtex','SO2tex','12PPDStex','GALURtex','23CAMPtex','GLUtex','DGMPtex','GSNtex','THYMtex','GLYBtex','NMNtex','GLCNtex','FE2tex','12PPDRtex','DALAtex','ALAtex','Zn2tex','HCINNMtex','ACGAL1Ptex','TSULtex','THMDtex','ACNAMtex','CGLYtex','DOPAtex','GTHRDtex','AGMtex','G3PStex','PSCLYStex','HOMtex','GBBTNtex','DMStex','HG2tex','PItex','IDONtex','GLCtex','TYRtex','MOBDtex','ASNtex','ACGALtex','NO3tex','NAtex','PACALDtex','PPPNtex','DSERtex','ACMUMtex','PPALtex','HIStex','DINStex','TCYNTtex','SULFACtex','OCTAtex','CD2tex','URAtex','GALCTtex','TUNGStex','SO3tex','METDtex','TMAOtex','CYANtex','MSO3tex','TMAtex','GALCTNLtex','ALLtex','PYRtex','D-LACtex','BUTtex','XMPtex','MMETtex','5DGLCNtex','ALLTNtex','G3PCtex','CYStex','GLYCAtex','MNtex','G3PEtex','ASO3tex','TYRPtex','GLYtex','L-LACtex','FORtex','PNTOtex','ETOHtex','SPMDtex','HPPPNtex','GDPtex','BALAtex','FRULYStex','TARTRtex','3GMPtex','MNLtex','DCMPtex','AMPtex','ACGAtex','ACACtex','SUCCtex','FALDtex','PEAMNtex','SUCRtex','UDPGALtex','PPAtex','PROtex','XANtex','PPTtex','ASPtex','HXAtex','SKMtex','HYXNtex','TREtex','CO2tex','PROGLYtex','MALtex','ILEtex','GLCUR1Ptex','UREAtex','DAPtex','GLNtex','CSNtex','PTRCtex','XYLtex','O2tex','DAMPtex','G3PGtex','3PEPTtex','VALtex','AKGtex','METtex','ASCBtex','SBTtex','3CMPtex','GLYC2Ptex','GLYALDtex','G6Ptex','NO2tex','PSERtex','CYTDtex','H2tex','MANGLYCtex','DUMPtex','LYXtex','34dhpactex','R5Ptex','ARBtex','GAL1Ptex','FRUURtex','MG2tex','METSOX1tex','TAURtex','GALTtex','UDPGLCURtex','CYNTtex','23CCMPtex','G1Ptex','GLCRtex','IMPtex','RMNtex','DHAtex','GTPtex','FUCtex','ANHGMtex','GLYCLTtex','GALtex','CITtex','23CUMPtex','LCTStex','H2O2tex','OROTtex','DCAtex','NACtex','ACALDtex','CYSDtex','G3PItex','ISETACtex','ACGAM1Ptex','INSTtex','ABUTtex','GTHOXtex','DMSOtex','F6Ptex','GALCTNtex','26DAHtex','MAN6Ptex','GAMtex','GLYC3Ptex','GLCURtex','NI2tex','DIMPtex','THRPtex','MANtex','GMPtex','CU2tex','THRtex','XYLUtex','DTMPtex','TYMtex','4PEPTtex','ADEtex','RIBtex','H2Otex','ETHSO3tex','CA2tex','BUTSO3tex','3UMPtex','CUtex','4HOXPACDtex','NH4tex','UACGAMtex','Ktex','FE3tex','MALDtex','FRUtex','PHEtex','FUMtex','N2Otex','H2Stex','CMPtex','DDGLCNtex','COBALT2tex','CHLtex',], 'protein-comments' : ["""(OmpF is a member of the General Bacterial Porin (GBP) family. X-ray crystallography has determined the three-dimensional
structure of the OmpF porin to be a trimeric structure with each monomer consisting of 16 antiparallelβ strands |CITS: [1380671]|.
It allows the passage of solutes such as sugars, ions, and amino acids which are less than 600 daltons, with a weak preference for cationic molecules |CITS: [1380671]|.
OmpF is tightly but noncovalently associated with the peptidoglycan layer |CITS: [2903556]|.
Double OmpC-OmpF mutants and OmpR mutants (incapable of synthesizing OmpC and OmpF) survive poorly in comparison to
single mutants of OmpC or OmpF when suspended in filtered-autoclaved water or sea water. This suggests that these two porins are crucial for entry into survival mode |CITS: [14633108]|.
Targeting of OmpF to the Sec-translocase for transport across the inner membrane
is SecB-dependent |CITS:[16352602]|.)""","""NIL""",]},
'B2224' : {'ecocyc-rxns': {"""ACETYL-COA-ACETYLTRANSFER-RXN""": """2 acetyl-CoA = acetoacetyl-CoA + coenzyme A""",},'ucsd-rxns' : ['ACACT1r',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B2923' : {'ecocyc-rxns': {},'ucsd-rxns' : ['LYSt3pp','ARGt3pp',], 'protein-comments' : ["""(The ArgO (YggA) protein is a member of the LysE family of lysine efflux transporters |CITS: [99257453]|.
Based on sequence similarity, ArgO may function as a proton-driven amino acid efflux system.
Null mutations in both the argO and the argP genes cause hypersensitivity to canavanine, an arginine analog. ArgO
expression is regulated by ArgP, and transcription of argO is induced by exogenous arginine |CITS: [15150242]|.
ArgO = "arginine outward transport" |CITS: [15150242]|)""",]},
'B2221' : {'ecocyc-rxns': {"""ACETOACETYL-COA-TRANSFER-RXN""": """acetoacetate + acetyl-CoA = acetoacetyl-CoA + acetate""","""ACECOATRANS-RXN""": """an acyl-CoA + acetate = a fatty acid + acetyl-CoA""",},'ucsd-rxns' : ['BUTCT','HXCT','ACACCT',], 'protein-comments' : ["""(Based on sequence similarity, AtoD is predicted to be an acetate CoA-transferase |CITS: [12952533]|.)""","""NIL""","""NIL""",]},
'B3493' : {'ecocyc-rxns': {"""TRANS-RXN-114""": """H+[periplasmic space] + phosphate[periplasmic space] =H+[cytosol] + phosphate[cytosol] """,},'ucsd-rxns' : ['PIt2rpp',], 'protein-comments' : ["""(The PitA phosphate transporter is a member of the Inorganic Phosphate Transporter (PiT) family. It is
responsible for the low-affinity transport of inorganic phosphate. Whole cell transport assays determined
that PitA has a Km of approximately 38 μM for inorganic phosphate transport
|CITS: [81026213]|. Transposon mutagenesis suggests that PitA may also transport Zn (II)
|CITS: [20179665]|. Cells with insertional mutation in PitA showed increased resistance to Zn (II)
|CITS: [20179665]|. This transporter is constitutively expressed. This transport is powered by proton-motive
force and transport can be abolished with uncouplers or respiration inhibitors |CITS: [91041716]|.)""",]},
'B2222' : {'ecocyc-rxns': {"""ACETOACETYL-COA-TRANSFER-RXN""": """acetoacetate + acetyl-CoA = acetoacetyl-CoA + acetate""","""ACECOATRANS-RXN""": """an acyl-CoA + acetate = a fatty acid + acetyl-CoA""",},'ucsd-rxns' : ['BUTCT','HXCT','ACACCT',], 'protein-comments' : ["""(Based on sequence similarity, AtoA is predicted to be an acetate CoA-transferase |CITS: [12952533]|.)""","""NIL""","""NIL""",]},
'B1325' : {'ecocyc-rxns': {},'ucsd-rxns' : ['ALAGLUE',], 'protein-comments' : ["""(YcjG is an L-Ala-D/L-Glu epimerase (of the enolase superfamily) that may act on murein |CITS: [11747447]|. The substrate specificity of the enzyme is not strict |CITS: [11747447]|. Kinetic characterization is performed; the k(cat)/K(M) with L-Ala-D/L-Glu as a substrate is about 10(4) per M per sec|CITS: [11747447]|.
The crystal structure has been determined |CITS: [11747448]|.)""",]},
'B2388' : {'ecocyc-rxns': {"""GLUCOKIN-RXN""": """β-D-glucose + ATP = β-D-glucose-6-phosphate + ADP""",},'ucsd-rxns' : ['HEX1',], 'protein-comments' : ["""NIL""",]},
'B1326' : {'ecocyc-rxns': {"""RXN0-961""": """L-Ala-γ-D-Glu-Dap + H2O -> L-Ala-γ-D-Glu + meso-diaminopimelate""",},'ucsd-rxns' : ['LADGMDH',], 'protein-comments' : ["""(MpaA is a murein peptide amidase that may act with YcjG in murein recycling |CITS: [12511517]|.
An mpaA mutation greatly enhances the murein tripeptide hydrolysis defect of an mpl mutant |CITS: [12511517]|.
MpaA appears to be cytoplasmic, as no signal peptide is evident |CITS: [12511517]|.
MpaA has similarity to Bacillus sphaericus ENP1 protein |CITS: [12511517]|.)""",]},
'B2810' : {'ecocyc-rxns': {"""RXN0-279""": """3-sulfinoalanine = L-alanine + sulphur dioxide""",},'ucsd-rxns' : ['CYSSADS',], 'protein-comments' : ["""NIL""","""(CsdA and CsdE combine to form the CSD sulfur-generating system. CsdA is a cysteine sulfinate
desulfinase. It is a pyridoxal 5'-phosphate enzyme and also has activity with L-selenocysteine and
L-cysteine. The mechanism of L-cysteine desulfurization is different from that of L-selenocysteine degradation
|CITS: [10739946] [97426379]|. CsdA activity doubles in the presence of CsdE, which
contains a cysteine that acts to accept sulfur liberated via the desulfinase activity of CsdA |CITS: [15901727]|.)""",]},
'B3256' : {'ecocyc-rxns': {"""ACETYL-COA-CARBOXYLTRANSFER-RXN""": """ATP + acetyl-CoA + HCO3- + H+ = malonyl-CoA + phosphate + ADP""","""BIOTIN-CARBOXYL-RXN""": """a biotin-BCCP (dimer) + CO2 + ATP = carboxy-biotin-BCCP + phosphate + ADP""",},'ucsd-rxns' : ['ACCOAC',], 'protein-comments' : ["""(Mutations in the homologous and functionally identical subunit in mammalian proprionyl-CoA carboxylase and
3-methylcrotonyl-CoA carboxylase result in the metabolic deficiency diseases of propionic acidemia or
methylcrotonylglycinuria. Kinetic analysis of mutants analogous to the disease-causing mutants has been
performed to determine the function of those residues |CITS: [14960587]|.)""","""NIL""","""(The enzyme |FRAME:ACETYL-COA-CARBOXYLMULTI-CPLX| is one of the key enzymes in the
biosynthesis of fatty acids (see |FRAME: FASYN-INITIAL-PWY|).
The enzyme belongs to the family of enzymes that catalyze
the intermolecular transfer of carboxyl groups via the transient formation of a carboxyphosphate
intermediate covalently linked to a biotin prosthetic group |CITS: [15749055]|.
The E. coli enzyme complex is composed of two catalytic units and one carrier protein,
encoded by four different genes.
The catalytic units are |FRAME:BIOTIN-CARBOXYL-CPLX| (BC), a homodimer encoded by the
|FRAME: EG10276| gene, and |FRAME:ACETYL-COA-CARBOXYLMULTI-CPLX| (ACCT), an
α2β2 tetramer, encoded by the |FRAME:EG11647| and
|FRAME: EG10217| genes.
The carrier protein is the |FRAME:BCCP-CPLX| (BCCP), a homodimer encoded by the |FRAME:EG10275| gene.
The BCCP monomer is biotinylated by the enzyme |FRAME:BIOTINLIG-ENZRXN|.
Following dimerization of the biotinylated monomers, |FRAME:BIOTIN-CARBOXYL-CPLX| (BC) catalyzes the addition
of |FRAME: CARBON-DIOXIDE| to the carrier protein dimer, forming |FRAME:Carboxybiotin-BCCP| (carboxy-BCCP).
|FRAME:Carboxybiotin-BCCP|
in turn is the substrate for ACCT, which transfers the carboxy group to |FRAME:ACETYL-COA|,
resulting in the formation of |FRAME:MALONYL-COA| and the regeneration of |FRAME:BCCP-CPLX|.
Both biotinylation and carboxylation of the carrier protein require ATP, while the last step, transfer of the carboxy
group to |FRAME: ACETYL-COA|, does not |CITS: [15749055]|.)""",]},
'B3255' : {'ecocyc-rxns': {"""ACETYL-COA-CARBOXYLTRANSFER-RXN""": """ATP + acetyl-CoA + HCO3- + H+ = malonyl-CoA + phosphate + ADP""",},'ucsd-rxns' : ['ACCOAC',], 'protein-comments' : ["""NIL""","""(The accB gene encodes the biotin carboxyl carrier protein (BCCP), a component of acetyl CoA carboxylase |CITS: [2575489]|. AccB is active as a dimer |CITS: [11495922]|.
The kinetics of the biotinylation reaction have been determined, and the N terminus does not appear to have any role in the modification |CITS: [8631788]|. Biotinylation causes a large structural change in the C-terminal region of the protein |CITS: [9325338]|. Biotinylation results in loss of conformational flexibility of the biotin interaction region |CITS: [10048324]|; a "thumb" domain comprising amino acids 94-101 fastens the biotin moiety to the surface of the protein |CITS: [10213607]| and this interaction results in increased protein stability |CITS: [11943781]|. This thumb domain is important for acetyl CoA carboxylase activity |CITS: [11495922], [10213607]|. Unbiotinylated AccB C-terminal domain dimerizes, and biotinylated AccB C-terminal domain is monomeric |CITS: [9325338]|.
AccB appears to interact with the C terminus of the BirA biotin ligase |CITS: [11714929]|. The interaction of BirA with AccB BirA-BCCP binding may preclude BirA dimerization and therefore DNA binding and transcriptional repressor activity of BirA |CITS: [11714930]|.
A crystal structure of the biotinyl domain is presented at 1.8 angstrom resolution |CITS: [8747466]|. An NMR structure of the C-terminal domain has also been determined |CITS: [9398236], [10213607]| and implications with respect to specificity of protein-protein interactions are discussed |CITS: [9398236]|. Structural characterization of biotin carboxyl carrier protein (BCCP) by circular dichroism indicates that the biotin moiety may be partly engulfed within the protein rather than fully exposed in solution |CITS: [5438]|. Secondary structure predictions have been made |CITS: [8102604]|.
Mutation of the MKM biotinylation sequence reveals substrate requirements; the position of the lysine is critical and the flanking methionines are not |CITS: [9445386]|. Production of a protein with a mutation of the biotinylated lysine residue partially complements the heat sensitivity of another accB mutant, probably due to formation of mutant heterodimers |CITS: [11495922]|. A fabE/accB mutation is shown to disrupt biotinylation |CITS: [1370469]|. E119K and E147K mutant proteins exhibit defects in biotinylation that are due to defects in interaction with BirA, the biotin ligase |CITS: [9880519]|. Mutation of residue G133, G143, or V146 causes structural disruption of the protein |CITS: [9880519]|. A linker region N-terminal to the biotinoyl domain is also essential for function (but not required for biotinylation) |CITS: [11956202]|. Mutations in accB or accC suppress the inviability of an htrB mutant at 42 deg, which is due to accumulation of excess phospholipids |CITS: [1358874]|.
AccB has 57% identity to Anabaena sp. strain PCC 7120 biotin carboxyl carrier protein |CITS: [8102363]| and has similarity to biotin carboxyl carrier proteins from Pseudomonas aeruginosa |CITS: [7693652]|, Mycobacterium leprae |CITS: [7909542]|, Mycobacterium tuberculosis |CITS: [7909542]|, Bacillus subtilis |CITS: [7592499]|, Glycine max (soybean) |CITS: [10069834]|, Sulfolobus metallicus |CITS: [10591844]|, Lactobacillus plantarum |CITS: [11133475]|, Arabidopsis thaliana |CITS: [11299381]|, and Aquifex aeolicus |CITS: [12631286]|. AccB has similarity to the putative protein encoded by ORF2 of Lactobacillus sanfranciscensis DSM20451T |CITS: [9851037]|. AccB also has similarity to Streptomyces venezuelae ISP5230 JadJ protein, which is involved in biosynthesis of the polyketide antibiotic jadomycin B |CITS: [10784049]|. Pseudomonas aeruginosa AccB functionally complements conditional lethality of an accB mutation in E. coli|CITS: [7693652]|.
AccB exhibits an abnormally large apparent molecular weight of 22.5 kDa, compared to the predicted molecular weight of about 16.7 kDa |CITS: [1370469]|.
Purification of AccB is described |CITS: [8631788]|.
AccB peptides have been fused to exogenous proteins for use as biotinylation signals that facilitate purification |CITS: [7827508], [10357213]|.
Reviews: |CITS: [12121720], [10470036]|.
)""","""NIL""","""(Biotin carboxyl carrier protein (BCCP) plays a central role
in the acetyl-CoA carboxylase complex. The overall carboxylase
reaction takes place in two distinct half-reactions. BCCP, which
contains a biotinyl prosthetic group covalently attached to a specific
lysyl residue, is carboxylated in the first partial reaction. In the
second partial reaction the carboxyl group is transferred to an
acceptor and BCCP is regenerated for further carboxylation. |CITS:
[77187896]|.
On the other hand, BCCP amino terminal is able to bind to DNA; this means, BCCP autoregulates its coding
gene expression (the accBD operon) |CITS:[14594796]|.)""","""NIL""","""(The enzyme |FRAME:ACETYL-COA-CARBOXYLMULTI-CPLX| is one of the key enzymes in the
biosynthesis of fatty acids (see |FRAME: FASYN-INITIAL-PWY|).
The enzyme belongs to the family of enzymes that catalyze
the intermolecular transfer of carboxyl groups via the transient formation of a carboxyphosphate
intermediate covalently linked to a biotin prosthetic group |CITS: [15749055]|.
The E. coli enzyme complex is composed of two catalytic units and one carrier protein,
encoded by four different genes.
The catalytic units are |FRAME:BIOTIN-CARBOXYL-CPLX| (BC), a homodimer encoded by the
|FRAME: EG10276| gene, and |FRAME:ACETYL-COA-CARBOXYLMULTI-CPLX| (ACCT), an
α2β2 tetramer, encoded by the |FRAME:EG11647| and
|FRAME: EG10217| genes.
The carrier protein is the |FRAME:BCCP-CPLX| (BCCP), a homodimer encoded by the |FRAME:EG10275| gene.
The BCCP monomer is biotinylated by the enzyme |FRAME:BIOTINLIG-ENZRXN|.
Following dimerization of the biotinylated monomers, |FRAME:BIOTIN-CARBOXYL-CPLX| (BC) catalyzes the addition
of |FRAME: CARBON-DIOXIDE| to the carrier protein dimer, forming |FRAME:Carboxybiotin-BCCP| (carboxy-BCCP).
|FRAME:Carboxybiotin-BCCP|
in turn is the substrate for ACCT, which transfers the carboxy group to |FRAME:ACETYL-COA|,
resulting in the formation of |FRAME:MALONYL-COA| and the regeneration of |FRAME:BCCP-CPLX|.
Both biotinylation and carboxylation of the carrier protein require ATP, while the last step, transfer of the carboxy
group to |FRAME: ACETYL-COA|, does not |CITS: [15749055]|.)""",]},
'B3789' : {'ecocyc-rxns': {"""DTDPGLUCOSEPP-RXN""": """α-D-glucose 1-phosphate + dTTP = dTDP-D-glucose + diphosphate""",},'ucsd-rxns' : ['G1PTT',], 'protein-comments' : ["""NIL""",]},
'B3258' : {'ecocyc-rxns': {"""TRANS-RXN-117""": """Na+[periplasmic space] + pantothenate[periplasmic space] =Na+[cytosol] + pantothenate[cytosol] """,},'ucsd-rxns' : ['PNTOt4pp',], 'protein-comments' : ["""(PanF is a pantothenate transporter which probably functions as a
panthothenate/proton symporter. Whole cell transport assays have
shown that the cloned panF gene can complement panF
mutants with panthothenate transport defects |CITS: [90299808]|.
Overexpression of panF lead to increased panthothenate
accumulation. Whole cell transport experiments have shown that
PanF mediates high affinity panthothenate transport with a Km of
approx 0.4 μM and panthothenate uptake was stimulated by the
presence of sodium ions |CITS: [85207433]|. PanF is a member of the
SSS family of sodium/solute symporters, supporting the notion that
it functions as a sodium/panthothenate symporter |CITS: [94304911]|.
Imported panthothenate is phosphorylated by panthothenate kinase, a
key step in Coenzyme A synthesis.)""",]},
'B1296' : {'ecocyc-rxns': {},'ucsd-rxns' : ['PTRCt2pp',], 'protein-comments' : ["""(The YcjJ protein is a member of the
APC superfamily of amino acid transporters.
Based on sequence similarity, YcjJ may function as a proton-driven
amino acid uptake system.
PuuP is a putrescine importer |CITS: [15590624]|.)""",]},
'B3788' : {'ecocyc-rxns': {"""DTDPGLUCDEHYDRAT-RXN""": """dTDP-D-glucose = H2O + dTDP-4-dehydro-6-deoxy-D-glucose""",},'ucsd-rxns' : ['TDPGDH',], 'protein-comments' : ["""NIL""",]},
'B3846' : {'ecocyc-rxns': {"""KETOACYLCOATHIOL-RXN""": """an acyl-CoA + acetyl-CoA = a 3-ketoacyl-CoA + coenzyme A""","""OHBUTYRYL-COA-EPIM-RXN""": """a D-3-hydroxyacyl-CoA = an L-3-hydroxyacyl-CoA""","""OHACYL-COA-DEHYDROG-RXN""": """NAD+ + an L-3-hydroxyacyl-CoA = NADH + a 3-ketoacyl-CoA""","""ENOYL-COA-HYDRAT-RXN""": """H2O + a trans-2-enoyl-CoA = an L-3-hydroxyacyl-CoA""","""ENOYL-COA-DELTA-ISOM-RXN""": """a cis-3-enoyl-CoA = a trans-2-enoyl-CoA""",},'ucsd-rxns' : ['HACD3i','HDCOAI','HACD8i','HACD4i','HACD5i','HACD6i','HACD7i','HACD1i','ECOAH8','ECOAH6','ECOAH7','ECOAH4','ECOAH5','ECOAH2','ECOAH3','ECOAH1','ODECOAI','HACD2i','TDECOAI',], 'protein-comments' : ["""NIL""","""(The alpha subunit has four enzymatic activities associated
with it. It is part of a multienzyme complex. Two of the activities,
enoyl-CoA hydratase (EC 4.2.1.17) and 3-OHacyl-CoA epimerase (EC
5.1.2.3) are carried out by the same N terminal active site. |CITS:
[93203257]|)""","""NIL""",]},
'B4036' : {'ecocyc-rxns': {"""RXN0-2543""": """maltose[extracellular space] =maltose[cytosol] ""","""RXN0-1804""": """non-specific ion/solute[extracellular space] =non-specific ion/solute[periplasmic space] ""","""RXN0-1741""": """maltose[extracellular space] =maltose[periplasmic space] """,},'ucsd-rxns' : ['GLCtexi','MALTHXtexi','MALTPTtexi','MALTTRtexi','MALTtexi','14GLUCANtexi','MALTTTRtexi',], 'protein-comments' : ["""(LamB is a member of the Sugar Porin (SP) family. It has been characterized via X-ray crystallography to have an
18-stranded antiparallel beta-barrel structure forming the channel. |CITS: [7824948]| It was originally discovered as a
receptor for the bacteriophage lambda. |CITS: [4201774]| It specifically facilitates the diffusion of maltose and other
maltodextrins (α1-4 linked polyglucosyls) across the outer membrane. |CITS: [9299337]| In order to facillitate
diffusion of malodextrins, it must form a homotrimer. |CITS: [7824948]|
Targeting of LamB to the Sec-translocase for transport across the inner membrane
is SecB-dependent |CITS:[16352602]|.)""","""NIL""",]},
'B0368' : {'ecocyc-rxns': {"""RXN0-299""": """taurine + α-ketoglutarate + O2 = aminoacetaldehyde + sulfite + succinate + CO2""",},'ucsd-rxns' : ['TAUDO',], 'protein-comments' : ["""(E. coli can utilize aliphatic sulfonates as sulfur sources for growth. Taurine dioxygenase is a non-heme iron
oxidase that catalyzes the oxygenolytic release of sulfite from taurine. The enzyme requires α-ketoglutarate
and Fe2+, and is stimulated by ascorbate. TauD is expressed only under conditions of sulfate
starvation |CITS: [96404792][97435261]|.
Each subunit of TauD binds a single Fe2+ molecule |CITS: [10563813]|. Kinetic analysis of the enzyme
has been performed |CITS: [10563813][12642663][15225039][15751960][15924433]|. The presence of an oxidized
Fe intermediate involved in hydrogen abstraction from the C1 carbon of taurine has been suggested
|CITS: [12809506][14570457]|.
Crystal structures of TauD have been solved |CITS: [11955067][12741810]|.
Review: |CITS: [11479697]|)""","""NIL""",]},
'B3845' : {'ecocyc-rxns': {"""KETOACYLCOATHIOL-RXN""": """an acyl-CoA + acetyl-CoA = a 3-ketoacyl-CoA + coenzyme A""",},'ucsd-rxns' : ['KAT8','KAT1','KAT2','KAT3','KAT4','KAT5','KAT6','KAT7',], 'protein-comments' : ["""NIL""","""(The beta subunit has one enzymatic activity associated with
it and is part of a multienzyme complex.)""","""NIL""",]},
'B0047' : {'ecocyc-rxns': {"""TRANS-RXN-42""": """H+[periplasmic space] + K+[cytosol] =H+[cytosol] + K+[periplasmic space] """,},'ucsd-rxns' : ['Kt3pp',], 'protein-comments' : ["""(KefB and KefC are two independent glutathione-regulated potassium efflux
systems, which play a role in responding to changes in osmotic
pressure and in protecting the cell from electrophile toxicity. Mutations
in kefB and kefC affect potassium efflux at neutral pH, can
be complemented by the cloned genes and probably function via potassium/proton
antiport |CITS: [85200098] [87279929]|. Potassium efflux by KefB or KefC
is activated by adducts formed by reaction of glutathione with electrophilic
compounds such as N-ethylmaleimide, methylglyoxal and
chlorodinitrobenzene |CITS: [95020661] [90286917]|. Potassium efflux mediated by
KefB and KefC leads to acidification of the cytoplasm, which protects the cell
from electrophile toxicity |CITS: [97175522] [96130836]|. KefB and KefC differ
in their activation by methylglyoxal, with KefC only weakly activated
|CITS: [99194803]|. KefC is a member of the CPA2 family of monovalent cation/proton
antiporters. In addition to KefB and KefC, additional unidentified potassium efflux systems
exist.
)""",]},
'B3843' : {'ecocyc-rxns': {"""3-OCTAPRENYL-4-OHBENZOATE-DECARBOX-RXN""": """3-octaprenyl-4-hydroxybenzoate = 2-octaprenylphenol + CO2""",},'ucsd-rxns' : ['OPHBDC',], 'protein-comments' : ["""(3-Octaprenyl-4-hydroxybenzoate decarboxylase catalyzes the
third reaction in ubiquinone biosynthesis. The enzyme has not been
studied fully, but it is known that for optimal activity the enzyme
requires Mn2+, a membrane fraction (or phospholipids) and an
unidentified soluble co-factor. There is a second decarboxylase present in
E. coli, the ubiX gene product. It is present in much lower levels than the
ubiD encoded enzyme. |CITS: [ColiSalII] [76253689] [20485580]|
A mutant shows a defect in the aerobic and anaerobic ubiquinone biosynthesis pathways |CITS: [365223]|. A ubiD mutation (in combination with a ubiX mutation) may contribute to the thiol hypersensitivity exhibited by an IS16 mutant; this sensitivity is associated with low ubiquinone abundance |CITS: [9658014]|.
Regulation has been described |CITS: [12799002]|. Gene expression shows dependence on carbon source and regulation via Fnr, ArcA and HemA |CITS: [12799002]|.)""","""NIL""",]},
'B0019' : {'ecocyc-rxns': {"""TRANS-RXN-129""": """Na+[cytosol] + 2 H+[periplasmic space] =Na+[periplasmic space] + 2 H+[cytosol] """,},'ucsd-rxns' : ['NAt3_2pp',], 'protein-comments' : ["""(NhaA is a sodium ion/proton antiporter that uses the proton electrochemical gradient to expel sodium ions
from the cytoplasm and functions primarily in the adaptation to high salinity and alkaline pH. NhaA has
been purified and reconstituted into sodium-loaded proteoliposomes and demonstrated to transport sodium
ions and protons with a 1:2 stoichiometry. This value is independent of pH between 7.2 and 8.1
|CITS:[8383669]|. Electron cryo-microscopic analysis has suggested a 12 transmembrane helical structure
of NhaA, with both N and C termini located in the cytoplasm |CITS:[10638764]|. The structure of NhaA has
been determined by X-ray crystallography to a resolution of 3.45 angstroms |CITS:[15988517]|. One of the
most striking features of NhaA is its extreme sensitivity to pH. The activity of NhaA increases 2000-fold
between pH 6.5 and 8.5 |CITS:[9398175]|. At the protein level, activation of the protein by pH confers a
conformational change. This was demonstrated by probing intact membrane vesicles at various pH values
with trypsin. The protein remains relatively uncleaved at low pH, in contrast to at high pH when the
trypsin-cleavable sites become exposed |CITS:[9398175]|. Insertion mutation experiments have suggested
the involvement of loop VIII-IX in this pH-induced conformational change |CITS:[10455127]|. Northern
hybridization and analysis of nhaA-lacZ gene fusion has demonstrated that nhaA
transcription is dependent on NhaR, a positive regulator of the LysR family, and sodium ion, an
environmental signal for nhaA transcription. Transcription of the two nhaA promoters has
been studied |CITS:[11133959]|. 2-aminoperimidine is a specific inhibitor of NhaA |CITS:[15642346]|.
Review: |CITS:[15282168]|
)""",]},
'B2988' : {'ecocyc-rxns': {"""GSPSYN-RXN""": """spermidine + glutathione + ATP = glutathionylspermidine + ADP + phosphate""","""GSPAMID-RXN""": """glutathionylspermidine + H2O = glutathione + spermidine""",},'ucsd-rxns' : ['GSPMDA','GSPMDS',], 'protein-comments' : ["""NIL""","""(The enzyme is most likely a dimer, although a trimeric
structure may be possible. |CITS: [95294007]|)""",]},
'B3960' : {'ecocyc-rxns': {"""ARGSUCCINLYA-RXN""": """L-arginino-succinate = L-arginine + fumarate""",},'ucsd-rxns' : ['ARGSL',], 'protein-comments' : ["""(Argininosuccinate lyase catalyzes the final step in the L-arginine biosynthesis pathway.
A crystal structure of argininosuccinate lyase has been solved at 2.44 Å resolution; the enzyme appears to be
tetrameric, with a dimer as the asymmetric unit of this crystal form |CITS: [15502303]|.
ArgH expression is repressed by the addition of arginine or ornithine to the medium |CITS: [770426]|.)""",]},
'B0049' : {'ecocyc-rxns': {"""3.6.1.41-RXN""": """H2O + P(1),P(4)-bis(5'-adenosyl)tetraphosphate -> 2 ADP""",},'ucsd-rxns' : ['GP4GH','AP5AH','AP4AH',], 'protein-comments' : ["""(The apaH gene encodes diadenosine tetraphosphatase (diadenosine 5', 5'''-P1, P4-tetraphosphate pyrophosphohydrolase) |CITS: [2995325]|. Substrate specificity |CITS: [2820468], [2554885], [2172926]| and reaction kinetics |CITS: [2172926]| have been examined. The enzyme is not inhibited by fluoride |CITS: [2159411]|.
An apaH mutation leads to elevated abundance of diadenosine tetraphosphate (Ap4A) |CITS: [2544886], [2157025]|. An apaH mutant exhibits defects in transcription, including defects in sigmaF-mediated gene regulation and in catabolite repression |CITS: [2544886]|. An apaH mutation also affects sensitivity to kasugamycin, possibly as a result of a general defect in stress resistance |CITS: [2157025]|. An apaH mutant exhibits decreased resistance to heat, compared to wild type |CITS: [1935909]|, and this phenotype is suppressed by ClpB overproduction |CITS: [8468292]|. The cfcB1 mutation is an apaH allele; the mutation causes cell cycle defects that indicate that Ap4A regulates the initiation of cell division |CITS: [9286857]|. Overproduction causes decreased diadenosine tetraphosphate abundance |CITS: [2995325]|. Overproduction does not alter the profile of proteins produced upon heat shock or oxidative damage |CITS: [3038851]|. Overproduction does not increase resistance to H2O2 |CITS: [3038851]|.
ApaH has similarity to a protein from Klebsiella aerogenes |CITS: [1551851]| and to Bacillus subtilis PrpE |CITS: [12059787]|. ApaH also has similarity to serine/threonine protein phosphatases from eukaryotes |CITS: [8119291]|. The ApaH protein of Salmonella enterica serovar Typhimurium is required for wild-type invasion of human cells in vitro |CITS: [12824172]|. Haemophilus parasuis ApaH is associated with virulence in swine |CITS: [14519336]|.
Regulation has been described |CITS: [3031429], [2670894]|.)""",]},
'B0048' : {'ecocyc-rxns': {"""DIHYDROFOLATEREDUCT-RXN""": """NADP+ + tetrahydrofolate = NADPH + 7,8-dihydrofolate""",},'ucsd-rxns' : ['DHFR',], 'protein-comments' : ["""(Review: |CITS: [15139807]|)""",]},
'B0366' : {'ecocyc-rxns': {"""ABC-64-RXN""": """taurine[periplasmic space] + ATP + H2O =taurine[cytosol] + ADP + phosphate """,},'ucsd-rxns' : ['BUTSO3abcpp','ISETACabcpp','TAURabcpp',], 'protein-comments' : ["""(ATP-binding component of ABC-transporter)""","""(The TauABC transporter belongs to the ATP Binding Cassette (ABC)
superfamily |CITS: [96381453]|, and is believed to be responsible for taurine uptake
in E. coli |CITS: [96404792]|. E. coli rely on organosulfur compounds
such as taurine as sources of sulfur when the level of inorganic sulfate
available in the invironment is low |CITS: [96404792]|. Disruption of the tauABC
genes resulted in the loss of the ability to utilize taurine
(2-aminoethanesulfonate) as a source of sulfur but did not affect the
utilization of a range of other aliphatic sulfonates as sulfur sources.
Taurine utilization was restored when the tauABC mutants
were complemented with a clone of the tauABC locus |CITS: [96404792]|. TauA
contains a N-terminal signal sequence, indicating that it is probably
located in the periplasm, and therefore may function as the substrate
binding component of the ABC transporter |CITS: [96404792]|. TauC is the membrane
component of the TauABC taurine ABC transporter |CITS:[8808933]|. Membrane topology
predictions using experimentally determined C terminus locations indicate that TauC has
6 transmembrane helices and the C-terminus is located in the cytoplasm |CITS:[15044727]|
TauB and TauC show strong sequence similarities to ATP-binding components and
membrane components, respectively, of other members of the ABC
superfamily |CITS: [96404792]|. Expression of tauABC is induced by sulfate
starvation, and analysis of LacZ fusions showed that the tauABC
operon is repressed by the presence of sulfur containing compounds, such as sulfate,
cysteine, cystine, ethanesulfonate, and lanthionine |CITS: [96404792]|.)""",]},
'B0367' : {'ecocyc-rxns': {"""ABC-64-RXN""": """taurine[periplasmic space] + ATP + H2O =taurine[cytosol] + ADP + phosphate """,},'ucsd-rxns' : ['BUTSO3abcpp','ISETACabcpp','TAURabcpp',], 'protein-comments' : ["""(membrane component of ABC transporter)""","""(The TauABC transporter belongs to the ATP Binding Cassette (ABC)
superfamily |CITS: [96381453]|, and is believed to be responsible for taurine uptake
in E. coli |CITS: [96404792]|. E. coli rely on organosulfur compounds
such as taurine as sources of sulfur when the level of inorganic sulfate
available in the invironment is low |CITS: [96404792]|. Disruption of the tauABC
genes resulted in the loss of the ability to utilize taurine
(2-aminoethanesulfonate) as a source of sulfur but did not affect the
utilization of a range of other aliphatic sulfonates as sulfur sources.
Taurine utilization was restored when the tauABC mutants
were complemented with a clone of the tauABC locus |CITS: [96404792]|. TauA
contains a N-terminal signal sequence, indicating that it is probably
located in the periplasm, and therefore may function as the substrate
binding component of the ABC transporter |CITS: [96404792]|. TauC is the membrane
component of the TauABC taurine ABC transporter |CITS:[8808933]|. Membrane topology
predictions using experimentally determined C terminus locations indicate that TauC has
6 transmembrane helices and the C-terminus is located in the cytoplasm |CITS:[15044727]|
TauB and TauC show strong sequence similarities to ATP-binding components and
membrane components, respectively, of other members of the ABC
superfamily |CITS: [96404792]|. Expression of tauABC is induced by sulfate
starvation, and analysis of LacZ fusions showed that the tauABC
operon is repressed by the presence of sulfur containing compounds, such as sulfate,
cysteine, cystine, ethanesulfonate, and lanthionine |CITS: [96404792]|.)""",]},
'B3967' : {'ecocyc-rxns': {"""GLUTRACE-RXN""": """L-glutamate = D-glutamate""",},'ucsd-rxns' : ['GLUR',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B3849' : {'ecocyc-rxns': {"""TRANS-RXN-3""": """H+[periplasmic space] + K+[periplasmic space] =H+[cytosol] + K+[cytosol] """,},'ucsd-rxns' : ['Kt2pp',], 'protein-comments' : ["""(TrkH is a potassium ion transporter, closely related to the TrkG
potassium ion transporter. Inactivation of either trkG or
trkH genes affects the kinetics of potassium uptake
|CITS: [95204366]|. Both TrkG and TrkH appear to be low affinity
transporters for potassium (Km of 1-6 mM). Both TrkG and TrkH
appear to function in conjunction with TrkA, a peripheral membrane
binding protein that binds NAD+ and is essential for TrkG/H activity
|CITS: [89380255] [94018648]|. TrkE, an ATP binding protein, additionally
is required for TrkH activity and affects the kinetics of TrkG activity
|CITS: [91100357]|. Both TrkA and TrkE probably play regulatory roles.
Interactions between TrkG and TrkH remain to be clarified. TrkG and
TrkH are members of the Trk family of potassium ion transporters and
probably function as potassium ion/proton symporters.)""",]},
'B2501' : {'ecocyc-rxns': {"""POLYPHOSPHATE-KINASE-RXN""": """ATP + (POLYPHOSPHATE)(N) = ADP + (polyphosphate)(n+1)""",},'ucsd-rxns' : ['PPK2r','PPKr',], 'protein-comments' : ["""NIL""","""(The role of polyphosphate (poly(Pi)) in E. coli is still not fully understood; it may
function in energy storage. Polyphosphate kinase (PPK) has several
enzymatic activities. It catalyzes the synthesis of
poly(Pi) through the transfer of a phosphoryl group of ATP to a poly(Pi)
polymer. This reaction is readily reversible. PPK is most active with poly(Pi)
substrates of chain lengths greater than 132 phosphoryl units. Activity
decreases with decreasing chain length. In the reverse reaction ATP is synthesized
from poly(Pi). PPK can also act as a nucleoside diphosphate kinase (NDK), converting
GDP, CDP and UDP to their respective nucleoside triphosphates, in the reverse of the
poly(Pi) synthesis reaction. Finally, GDP acts on a subterminal linkage of poly(Pi),
transferring a pyrophosphoryl group and generating linear guanosine tetraphosphate (ppppG).
PPK can also autophosphorylate. These various activities differ in their biochemical optima,
subunit organization and in responses to chemical agents.
PPK has also been identified as a component of the E. coli RNA degradosome |CITS: [9383162]|.
Mutants lacking PPK do not survive stationary phase. After a period of amino acid
starvation PPK is important to the cell to increase intracellular protein degradation
to provide amino acids for synthesis of new enzymes.
PPK can combine with adenylate kinase to catalyze the formation of ADP from AMP
and poly(Pi). This polyP:AMP phosphotransferase (PAP) activity requires both
enzymes acting together. |CITS: [ColiSalII] [90307693]
[92265199] [93054553] [94165003] [97121395] [97470945] [97165039]
[96200110] [97288062] [20056233] [20127873] [20570450]|
The basic functional unit of homotetrameric polyphosphate kinase is
a dimer. However the enzyme has diverse functions
involving different subunit organizations and conformations.
When synthesizing ppppG the enzyme is a trimer and when
autophosphorylating it is a tetramer. |CITS: [20127873]|
Crystal structures have been determined for polyphosphate kinase
on its own and binding AMP-PNP |CITS: [15947782]|.)""","""(The degradosome is a large, multiprotein complex involved in RNA degradation.
It consists of the RNA degradation enzymes RNase E and PNPase, as well
as the ATP-dependent RNA helicase RhlB and the metabolic enzyme enolase |CITS: [7891559][7510217][8610017]|.
Polyphosphate kinase
and the chaperone protein DnaK are also associated with and may be components of
the degradosome |CITS: [9383162][8632981]|. A "minimal" degradosome
composed of only RNase E, PNPase and RhlB degrades malEF REP RNA in an
ATP-dependent manner in vitro, with activity equivalent to purified
whole degradosomes. RNase E enzymatic function is dispensible for this test
case, whereas PNPase must be catalytically active and incorporated into the degradosome
for degradation to occur |CITS: [10521403]|. Based on immunogold
labeling studies, RhlB and RNase E are present in equimolar quantities in
the degradosome, which is tethered to the cytoplasmic membrane via the
amino-terminus of RNase E |CITS: [11134527]|.
RNase E provides the organizational structure for the degradosome. Its
carboxy-terminal half binds PNPase, RhlB and enolase, and the loss of
this portion of the protein prevents degradation of a number of
degradosome substrates, including the ptsG and mukB mRNAs and RNA I |CITS: [8682798][9732274][15522087]|.
This
scaffold region is flexible, with isolated segments of increased structure
that may be involved in binding other degradosome constituents |CITS: [15236960]|.
RNase E binding to partner proteins can
be selectively disrupted. Loss of RhlB and enolase binding results
in reduced degradosome activity. Conversely, disrupted PNPase
binding yields increased activity. Strains any alteration in RNase E
binding do not grow as well as wild type |CITS: [12207692]|.
The amino-terminal half of RNase E contains
sequences involved in oligomerization |CITS: [9732274]|.
In vitro purified degradosome generates 147-nucleotide RNase E
cleavage intermediates from rpsT mRNA. Continuous cycles of polyadenylation
and PNPase cleavage are necessary and sufficient to break down
these intermediates, though RNase II can block this second degradation
step |CITS: [9642084]|. RNAs with 3' REP stabilizers or stem loops
must be polyadenylated to allow breakdown by the degradosome |CITS: [14731278][9933592]|.
Poly(G) and poly(U) tails do not allow degradation, though addition of a stretch
of mixed nucleotides copied from within a coding region has stimulated
degradation of a test substrate |CITS: [9933592]|.
The degradosome copurifies with fragments from its RNA substrates, including
rRNA fragments derived from cleavage of 16S and 23S rRNA by
RNase E, 5S rRNA and ssrA RNA |CITS: [9501232][10535935]|.
The DEAD-box helicases SrmB, RhlE and CsdA bind RNase E in vitro
at a different site than RhlB. RhlE and CsdA can both replace RhlB in
promoting PNPase activity in vitro |CITS: [15554979]|.
CsdA is induced by cold shock, and following a shift to 15 degrees C
it copurifies with the degradosome |CITS: [15554978]|.
At least two poly(A)-binding proteins interact with the degradosome. The
cold-shock protein CspE inhibits internal cleavage and breakdown of
polyadenylated RNA by RNase E and PNPase by blocking digestion through
the poly(A) tail. S1, a component of the 30S ribosome, binds to RNase E
and PNPase without apparent effect on their activities |CITS: [11390393]|.
The global effects of mutations in degradeosome constituents on mRNA levels have
been evaluated using microarrays |CITS: [14981237]|.)""",]},
'B0586' : {'ecocyc-rxns': {"""ENTMULTI-RXN""": """6 ATP + 3 L-serine + 3 2,3-dihydroxybenzoate = 6 diphosphate + 6 AMP + enterobactin""","""ENTF-RXN""": """ATP + L-serine = diphosphate + L-Seryl-AMP""",},'ucsd-rxns' : ['SERASr',], 'protein-comments' : ["""NIL""","""(Apo-serine activating enzyme is phosphopantetheinylated posttranslationally
resulting in the active enzyme form, serine activating enzyme.)""","""NIL""",]},
'B2021' : {'ecocyc-rxns': {"""HISTAMINOTRANS-RXN""": """imidazole acetol-phosphate + L-glutamate = L-histidinol-phosphate + α-ketoglutarate""",},'ucsd-rxns' : ['HSTPT',], 'protein-comments' : ["""NIL""","""(Histidinol-phosphate aminotransferase (HisC) catalyzes the conversion of imidazole
acetol-phosphate to histidinol-phosphate as part of the histidine biosynthesis
pathway.
HisC is presumed to catalyze the conversion of imidazole acetol-phosphate to
histidinol-phosphate based on extensive characterization of its homolog
in S. typhimurium |CITS: [5337155][5337156]|.
A number of crystal structures have been determined for the functional HisC
dimer. HisC has
been crystallized on its own to 2 Å, with histidinol-phosphate to
2.2 Å and with N-(5'-phosphopyridoxyl)-L-glutamate to 2.3 Å |CITS: [11294630]|.
It has also been crystallized with
pyridoxamine-5'-phosphate to 1.5 Å, as an internal aldimine with
pyridoxal-5'-phosphate to 2.2 Å and in a covalent complex with
pyridoxal-5'-phosphate and L-histidinol to 2.2 Å |CITS: [11518529]|.
Spectroscopic and pK(a) analyses of HisC have also been carried out |CITS: [12686152]|.)""",]},
'B0352' : {'ecocyc-rxns': {"""MHPELY-RXN""": """4-hydroxy-2-ketovalerate = acetaldehyde + pyruvate""",},'ucsd-rxns' : ['HOPNTAL',], 'protein-comments' : ["""NIL""",]},
'B2020' : {'ecocyc-rxns': {"""HISTALDEHYD-RXN""": """histidinal + NAD+ + H2O -> L-histidine + NADH""","""HISTOLDEHYD-RXN""": """histidinol + NAD+ -> histidinal + NADH""",},'ucsd-rxns' : ['HISTD',], 'protein-comments' : ["""NIL""","""(The catalytically active form of this bifunctional enzyme has
been shown to be a dimer.|CITS: [86310273]| This enzyme is an example of
a bifunctional NAD-linked dehydrogenase, where one polypeptide chain possesses
two active sites, one being an alcohol dehydrogenase and the other an aldehyde
dehydrogenase.|CITS: [82027194]|
The enzyme functions by carrying out the first oxidation
step at an active site on one subunit and then passes the intermediate
to a vicinal site on the adjacent subunit, despite the fact that both
subunits are identical.|CITS: [86310273]| The dimeric active protein has
been proposed to carry out two sequential reactions, moving the
intermediate from an active center on one subunit to another on the
second subunit.|CITS: [86310274]|
intragenic complementation occurs)""",]},
'B0875' : {'ecocyc-rxns': {"""TRANS-RXN-145""": """H2O[periplasmic space] =H2O[cytosol] """,},'ucsd-rxns' : ['H2Otpp',], 'protein-comments' : ["""(AqpZ is a water channel, or aquaporin, that allows bi-directional passive diffusion
of water in E. coli. It is a member of the Major Intrinsic Protein (MIP) family,
which includes channel proteins such as aquaporins and glycerol facilitators. AqpZ
forms a tetramer of four channels |CITS:[14630323]|. Electron microscopic analysis
to a resolution of 8 angstroms of two-dimensional crystals of purified, solubilized
AqpZ shows the protein forms a homotetramer |CITS:[10518953]|. X-ray analysis of
purified AqpZ crystals has also been performed |CITS:[14993693]|. The crystal
structure of the tetrameric AqpZ has been determined to a resolution of 3.2 angstroms
and shows two conformations in the narrowest portion of the channels. One allows
passage of water through the channel, while the other blocks the channel. This allows
for regulation of diffusion of water through the pores |CITS:[16239219]|. AqpZ has an
important role in the osmoregulatory response since it allows E. coli to adapt to
osmotic variations by rapid diffusion of water molecules |CITS:[20392456]|. Water
channel activity has been demonstrated by expression of aqpZ in
Xenopus oocytes, which produced a marked increase in osmotic water
permeability |CITS:[96094287]|. In an aqpZ knockout strain, disruption of
aqpZ is not lethal for the organism, although it greatly reduces the growth
rate and size of the bacterial colonies |CITS:[98188253]|. In response to a
hypoosmotic downshock, a sudden influx of water into the bacterial cells through
AqpZ leads to an increase in intracellular pressure to within the range needed for
growth and survival. Northern analysis confirmed the monocistronic nature of the
aqpZ gene. Regulatory studies performed with an aqpZ-lacZ gene
fusion demonstrated that expression of the gene is dependent upon the extracellular
osmolality |CITS:[98188253]|.)""",]},
'B2523' : {'ecocyc-rxns': {},'ucsd-rxns' : ['AMPTASEPG','AMPTASECG',], 'protein-comments' : ["""(The pepB gene encodes an aminopeptidase (AP) |CITS: [372108]|.)""",]},
'B1101' : {'ecocyc-rxns': {"""TRANS-RXN-157""": """phosphoenolpyruvate + β-D-glucose[periplasmic space] =β-D-glucose-6-phosphate[cytosol] + pyruvate """,},'ucsd-rxns' : ['ACGAptspp','GLCptspp',], 'protein-comments' : ["""(contains PTS Enzyme IIB and IIC domains)""","""(PtsG/Crr, the glucose-specific PTS permease, belongs to the functional
superfamily of the phosphoenolpyruvate (PEP)-dependent, sugar
transporting phosphotransferase system (PTS). The PTS transports
and simultaneously phosphorylates its sugar substrates in a process
called group translocation. PtsG/Crr takes up exogenous glucose,
releasing the phosphate ester into the cell cytoplasm in preparation
for metabolism, primarily via glycolysis|CITS: [8246840]|. It can also transport
the nonmetabolizable glucoside, methyl α-glucoside
with 10-fold lower affinity.
The Enzyme IIGlc complex possesses two domains
in a single polypeptide chain with the domain order IIC-IIB (PtsG),
and it functions with an additional polypeptide chain, the Crr
or IIAGlc protein. The IIC domain of PtsG
has been reported to possess 8 transmembrane α-helical
segments |CITS: [8505291]|. The IIB domain of PtsG and IIAGlc
are localized to the cytoplasmic side of the membrane. The overall
PTS-mediated phosphoryl transfer reaction, requiring the two general
energy coupling proteins of the PTS, Enzyme I and HPr, as well
as the three domains of the Enzyme II complex is:
PEP --> Enzyme I(his~~P)
--> HPr(his~~P)
--> IIA(his~~P) -->
IIB(cys~~P) -(IIC)-> glucose-6-P.
PtsG transports glucose with low micromolar affinity.
The ptsG operon in wild type E. coli K12 is 5-10x
inducible by growth in the presence of glucose, but some E.
coli strains synthesize PtsG constitutively. IIAGlc
is synthesized constitutively from its own promoter, but it is
also slightly inducible as a result of read through from the weaker
ptsH promoter of the pts operon. ptsG but
not crr is subject to positive control by the cyclic AMP-cyclic
AMP receptor protein (CRP) complex. The ptsG operon contains
only the ptsG gene encoding the Enzyme IICBGlc.
Both the IIAGlc protein and the IIBGlc
domain of the PtsG protein have been solved in 3-dimensions by
X-ray crystallography and NMR spectroscopy, and the 3-dimensional
structure of the complex of IIAGlc with HPr
has also been solved |CITS: [1911744],[8418852],[8784182]|. PtsG was shown to exist in two forms. It is
oligomeric within the membrane and monomeric in its soluble form in the cytoplasm. Both forms exhibit
PEP-dependent sugar phosphorylation and sugar phosphate-dependent transphosphorylation activities,
though the kinetic properties of these reactions differ between the two forms of the protein
|CITS:[15576795]|.)""",]},
'B0186' : {'ecocyc-rxns': {"""LYSDECARBOX-RXN""": """L-lysine = CO2 + cadaverine""",},'ucsd-rxns' : ['LYSDC',], 'protein-comments' : ["""(There are two lysine decarboxylases in E. coli, encoded by the cadA and ldcC genes |CITS: [9534244], [9339543], [9226257]|. The ldcC gene product, lysine decarboxylase 2 (LDC2), differs from the cadA enzyme, LDC, in that it is weakly expressed, is more thermosensitive and
has activity over a broad range of pH with an optimum higher than LDC |CITS: [9534244]|.
Overproduction and purification is described |CITS: [9339543], [9226257], [9534244]|.
LdcC has 69% identity to CadA |CITS: [9226257], [9339543]|. LdcC has similarity to Hafnia alvei lysine decarboxylase |CITS: [9339543]|.
RpoS-dependent expression at stationary phase is described |CITS: [9692215]|.)""","""NIL""",]},
'B2032' : {'ecocyc-rxns': {},'ucsd-rxns' : ['O16GLCT1',], 'protein-comments' : ["""(No information about this protein was found by a literature search conducted on November 29, 2005.)""",]},
'B1102' : {'ecocyc-rxns': {"""RXN0-1702""": """ferric coprogen[extracellular space] =ferric coprogen[periplasmic space] """,},'ucsd-rxns' : ['CPGNtonex',], 'protein-comments' : ["""(FhuE is a protein which serves as a receptor for ferric-coprogen and ferric-rhodotorulic acid. |CITS: [3032906]|
Uptake into the periplasm is facilitated by TonB coupling of inner membrane energy to power specific
uptake across the outer membrane. |CITS: [7830717]| FhuE appears to have a preference for Δ-absolute
configuration metal complexes. |CITS: [6234892]|)""",]},
'B2034' : {'ecocyc-rxns': {},'ucsd-rxns' : ['O16GALFT',], 'protein-comments' : ["""(WbbI (GalF) is not required for colanic acid biosynthesis |CITS: [8759852]|.
In E. coli O7:K1, GalF binds to and regulates GalU UDP-glucose pyrophosphorylase |CITS: [8971705]|. In E. coli K30, GalF is involved in biosynthesis of capsular polysaccharide, and transcription of the galF gene is activated by RcsB |CITS: [12581358]|.)""",]},
'B2035' : {'ecocyc-rxns': {},'ucsd-rxns' : ['O16AP1pp','O16AP2pp','O16AP3pp',], 'protein-comments' : ["""(Lipopolysaccharide (LPS) is a major component of the outer membrane in most gram-negative
bacteria. It consists of lipid A, core oligosaccharide, and O polysaccharide or O-specific antigen.
E. coli K-12 does not normally express O-specific LPS due to mutations in its laterally acquired
rfb gene cluster. rfc is found within the rfb gene cluster and encodes an O-antigen
polymerase |CITS:[7517390],[7517391]|. When the rfb-50 mutation of W3110 is complemented
with the rfb cluster from strain WG1, O16 O antigen is synthesized |CITS:[7517391]|.)""",]},
'B1107' : {'ecocyc-rxns': {"""3.2.1.52-RXN""": """EC# 3.2.1.52""",},'ucsd-rxns' : ['AGM4PH','AGMH','AGM3PH',], 'protein-comments' : ["""NIL""",]},
'B1676' : {'ecocyc-rxns': {"""PEPDEPHOS-RXN""": """pyruvate + ATP = ADP + phosphoenolpyruvate""",},'ucsd-rxns' : ['PYK',], 'protein-comments' : ["""(Pyruvate kinase I and pyruvate kinase II differ in physical and chemical properties as well as in their kinetic behavior.
Although the two enzymes are under independent genetic control, they do coexist in a wide range of nutritional and
metabolic states |CITS:[83114522][84029179]|. The two enzymes are not interconvertible. Both show positive
cooperative effects with respect to the substrate phosphoenolpyruvate |CITS:[83114522]|. Pyruvate kinase I has a
low nucleotide specificity and the 5'-diphosphates of guanosine, inosine, uridine and cytidine can all serve as
phospho acceptors |CITS: [90336973]|. Pyruvate kinase I from E. coli, unlike pyruvate kinase II, is remarkably
stable |CITS:[91315755]|.
A free N-terminal amino acid can be detected in both forms of pyruvate kinase; it corresponds to methionine for
type I and serine for type II |CITS:[83114522]|. Comparison with the known primary structures shows that bacterial
enzymes lack a substantial portion of the N-terminal sequence with respect to pyruvate kinases from vertebrates
|CITS:[91315755]|.
Regulation has been described |CITS: [8550429]|. Gene expression levels, enzyme activities, metabolite
concentrations and metabolic flux have been measured in a pykF mutant strain |CITS: [12802531][15158258]|.)""","""NIL""",]},
'B2038' : {'ecocyc-rxns': {"""DTDPRHAMSYNTHMULTI-RXN""": """dTDP-4-dehydro-6-deoxy-D-glucose + NADH = dTDP-α-L-rhamnose + NAD+ + H+""","""DTDPDEHYDRHAMEPIM-RXN""": """dTDP-4-dehydro-6-deoxy-D-glucose = dTDP-4-dehydro-6-deoxy-L-mannose""",},'ucsd-rxns' : ['TDPDRE',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B1661' : {'ecocyc-rxns': {"""2.1.1.79-RXN""": """a phospholipid olefinic fatty acid + S-adenosyl-L-methionine = a phospholipid cyclopropane fatty acid + S-adenosyl-L-homocysteine""",},'ucsd-rxns' : ['CFAS180E','CFAS180G','CFAS160G','CFAS160E',], 'protein-comments' : ["""(Cyclopropane fatty acid (CFA) synthase catalyzes a modification
of the acyl chains of phospholipid bilayers through methylenation of unsaturated fatty acyl chains to their cyclopropane derivatives |CITS: [380648]|. It is one of the few enzymes known to act on the nonpolar portion of
phospholipids dispersed in a vesicle. The enzyme acts on the double
bond of a phospholipid unsaturated fatty acid residue, which must be
9-11 carbon atoms removed from the glycerol backbone of the
molecule. |CITS: [380648] [7024727] [1445840] [9409147] [9882672]|
The enzyme is approximately 90 kD in molecular weight |CITS: [380648]|, whereas a Cfa monomer is approximately 44 kD in molecular weight |CITS: [1445840]|, indicating that the enzyme is homodimeric.
CFA synthase shows some association with the cytoplasmic membrane and shows specific binding to unsaturated fatty acid- or cyclopropane fatty acid-containing phospholipid vesicles |CITS: [380648]|.
Mutants show a reduced resistance to acid shock |CITS: [10411742]| and to freeze-thaw cycles |CITS: [3519583]|, compared to wild type. Mutants do not exhibit obvious phenotypic defects under a range of other conditions |CITS: [1107324]|. Overproduction does not cause obvious growth defects |CITS: [6325391]|. A cfa rpoS double mutant shows enhanced acid sensitivity compared to either single mutant |CITS: [10411742]|.
Purification of the enzyme is described |CITS: [380648], [1445840]|. The enzyme exhibits a short half life |CITS: [8022273]|.
Regulation has been described |CITS: [7007364], [6325391], [9882672], [8022273], [10411742], [10894739], [11786251]|. An RpoS-dependent promoter directs stationary-phase transcription, while a sigma 70-type promoter directs constitutive transcription |CITS: [8022273]|. Phospholipid-mediated enzyme stabilization |CITS: [8022273]| and degradation by a heat-shock-dependent mechanism |CITS: [10894739]| also have regulatory effects. Moderate aciditity (pH 5) induces gene expression, resulting in an acid-acclimation effect |CITS: [10411742]|. Stringent control regulation has been observed, with increases in enzyme activity upon entry into stationary phase and during isoleucine starvation |CITS: [7007364]|. The nucleotide guanosine-3',5'-bisdiphosphate (ppGpp) has an indirect regulatory effect via induction of rpoS |CITS: [9882672]|.
Review: |CITS: [9409147]|.)""","""NIL""",]},
'B1662' : {'ecocyc-rxns': {"""RIBOFLAVIN-SYN-RXN""": """2 6,7-dimethyl-8-(1-D-ribityl)lumazine = 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione + riboflavin""",},'ucsd-rxns' : ['RBFSa',], 'protein-comments' : ["""(Riboflavin synthase catalyzes the final step in riboflavin biosynthesis, the formation of the carbocyclic ring of riboflavin
by dismutation of 6,7-dimethyl-8-ribityllumazine. No homolog of this enzyme exists in humans, and it is therefore an
attractive target for antimicrobial agents against microbes that are dependent on endogenous synthesis of riboflavin.
A recombinant N-terminal domain fragment dimerizes and is able to bind riboflavin |CITS: [11488927]|.
Catalytically relevant amino acid residues have been identified by mutagenesis |CITS: [11278450]|. A kinetically
competent reaction intermediate has been identified |CITS: [11404482]|, and the enzyme kinetics have been studied
under single turnover conditions |CITS: [14504292][15843156]|.
Solution and crystal structures of N-terminal riboflavin-binding domain fragments and the riboflavin synthase
homotrimer have been solved |CITS: [11399071][11377200][12927541]|.
Reviews: |CITS: [10940330][16042598]|)""","""NIL""",]},
'B0394' : {'ecocyc-rxns': {"""FRUCTOKINASE-RXN""": """fructose + ATP -> D-fructose-6-phosphate + ADP""",},'ucsd-rxns' : ['HEX7',], 'protein-comments' : ["""(In the absence of the usual PTS-mediated route of fructose uptake, Mak catalyzes phosphorylation of fructose after
its entry into the cell via PtsGF |CITS: [10677538]|.
Mak shows trace activity in wild-type cells |CITS: [11361065]|. An A24D mutation causes increased Mak activity
|CITS: [11361065]|. The A24D mutant protein is more stable than wild-type Mak |CITS: [11742072]|.
Overexpression of yajF rescues the glucose auxotrophy of a glucokinase mutant, and the YajF protein
functions as a rudimentary glucokinase in vitro |CITS: [15157072]|. When a glucokinase-deficient strain is
placed under selective pressure for growth on glucose, a spontaneous mutation in the predicted promoter region of
yajF arises, regenerating a sigma70 consensus sequence and leading to a 94-fold increase in the expression
of yajF |CITS: [16086580]|.
Review: |CITS: [11361065]|.)""",]},
'B1744' : {'ecocyc-rxns': {"""SUCCGLUDESUCC-RXN""": """N2-succinylglutamate + H2O = succinate + L-glutamate""",},'ucsd-rxns' : ['SGDS',], 'protein-comments' : ["""(The subunit structure has not been determined.)""",]},
'B0403' : {'ecocyc-rxns': {"""MALTET-RXN""": """maltotetraose + H2O = maltotriose + β-D-glucose""","""MALTODEXGLUCOSID-RXN""": """H2O + (1,4-α-D-glucosyl)(N) = (1,4-α-D-glucosyl)(n-1) + α-D-glucose""",},'ucsd-rxns' : ['MLTG3','MLTG5','MLTG4','MLTG1','MLTG2',], 'protein-comments' : ["""NIL""",]},
'B0401' : {'ecocyc-rxns': {"""TRANS-RXN-126B""": """Na+[periplasmic space] + L-leucine[periplasmic space] =Na+[cytosol] + L-leucine[cytosol] ""","""TRANS-RXN-126A""": """Na+[periplasmic space] + L-valine[periplasmic space] =Na+[cytosol] + L-valine[cytosol] ""","""TRANS-RXN-126""": """Na+[periplasmic space] + L-isoleucine[periplasmic space] =Na+[cytosol] + L-isoleucine[cytosol] """,},'ucsd-rxns' : ['LEUt2rpp','VALt2rpp','ILEt2rpp',], 'protein-comments' : ["""(BrnQ is a probable branched chain amino acid transporter. BrnQ
is highly similar to the Salmonella typhimurium BrnQ branched
chain amino acid transporter |CITS: [90241621]| and very probably
corresponds to the Liv-II branched chain amino acid transport
system in E. coli, which has been shown to transport leucine,
valine, and isoleucine |CITS: [79048215]|.
BrnQ is a member of the LIVCS family of branched chain amino acid
transporters and probably functions as a sodium/branched chain amino
acid symporter.)""",]},
'B3403' : {'ecocyc-rxns': {"""PEPCARBOXYKIN-RXN""": """oxaloacetate + ATP = CO2 + phosphoenolpyruvate + ADP""",},'ucsd-rxns' : ['PPCK',], 'protein-comments' : ["""NIL""",]},
'B0404' : {'ecocyc-rxns': {"""3.1.4.14-RXN""": """H2O + acyl carrier protein = apo-[acyl-carrier protein] + pantetheine 4'-phosphate""",},'ucsd-rxns' : ['FA120ACPHi','FA100ACPHi','FA160ACPHi','FA141ACPHi','FA140ACPHi','FA161ACPHi','FA80ACPHi',], 'protein-comments' : ["""(acpH encodes acyl carrier protein (ACP) phosphodiesterase |CITS:[16107329]|.)""",]},
'B2131' : {'ecocyc-rxns': {},'ucsd-rxns' : ['GLYBabcpp','CHLabcpp',], 'protein-comments' : ["""(periplasmic binding component of ABC transporter)""","""(YehX, YehW, YehY, YehZ are uncharacterized members
of the ABC superfamily of transporters |CITS: [99091701]|.
YehX is the putative ATP binding component, YehW and YehY
are the membrane components, and YehZ is the putative
periplasmic binding protein. Based on sequence similarity
they probably function together as an ATP-dependant
osmoprotection transporter. The yehX, yehW,
yehY, and yehZ genes are located
within a single operon.
Osmotic shock and entry into stationary phase induced transcription of the yehZYXW operon,
which was dependent upon σs |CITS:[15251200]|.)""",]},
'B2130' : {'ecocyc-rxns': {},'ucsd-rxns' : ['GLYBabcpp','CHLabcpp',], 'protein-comments' : ["""(membrane component of ABC transporter)""","""(YehX, YehW, YehY, YehZ are uncharacterized members
of the ABC superfamily of transporters |CITS: [99091701]|.
YehX is the putative ATP binding component, YehW and YehY
are the membrane components, and YehZ is the putative
periplasmic binding protein. Based on sequence similarity
they probably function together as an ATP-dependant
osmoprotection transporter. The yehX, yehW,
yehY, and yehZ genes are located
within a single operon.
Osmotic shock and entry into stationary phase induced transcription of the yehZYXW operon,
which was dependent upon σs |CITS:[15251200]|.)""",]},
'B2133' : {'ecocyc-rxns': {"""DLACTDEHYDROGFAD-RXN""": """ubiquinone-8 + D-lactate = ubiquinol-8 + pyruvate""",},'ucsd-rxns' : ['LDH_D2','LDH_D',], 'protein-comments' : ["""(The protein is membrane associated |CITS: [7046793]|.)""",]},
'B2132' : {'ecocyc-rxns': {"""3.2.1.21-RXN""": """EC# 3.2.1.21""",},'ucsd-rxns' : ['LACZpp',], 'protein-comments' : ["""(BglX is a periplasmic β-D-glucosidase.
The enzymatic activity of BglX was evaluated with the
artificial substrate o-nitrophenyl β-D-glucopyranoside.
It has a Km of 18mM and a Vmax of 3 μM/minute for this
substrate. The actual, in vivo substrate of BglX
is unknown. Deletion of bglX has no apparent effect, and
overexpression of BglX does not aid growth on |FRAME: CPD-1141|,
|FRAME: CPD-1142| or |FRAME: CELLOBIOSE| |CITS: [8757730]|.)""",]},
'B1062' : {'ecocyc-rxns': {"""DIHYDROOROT-RXN""": """dihydroorotate + H2O = carbamoyl-L-aspartate""",},'ucsd-rxns' : ['DHORTS',], 'protein-comments' : ["""NIL""","""(Dihydroorotase catalyzes the cyclization of carbamoyl-aspartate to dihydroorotate.
The structure of dihydroorotase has been determined to 1.7 Å resolution.
Each subunit has a TIM motif with eight parallel β strands flanked by α
helices, as well as a binuclear zinc center with two ions 3.6 Å apart |CITS: [11401542]|.
A 1.9 Å structure resolved in the presence of dihydroorotate
shows that a loop in PyrC is in a different conformation in each subunit of the dimer |CITS: [15826651]|.
A mechanism has been proposed for the dihydroorotase reaction |CITS: [15610022]|.
The subunits operate cooperatively during catalysis |CITS: [15826651]|.
PyrC actually has two isoelectric points, a major band at pH 4.97 and a minor one at pH 5.26 |CITS: [6142052]|.
Translation of pyrC is regulated by transcription start site selection. When
CTP is abundant, a site distal to the start codon is chosen, allowing formation of a hairpin that
blocks ribosome binding. Otherwise, a proximal site is chosen that prevents hairpin
formation, allowing translation |CITS: [1345912][7909541][7910603]|.)""",]},
'B2134' : {'ecocyc-rxns': {"""RXN0-3461""": """EC# 3.4.99.-""",},'ucsd-rxns' : ['MDDEP3pp','MDDEP2pp','MDDEP4pp','MDDEP1pp',], 'protein-comments' : ["""(PbpG is a D-alanyl-D-alanine endopeptidase and a member of the family of penicillin-binding proteins.
It is a soluble, perisplasmic protein that is loosely membrane associated. Both PbPG and its cleavage
derivative, Pbp 8 have D-alanyl-D-alanine endopeptidase activity capable of cleaving the bonds in
murein sacculi but not in dimeric muropeptides |CITS: [7925376]|.
PbpG has consensus motifs putting it in the family of penicillin-binding endopeptidases, as well
as a signal-sequence cleavage site where its amino-terminus is clipped and a site near
the carboxy-terminus where OmpT cleaves it to yield the derivative protein PbP 8 |CITS: [7721700]|.
This latter cleavage is a preparation artifact, as it only occurs following cell lysis or
freeze-thaw perturbation of membranes |CITS: [8282705]|.
PbpG also binds soluble lytic murein transglycosylase, stimulating its
enzymatic activity via direct interaction and stabilizing it in vitro |CITS: [8063800]|.)""",]},
'B3409' : {'ecocyc-rxns': {"""TRANS-RXN-8""": """Fe2+[periplasmic space] =Fe2+[cytosol] """,},'ucsd-rxns' : ['FE2abcpp',], 'protein-comments' : ["""(FeoB is a ferrous iron uptake system belonging to the Ferrous Iron Uptake (FeoB) transporter family |CITS:
[94012482]|. Insertional mutations in feoB showed defective ferrous iron uptake activity that was
restored upon complementation by the cloned gene |CITS: [94012482]|. Sequence analysis of FeoB revealed its
homology to GTP-binding proteins, indicating that FeoB-mediated ferrous uptake might involve GTP or
ATP hydrolysis |CITS: [94012482]|. However, the specific mechanism and kinetic properties of FeoB have not
yet been characterized. The feoB gene is located in an operon with feoA, which may also be
involved in ferrous iron uptake |CITS: [94012482]|. The feo operon appears to be regulated by the Fur
iron regulatory protein |CITS: [94012482]|.)""",]},
'B2485' : {'ecocyc-rxns': {"""RXN0-3283""": """2 H+ + 2 e- -> H2""",},'ucsd-rxns' : ['FHL',], 'protein-comments' : ["""NIL""","""(On the basis of sequence similarity to hycBCDEFG, which encodes hydrogenase 3, the ten-gene
cluster hyfABCDEFGHIJ was presumed to encode a hydrogenase that interacts with formate dehydrogenase
(FdhF) to produce an active formate hydrogenlyase complex. The complex cleaves formate to dihydrogen and
carbon dioxide |CITS: [9387241]|. In support of this presumption, an H+-K+ exchange
activity was detected in osmotically stressed cells of wildtype but not in similarly treated cells from an hyf
mutant |CITS: [11817571]|. Further, formate-dependent expression of an hyf-lac fusion was reported to occur
with FhlA as an activator |CITS: [1246353]|. However, subsequent experiments indicate that the hyf operon is
probably silent in E. coli, at least under the environmental conditions examined, because mutant strains that
cannot make hydrogenases 1, 2, and 3 lack hydrogenase activity and fusion strains express significant activity only
in the presence of high levels of HyfR |CITS: [14702328]|.)""",]},
'B2484' : {'ecocyc-rxns': {"""RXN0-3283""": """2 H+ + 2 e- -> H2""",},'ucsd-rxns' : ['FHL',], 'protein-comments' : ["""NIL""","""(On the basis of sequence similarity to hycBCDEFG, which encodes hydrogenase 3, the ten-gene
cluster hyfABCDEFGHIJ was presumed to encode a hydrogenase that interacts with formate dehydrogenase
(FdhF) to produce an active formate hydrogenlyase complex. The complex cleaves formate to dihydrogen and
carbon dioxide |CITS: [9387241]|. In support of this presumption, an H+-K+ exchange
activity was detected in osmotically stressed cells of wildtype but not in similarly treated cells from an hyf
mutant |CITS: [11817571]|. Further, formate-dependent expression of an hyf-lac fusion was reported to occur
with FhlA as an activator |CITS: [1246353]|. However, subsequent experiments indicate that the hyf operon is
probably silent in E. coli, at least under the environmental conditions examined, because mutant strains that
cannot make hydrogenases 1, 2, and 3 lack hydrogenase activity and fusion strains express significant activity only
in the presence of high levels of HyfR |CITS: [14702328]|.)""",]},
'B2487' : {'ecocyc-rxns': {"""RXN0-3283""": """2 H+ + 2 e- -> H2""",},'ucsd-rxns' : ['FHL',], 'protein-comments' : ["""(This is the larger of the two catalytic subunits.
This subunit contains the [Ni-Fe (CO)(CN)2] cluster.
|CITS: [98048487]|)""","""(The hyfG and I encoded subunits comprise the
functional hydrogenase 4. |CITS: [98048487]|)""","""(On the basis of sequence similarity to hycBCDEFG, which encodes hydrogenase 3, the ten-gene
cluster hyfABCDEFGHIJ was presumed to encode a hydrogenase that interacts with formate dehydrogenase
(FdhF) to produce an active formate hydrogenlyase complex. The complex cleaves formate to dihydrogen and
carbon dioxide |CITS: [9387241]|. In support of this presumption, an H+-K+ exchange
activity was detected in osmotically stressed cells of wildtype but not in similarly treated cells from an hyf
mutant |CITS: [11817571]|. Further, formate-dependent expression of an hyf-lac fusion was reported to occur
with FhlA as an activator |CITS: [1246353]|. However, subsequent experiments indicate that the hyf operon is
probably silent in E. coli, at least under the environmental conditions examined, because mutant strains that
cannot make hydrogenases 1, 2, and 3 lack hydrogenase activity and fusion strains express significant activity only
in the presence of high levels of HyfR |CITS: [14702328]|.)""",]},
'B2486' : {'ecocyc-rxns': {"""RXN0-3283""": """2 H+ + 2 e- -> H2""",},'ucsd-rxns' : ['FHL',], 'protein-comments' : ["""NIL""","""(On the basis of sequence similarity to hycBCDEFG, which encodes hydrogenase 3, the ten-gene
cluster hyfABCDEFGHIJ was presumed to encode a hydrogenase that interacts with formate dehydrogenase
(FdhF) to produce an active formate hydrogenlyase complex. The complex cleaves formate to dihydrogen and
carbon dioxide |CITS: [9387241]|. In support of this presumption, an H+-K+ exchange
activity was detected in osmotically stressed cells of wildtype but not in similarly treated cells from an hyf
mutant |CITS: [11817571]|. Further, formate-dependent expression of an hyf-lac fusion was reported to occur
with FhlA as an activator |CITS: [1246353]|. However, subsequent experiments indicate that the hyf operon is
probably silent in E. coli, at least under the environmental conditions examined, because mutant strains that
cannot make hydrogenases 1, 2, and 3 lack hydrogenase activity and fusion strains express significant activity only
in the presence of high levels of HyfR |CITS: [14702328]|.)""",]},
'B2481' : {'ecocyc-rxns': {"""RXN0-3283""": """2 H+ + 2 e- -> H2""",},'ucsd-rxns' : ['FHL',], 'protein-comments' : ["""(This subunit contains four 4Fe-4S clusters and
may be involved in electron transfer. |CITS: [98048487]| Sequence similarity suggests that it may also contain
β-barrel structure(s). |CITS: [12192075]|)""","""(On the basis of sequence similarity to hycBCDEFG, which encodes hydrogenase 3, the ten-gene
cluster hyfABCDEFGHIJ was presumed to encode a hydrogenase that interacts with formate dehydrogenase
(FdhF) to produce an active formate hydrogenlyase complex. The complex cleaves formate to dihydrogen and
carbon dioxide |CITS: [9387241]|. In support of this presumption, an H+-K+ exchange
activity was detected in osmotically stressed cells of wildtype but not in similarly treated cells from an hyf
mutant |CITS: [11817571]|. Further, formate-dependent expression of an hyf-lac fusion was reported to occur
with FhlA as an activator |CITS: [1246353]|. However, subsequent experiments indicate that the hyf operon is
probably silent in E. coli, at least under the environmental conditions examined, because mutant strains that
cannot make hydrogenases 1, 2, and 3 lack hydrogenase activity and fusion strains express significant activity only
in the presence of high levels of HyfR |CITS: [14702328]|.)""",]},
'B2029' : {'ecocyc-rxns': {"""6PGLUCONDEHYDROG-RXN""": """6-phospho-D-gluconate + NAD(P)+ = D-ribulose-5-phosphate + CO2 + NAD(P)H""",},'ucsd-rxns' : ['GND',], 'protein-comments' : ["""(A null mutation in the gnd gene encoding 6-phosphogluconate dehydrogenase does not affect the growth rate
significantly. However, cellular metabolism and metabolic flux is changed |CITS: [14661115][12670695]|.
Expression of 6-phosphogluconate dehydrogenase is growth rate regulated. Regulation is both
at transcriptional |CITS: [8282686]| and posttranscriptional (translation initiation) |CITS: [7592434]| levels.
The enzyme is a homodimer |CITS: [786365]|.)""","""NIL""",]},
'B2483' : {'ecocyc-rxns': {"""RXN0-3283""": """2 H+ + 2 e- -> H2""",},'ucsd-rxns' : ['FHL',], 'protein-comments' : ["""NIL""","""(On the basis of sequence similarity to hycBCDEFG, which encodes hydrogenase 3, the ten-gene
cluster hyfABCDEFGHIJ was presumed to encode a hydrogenase that interacts with formate dehydrogenase
(FdhF) to produce an active formate hydrogenlyase complex. The complex cleaves formate to dihydrogen and
carbon dioxide |CITS: [9387241]|. In support of this presumption, an H+-K+ exchange
activity was detected in osmotically stressed cells of wildtype but not in similarly treated cells from an hyf
mutant |CITS: [11817571]|. Further, formate-dependent expression of an hyf-lac fusion was reported to occur
with FhlA as an activator |CITS: [1246353]|. However, subsequent experiments indicate that the hyf operon is
probably silent in E. coli, at least under the environmental conditions examined, because mutant strains that
cannot make hydrogenases 1, 2, and 3 lack hydrogenase activity and fusion strains express significant activity only
in the presence of high levels of HyfR |CITS: [14702328]|.)""",]},
'B2482' : {'ecocyc-rxns': {"""RXN0-3283""": """2 H+ + 2 e- -> H2""",},'ucsd-rxns' : ['FHL',], 'protein-comments' : ["""NIL""","""(On the basis of sequence similarity to hycBCDEFG, which encodes hydrogenase 3, the ten-gene
cluster hyfABCDEFGHIJ was presumed to encode a hydrogenase that interacts with formate dehydrogenase
(FdhF) to produce an active formate hydrogenlyase complex. The complex cleaves formate to dihydrogen and
carbon dioxide |CITS: [9387241]|. In support of this presumption, an H+-K+ exchange
activity was detected in osmotically stressed cells of wildtype but not in similarly treated cells from an hyf
mutant |CITS: [11817571]|. Further, formate-dependent expression of an hyf-lac fusion was reported to occur
with FhlA as an activator |CITS: [1246353]|. However, subsequent experiments indicate that the hyf operon is
probably silent in E. coli, at least under the environmental conditions examined, because mutant strains that
cannot make hydrogenases 1, 2, and 3 lack hydrogenase activity and fusion strains express significant activity only
in the presence of high levels of HyfR |CITS: [14702328]|.)""",]},
'B2976' : {'ecocyc-rxns': {"""MALSYN-RXN""": """acetyl-CoA + H2O + glyoxylate = malate + coenzyme A""",},'ucsd-rxns' : ['MALS',], 'protein-comments' : ["""(There are two isozymes of malate synthase in E. coli. Malate synthase G, encoded by the glcB gene, is
responsible for almost all of the malate synthesis in cells metabolizing glyoxylate formed during growth on glycolate.
Malate synthase A, encoded by the aceB gene, is involved in the glyoxylate bypass. It metabolizes
glyoxylate formed in the dissimilation of acetate |CITS: [95010032]|.
The crystal and solution structures of the malate synthase G in various conformations have been determined
at 1.95 Å resolution |CITS: [10715138][12662935][12930982][15637152]|.
Expression of glcB is inducible by glycolate |CITS: [9880556]|.)""",]},
'B2028' : {'ecocyc-rxns': {"""UGD-RXN""": """H2O + 2 NAD+ + UDP-D-glucose = 2 NADH + UDP-D-glucuronate""",},'ucsd-rxns' : ['UDPGD',], 'protein-comments' : ["""(Overproduction of UDP-glucose dehydrogenase reduces production of K5 polysaccharide during exogenous expression of the K5 biosynthesis gene gluster |CITS: [12775214]|.
Udp UDP-glucose dehydrogenase activity is activated by tyrosine phosphorylation catalyzed by the tyrosine kinase Wzc |CITS: [12851388]|. Udp does not appear to be a good substrate for the tyrosine phosphorylase Wzb |CITS: [12851388]|.)""",]},
'B2489' : {'ecocyc-rxns': {"""RXN0-3283""": """2 H+ + 2 e- -> H2""",},'ucsd-rxns' : ['FHL',], 'protein-comments' : ["""(This is the smaller of the two catalytic subunits.
This subunit contains a 4Fe-4S cluster. |CITS: [98048487]|)""","""(The hyfG and I encoded subunits comprise the
functional hydrogenase 4. |CITS: [98048487]|)""","""(On the basis of sequence similarity to hycBCDEFG, which encodes hydrogenase 3, the ten-gene
cluster hyfABCDEFGHIJ was presumed to encode a hydrogenase that interacts with formate dehydrogenase
(FdhF) to produce an active formate hydrogenlyase complex. The complex cleaves formate to dihydrogen and
carbon dioxide |CITS: [9387241]|. In support of this presumption, an H+-K+ exchange
activity was detected in osmotically stressed cells of wildtype but not in similarly treated cells from an hyf
mutant |CITS: [11817571]|. Further, formate-dependent expression of an hyf-lac fusion was reported to occur
with FhlA as an activator |CITS: [1246353]|. However, subsequent experiments indicate that the hyf operon is
probably silent in E. coli, at least under the environmental conditions examined, because mutant strains that
cannot make hydrogenases 1, 2, and 3 lack hydrogenase activity and fusion strains express significant activity only
in the presence of high levels of HyfR |CITS: [14702328]|.)""",]},
'B2488' : {'ecocyc-rxns': {"""RXN0-3283""": """2 H+ + 2 e- -> H2""",},'ucsd-rxns' : ['FHL',], 'protein-comments' : ["""(This subunit contains two 4Fe-4S and one Fe-S
clusters. |CITS: [98048487]|)""","""(On the basis of sequence similarity to hycBCDEFG, which encodes hydrogenase 3, the ten-gene
cluster hyfABCDEFGHIJ was presumed to encode a hydrogenase that interacts with formate dehydrogenase
(FdhF) to produce an active formate hydrogenlyase complex. The complex cleaves formate to dihydrogen and
carbon dioxide |CITS: [9387241]|. In support of this presumption, an H+-K+ exchange
activity was detected in osmotically stressed cells of wildtype but not in similarly treated cells from an hyf
mutant |CITS: [11817571]|. Further, formate-dependent expression of an hyf-lac fusion was reported to occur
with FhlA as an activator |CITS: [1246353]|. However, subsequent experiments indicate that the hyf operon is
probably silent in E. coli, at least under the environmental conditions examined, because mutant strains that
cannot make hydrogenases 1, 2, and 3 lack hydrogenase activity and fusion strains express significant activity only
in the presence of high levels of HyfR |CITS: [14702328]|.)""",]},
'B4041' : {'ecocyc-rxns': {"""GLYCEROL-3-P-ACYLTRANSFER-RXN""": """sn-glycerol-3-phosphate + an acyl-ACP -> a 1-acyl-sn-glycerol-3P + acyl carrier protein""",},'ucsd-rxns' : ['G3PAT140','G3PAT180','G3PAT181','G3PAT160','G3PAT161','G3PAT141','G3PAT120',], 'protein-comments' : ["""NIL""",]},
'B1817' : {'ecocyc-rxns': {"""TRANS-RXN-167A""": """phosphoenolpyruvate + glucosamine[periplasmic space] =D-glucosamine-6-phosphate[cytosol] + pyruvate ""","""TRANS-RXN-157""": """phosphoenolpyruvate + β-D-glucose[periplasmic space] =β-D-glucose-6-phosphate[cytosol] + pyruvate ""","""TRANS-RXN-167""": """phosphoenolpyruvate + N-acetyl-D-glucosamine[periplasmic space] =N-acetyl-D-glucosamine-6-phosphate[cytosol] + pyruvate ""","""TRANS-RXN-165""": """phosphoenolpyruvate + mannose[periplasmic space] =mannose-6-phosphate[cytosol] + pyruvate ""","""TRANS-RXN-158A""": """phosphoenolpyruvate + fructose[periplasmic space] =D-fructose-6-phosphate[cytosol] + pyruvate """,},'ucsd-rxns' : ['GAMptspp','MANptspp','FRUpts2pp','GLCptspp','ACMANAptspp',], 'protein-comments' : ["""(contains PTS Enzyme IIA and IIB domains)""","""(ManXYZ, the mannose PTS permease, belongs to the functional superfamily
of the phosphoenolpyruvate (PEP)-dependent, sugar transporting
phosphotransferase system (PTS). The PTS transports and simultaneously
phosphorylates its sugar substrates in a process called group
translocation. ManXYZ takes up exogenous hexoses (mannose, glucose,
glucosamine, fructose, 2-deoxyglucose, mannosamine, N-acetylglucosamine,
etc.), releasing the phosphate esters into the cell cytoplasm
in preparation for metabolism, primarily via glycolysis |CITS: [8246840]|.
ManXYZ, the Enzyme IIMan complex, possesses
four domains in three polypeptide chains, ManX=IIABMan,
ManY=IICMan and ManZ=IIDMan.
They are members of the mannose PTS permease family, the "splinter
group", which is not homologous to most other PTS permeases.
The IIB and IIA domains (ManX) form a homodimer that is localized
to the cytoplasmic side of the membrane |CITS: [94086520]|. ManXYZ was shown to exist in two forms. It is
oligomeric within the membrane and monomeric in its soluble form in the cytoplasm. Both forms exhibit
PEP-dependent sugar phosphorylation and sugar phosphate-dependent transphosphorylation activities,
though the kinetic properties of these reactions differ between the two forms of the protein
|CITS:[15576795]|. IIC and IID are integral membrane proteins with six and one transmembrane
α-helical spanner(s), respectively |CITS: [8774730]|. The 3-dimensional structure of
IIAMan and the secondary structure of IIBMan
have been determined |CITS: [8676384] [9030753]|. The overall PTS-mediated phosphoryl
transfer reaction, requiring the two general energy coupling proteins
of the PTS, Enzyme I and HPr, as well as the three domains of
the Enzyme II complex is:
PEP --> Enzyme I(his~~P)
--> HPr(his~~P)
--> IIA(his~~P) -->
IIB(his~~P)-(IICD)-> hexose-6-P.
ManXYZ transports mannose with micromolar affinity.
The manXYZ operon is either constitutively expressed or
inducibly expressed in response to extracellular sugar substrates
depending on the E. coli strain examined. The Mlc protein
plays a role in transcriptional regulation of this operon |CITS: [98143423]|.
The manXYZ operon is also subject to positive control
by the cyclic AMP-cyclic AMP receptor protein (CRP) complex.
)""",]},
'B2315' : {'ecocyc-rxns': {"""RXN0-2921""": """methylene-H4PteGlu(n) + L-glutamate + ATP = methylene-H4PteGlu(n+1) + phosphate + ADP""","""FORMYLTHFGLUSYNTH-RXN""": """an N10-formyl-tetrahydrofolate + L-glutamate + ATP = 10-formyl-H4PteGlu(n+1) + ADP + phosphate""","""FOLYLPOLYGLUTAMATESYNTH-RXN""": """H4PteGlu(n) + L-glutamate + ATP = tetrahydropteroyl-[γ-Glu](n+1) + phosphate + ADP""","""DIHYDROFOLATESYNTH-RXN""": """L-glutamate + 7,8-dihydropteroate + ATP = 7,8-dihydrofolate + phosphate + ADP""",},'ucsd-rxns' : ['DHFS',], 'protein-comments' : ["""(folC codes for a bifunctional polypeptide.)""",]},
'B1814' : {'ecocyc-rxns': {"""THREDEHYD-RXN""": """L-threonine -> 2-oxobutanoate + ammonia""","""4.3.1.17-RXN""": """L-serine -> pyruvate + ammonia""",},'ucsd-rxns' : ['SERD_L','THRD_L',], 'protein-comments' : ["""(Properties of the anaerobically purified SdaA protein are consistent with the presence of a [4Fe-4S] cluster
|CITS: [15155761]|.)""",]},
'B1812' : {'ecocyc-rxns': {"""PABSYNMULTI-RXN""": """L-glutamine + chorismate = p-aminobenzoate + L-glutamate + pyruvate""","""PABASYN-RXN""": """L-glutamine + chorismate = 4-amino-4-deoxychorismate + L-glutamate""",},'ucsd-rxns' : ['ADCS','GLUN',], 'protein-comments' : ["""(Component I catalyzes the formation of ADC by binding
chorismate and ammonia.)""","""(Before the multienzyme character of this complex was known,
a single protein was thought to carry out the reaction of
para-aminobenzoate synthesis. It was known (now incorrectly)
as para-aminobenzoate synthase. This enzyme forms the
intermediate aminodeoxychorismate.
)""","""NIL""",]},
'B3959' : {'ecocyc-rxns': {"""ACETYLGLUTKIN-RXN""": """N-acetyl-L-glutamate + ATP = N-acetylglutamyl-phosphate + ADP""",},'ucsd-rxns' : ['ACGK',], 'protein-comments' : ["""(The crystal structure of the enzyme has been determined at 1.5 Å resolution, and a catalytic mechanism has been
proposed |CITS: [99322417][12005432][12875848]|. Site-directed mutagenesis has been used to validate the model
|CITS: [14623187]|.)""","""NIL""",]},
'B0810' : {'ecocyc-rxns': {"""ABC-12-RXN""": """ATP + L-glutamine[periplasmic space] + H2O =ADP + phosphate + L-glutamine[cytosol] """,},'ucsd-rxns' : ['GLNabcpp',], 'protein-comments' : ["""NIL""","""(The GlnHPQ high-affinity glutamine transport system is a member of the ATP-Binding Cassette (ABC)
Superfamily of transporters |CITS: [96381453]|. Based on sequence similarity, GlnH is the periplasmic
glutamine-binding protein, GlnQ is the ATP-binding component, and GlnP is the membrane component
of the ABC transporter. Mutation of glnP results in the impaired ability to transport glutamine as well
as the inability to utilized glutamine as a sole source of carbon |CITS: [82007680] [87115160]|. Expression
of the cloned glnHPQ genes on a plasmid vector restored the glnH, glnP, and
glnQ mutants' abilities to transport glutamine and utilize glutamine as a sole carbon source
|CITS: [87115160]|.)""",]},
'B2738' : {'ecocyc-rxns': {},'ucsd-rxns' : ['FCLPA',], 'protein-comments' : ["""(No information about this protein was found by a literature search conducted on April 25, 2006.)""",]},
'B0813' : {'ecocyc-rxns': {"""TRANS-RXN-242""": """H+[periplasmic space] + homoserine[cytosol] =H+[cytosol] + homoserine[periplasmic space] ""","""TRANS-RXN-244""": """H+[periplasmic space] + L-threonine[cytosol] =H+[cytosol] + L-threonine[periplasmic space] """,},'ucsd-rxns' : ['HOMt2pp','THRt2pp',], 'protein-comments' : ["""(RhtA is a threonine/homoserine exporter in the Drug/Metabolite Transporter superfamily (TC: 2.A.7). It is homologous to YdeD, an
exporter that translocates metabolites of the cysteine pathway of E. coli, is also a member of the Drug/Metabolite Exporter
family (TC: 2.A.7.3). RhtA has 10 putative transmembrane spanning alpha helices. RhtA may also export other amino acids such as
proline, serine, cysteine, and histidine based upon resistance phenotypes. |CITS: [12648727]|
)""",]},
'B1819' : {'ecocyc-rxns': {"""TRANS-RXN-167A""": """phosphoenolpyruvate + glucosamine[periplasmic space] =D-glucosamine-6-phosphate[cytosol] + pyruvate ""","""TRANS-RXN-157""": """phosphoenolpyruvate + β-D-glucose[periplasmic space] =β-D-glucose-6-phosphate[cytosol] + pyruvate ""","""TRANS-RXN-167""": """phosphoenolpyruvate + N-acetyl-D-glucosamine[periplasmic space] =N-acetyl-D-glucosamine-6-phosphate[cytosol] + pyruvate ""","""TRANS-RXN-165""": """phosphoenolpyruvate + mannose[periplasmic space] =mannose-6-phosphate[cytosol] + pyruvate ""","""TRANS-RXN-158A""": """phosphoenolpyruvate + fructose[periplasmic space] =D-fructose-6-phosphate[cytosol] + pyruvate """,},'ucsd-rxns' : ['GAMptspp','MANptspp','FRUpts2pp','GLCptspp','ACMANAptspp',], 'protein-comments' : ["""(contains a PTS Enzyme IID domain)""","""(ManXYZ, the mannose PTS permease, belongs to the functional superfamily
of the phosphoenolpyruvate (PEP)-dependent, sugar transporting
phosphotransferase system (PTS). The PTS transports and simultaneously
phosphorylates its sugar substrates in a process called group
translocation. ManXYZ takes up exogenous hexoses (mannose, glucose,
glucosamine, fructose, 2-deoxyglucose, mannosamine, N-acetylglucosamine,
etc.), releasing the phosphate esters into the cell cytoplasm
in preparation for metabolism, primarily via glycolysis |CITS: [8246840]|.
ManXYZ, the Enzyme IIMan complex, possesses
four domains in three polypeptide chains, ManX=IIABMan,
ManY=IICMan and ManZ=IIDMan.
They are members of the mannose PTS permease family, the "splinter
group", which is not homologous to most other PTS permeases.
The IIB and IIA domains (ManX) form a homodimer that is localized
to the cytoplasmic side of the membrane |CITS: [94086520]|. ManXYZ was shown to exist in two forms. It is
oligomeric within the membrane and monomeric in its soluble form in the cytoplasm. Both forms exhibit
PEP-dependent sugar phosphorylation and sugar phosphate-dependent transphosphorylation activities,
though the kinetic properties of these reactions differ between the two forms of the protein
|CITS:[15576795]|. IIC and IID are integral membrane proteins with six and one transmembrane
α-helical spanner(s), respectively |CITS: [8774730]|. The 3-dimensional structure of
IIAMan and the secondary structure of IIBMan
have been determined |CITS: [8676384] [9030753]|. The overall PTS-mediated phosphoryl
transfer reaction, requiring the two general energy coupling proteins
of the PTS, Enzyme I and HPr, as well as the three domains of
the Enzyme II complex is:
PEP --> Enzyme I(his~~P)
--> HPr(his~~P)
--> IIA(his~~P) -->
IIB(his~~P)-(IICD)-> hexose-6-P.
ManXYZ transports mannose with micromolar affinity.
The manXYZ operon is either constitutively expressed or
inducibly expressed in response to extracellular sugar substrates
depending on the E. coli strain examined. The Mlc protein
plays a role in transcriptional regulation of this operon |CITS: [98143423]|.
The manXYZ operon is also subject to positive control
by the cyclic AMP-cyclic AMP receptor protein (CRP) complex.
)""",]},
'B1818' : {'ecocyc-rxns': {"""TRANS-RXN-167A""": """phosphoenolpyruvate + glucosamine[periplasmic space] =D-glucosamine-6-phosphate[cytosol] + pyruvate ""","""TRANS-RXN-157""": """phosphoenolpyruvate + β-D-glucose[periplasmic space] =β-D-glucose-6-phosphate[cytosol] + pyruvate ""","""TRANS-RXN-167""": """phosphoenolpyruvate + N-acetyl-D-glucosamine[periplasmic space] =N-acetyl-D-glucosamine-6-phosphate[cytosol] + pyruvate ""","""TRANS-RXN-165""": """phosphoenolpyruvate + mannose[periplasmic space] =mannose-6-phosphate[cytosol] + pyruvate ""","""TRANS-RXN-158A""": """phosphoenolpyruvate + fructose[periplasmic space] =D-fructose-6-phosphate[cytosol] + pyruvate """,},'ucsd-rxns' : ['GAMptspp','MANptspp','FRUpts2pp','GLCptspp','ACMANAptspp',], 'protein-comments' : ["""(contains a PTS Enzyme IIC domain)""","""(ManXYZ, the mannose PTS permease, belongs to the functional superfamily
of the phosphoenolpyruvate (PEP)-dependent, sugar transporting
phosphotransferase system (PTS). The PTS transports and simultaneously
phosphorylates its sugar substrates in a process called group
translocation. ManXYZ takes up exogenous hexoses (mannose, glucose,
glucosamine, fructose, 2-deoxyglucose, mannosamine, N-acetylglucosamine,
etc.), releasing the phosphate esters into the cell cytoplasm
in preparation for metabolism, primarily via glycolysis |CITS: [8246840]|.
ManXYZ, the Enzyme IIMan complex, possesses
four domains in three polypeptide chains, ManX=IIABMan,
ManY=IICMan and ManZ=IIDMan.
They are members of the mannose PTS permease family, the "splinter
group", which is not homologous to most other PTS permeases.
The IIB and IIA domains (ManX) form a homodimer that is localized
to the cytoplasmic side of the membrane |CITS: [94086520]|. ManXYZ was shown to exist in two forms. It is
oligomeric within the membrane and monomeric in its soluble form in the cytoplasm. Both forms exhibit
PEP-dependent sugar phosphorylation and sugar phosphate-dependent transphosphorylation activities,
though the kinetic properties of these reactions differ between the two forms of the protein
|CITS:[15576795]|. IIC and IID are integral membrane proteins with six and one transmembrane
α-helical spanner(s), respectively |CITS: [8774730]|. The 3-dimensional structure of
IIAMan and the secondary structure of IIBMan
have been determined |CITS: [8676384] [9030753]|. The overall PTS-mediated phosphoryl
transfer reaction, requiring the two general energy coupling proteins
of the PTS, Enzyme I and HPr, as well as the three domains of
the Enzyme II complex is:
PEP --> Enzyme I(his~~P)
--> HPr(his~~P)
--> IIA(his~~P) -->
IIB(his~~P)-(IICD)-> hexose-6-P.
ManXYZ transports mannose with micromolar affinity.
The manXYZ operon is either constitutively expressed or
inducibly expressed in response to extracellular sugar substrates
depending on the E. coli strain examined. The Mlc protein
plays a role in transcriptional regulation of this operon |CITS: [98143423]|.
The manXYZ operon is also subject to positive control
by the cyclic AMP-cyclic AMP receptor protein (CRP) complex.
)""",]},
'B3416' : {'ecocyc-rxns': {"""MALTODEG-RXN""": """(glucose)n + (glucose)m = (glucose)n+m-1 + β-D-glucose""","""MALTDEG-RXN""": """H2O + maltose = 2 β-D-glucose""","""AMYLOMALT-RXN""": """maltotriose + maltose = maltotetraose + β-D-glucose""",},'ucsd-rxns' : ['AMALT4','AMALT3','AMALT2','AMALT1',], 'protein-comments' : ["""NIL""",]},
'B3666' : {'ecocyc-rxns': {"""TRANS-RXN-33""": """H+[periplasmic space] + β-D-glucose-6-phosphate[periplasmic space] =β-D-glucose-6-phosphate[cytosol] + H+[cytosol] """,},'ucsd-rxns' : ['F6Pt6_2pp','GAM6Pt6_2pp','G6Pt6_2pp','MAN6Pt6_2pp',], 'protein-comments' : ["""(UhpT is a hexose phosphate transporter that is a member of the Major Facilitator Superfamily (MFS) |CITS:
[93174460]|. UhpT has been purified and reconstituted into liposomes and demonstrated to transport hexose
6-phosphates via an inorganic phosphate antiport mechanism |CITS: [86250840]|. The transport system was
also shown to catalyze a reversible phosphate: phosphate exchange |CITS: [86250840]|. Using
phosphate-loaded proteoliposomes, and in the absence of any imposed cation motive gradient, hexose
6-phosphate accumulated in the proteoliposomes, and the Km for the transport of
2-deoxy-glucose-6-phosphate via UhpT was determined to be approximately 20 μM |CITS: [86250840]|.
Size separation chromatography and reconstitution at low lipid/protein ratios suggest that UhpT has a
monomeric functional unit |CITS: [90324210]|. Hydropathy analysis and PhoA fusions suggest that UhpT has
a 12 transmembrane segment topology with the amino and carboxy termini facing the cytoplasm |CITS:
[90202680]|.)""",]},
'B3665' : {'ecocyc-rxns': {"""ADENINE-DEAMINASE-RXN""": """H2O + adenine -> ammonia + hypoxanthine""",},'ucsd-rxns' : ['ADD',], 'protein-comments' : ["""(Ade is an adenine deaminase |CITS: [11440125]| that is thought to be cryptic, as activity has been detected in mutant strains but not in wild type |CITS: [12077137]|.
The activity shows dependence on Mn2+ and exhibits tight substrate specificity for adenine |CITS: [11440125]|. The enzyme activity has been characterized in detail |CITS: [11440125]|.
The enzyme is homodimeric |CITS: [11440125]|.
Ade has similarity to Bacillus subtilis adenine deaminase |CITS: [11440125]|.
Regulation has been described |CITS: [12077137]|. Transcription of the ade gene is activated by various promoter mutations |CITS: [12077137]|. Transcription is silenced by the H-NS protein in wild type |CITS: [12077137]|.)""","""NIL""",]},
'B0432' : {'ecocyc-rxns': {"""CYT-UBIQUINOL-OXID-RXN""": """ubiquinol-8 + O2 = ubiquinone-8 + 2 H2O""",},'ucsd-rxns' : ['CYTBO3_4pp',], 'protein-comments' : ["""(CyoA is subunit II of the cytochrome bo terminal oxidase complex encoded by cyoABCDE.
Crosslinking studies suggested that subunit II functions as a ubiquinone binding site of the cytochrome bo
terminal oxidase complex |CITS: [7961841]|. However, the crystal structure of the entire cytochrome bo
terminal oxidase complex suggests that a potential ubiquinone binding site is instead located in the membrane domain
of subunit I |CITS: [11017202]|.
The CyoA polypeptide contains two transmembrane helices |CITS: [2165491]|. CyoA is a lipoprotein; during
maturation, the protein is modified by attachment of fatty acids and protease cleavage at C25; however, the
posttranslational modification is not essential for assembly or activity of the cytochrome bo terminal oxidase
complex |CITS:[9298948][15126489]|.
The three-dimensional structure of the periplasmic fragment of CyoA has been determined to 2.3A resolution
|CITS:[8433374][8618822]|. A crystal structure of the entire cytochrome bo terminal oxidase complex
containing CyoA has been determined at 3.5 A resolution |CITS: [11017202]|.
Under anaerobic conditions, cyoA is repressed 140-fold compared to growth under aerobic conditions.
This regulation is in part due to repression by Fnr |CITS: [2172211]|.
)""","""NIL""",]},
'B0933' : {'ecocyc-rxns': {},'ucsd-rxns' : ['ETHSO3abcpp','SULFACabcpp','BUTSO3abcpp','ISETACabcpp','MSO3abcpp',], 'protein-comments' : ["""(ATP-binding component of ABC transporter)""","""(Deletion mutation studies |CITS:[10506196]| indicate that the ssuEADCB gene cluster codes for proteins that enable Escherichia coli
to utilize sulfonates other than taurine as a sulfur source. Based on sequence similarity SsuABC is the ABC type transport system with
SsuA being the periplasmic substrate-binding subunit, SsuB the ATP-binding subunit and SsuC the permease. ssuD and
ssuE encode an FMNH2-dependent monooxygenase and an NAD(P)H-dependent FMN reductase, respectively.)""",]},
'B3124' : {'ecocyc-rxns': {"""GKI-RXN""": """ATP + glycerate = 2-phosphoglycerate + ADP""",},'ucsd-rxns' : ['GLYCK2',], 'protein-comments' : ["""NIL""",]},
'B0622' : {'ecocyc-rxns': {"""RXN0-1842""": """a phospholipid + KDO2-lipid A -> hepta-acylated KDO2-lipid A + a glycerol ester""",},'ucsd-rxns' : ['LIPAHT2ex','LIPAHTex',], 'protein-comments' : ["""(A PagP homodimer catalyzes palmitate transfer from a phospholipid (sn-1 position) to lipid A or to a lipid A
precursor (N-linked hydroxymyristate on the proximal unit) |CITS: [11013210]|. The catalytic site localizes to the
exterior of the outer membrane, and enzyme activity may require outer membrane problems that result in
mislocalization of palmitate-donor phospholipids from the inner to the outer leaflet of the outer membrane
|CITS: [12357033]|. However, PagP does not appear to play an active role in translocation of phospholipid to the
outer leaflet of the outer membrane |CITS: [15319435]|.
Structural characterization of PagP has been performed by NMR |CITS: [12357033]|. The transition between two
distinct conformational states of PagP has been studied |CITS: [15210985]|. A crystal structure has been solved at
1.9 A resolution |CITS: [15272304]|.
Overexpression or deletion of pagP (crcA) together with cspE and crcB has effects on camphor resistance and DNA
supercoiling |CITS: [8844142][12904550]|, but the effect might only be due to cspE and crcB.
PagP has similarity to proteins of Yersinia and Bordetella |CITS: [11013210]|. Salmonella typhimurium PagP has been characterized |CITS: [7927792], [9712687], [9790526]|. Lipid A acylation by Salmonella typhimurium PagP is implicated in resistance to cationic antimicrobial peptides that are produced by vertebrate hosts to limit infection |CITS: [9790526]|. Transcription of Salmonella typhimurium pagP is activated by PhoP |CITS: [7927792]|. A PagP homolog of Legionella pneumophila is involved in infectivity and in stationary phase survival under Mg2+-limited conditions |CITS: [11401964]|.
Regulation has been described |CITS: [9790526][15126461]|. Acylation of Lipid A is upregulated under
low-Mg2+ conditions |CITS: [9790526]|.)""","""NIL""",]},
'B0621' : {'ecocyc-rxns': {"""TRANS-RXN-202A""": """succinate[cytosol] + fumarate[periplasmic space] =fumarate[cytosol] + succinate[periplasmic space] ""","""TRANS-RXN-202""": """H+[periplasmic space] + fumarate[periplasmic space] =fumarate[cytosol] + H+[cytosol] """,},'ucsd-rxns' : ['SUCFUMtpp','FUMt2_3pp',], 'protein-comments' : ["""(The DcuC transporter is one of three transporters known to be
responsible for the uptake of C4-dicarboxylates such as fumarate under
anaerobic conditions. A knockout mutant of dcuC in a dcuA
dcuB double mutant lost the ability to grow by fumarate respiration
and was unable to mediate fumarate/succinate exchange |CITS: [97113548]|.
Whole cell experiments using dcuA-C indicated that DcuC can mediate
both fumarate/succinate exchange and fumarate/proton symport |CITS: [97113548]|.
DcuC is the prototype of the DcuC family of dicarboxylate uptake
transporters. Whether dcuC has a role outside of fumarate respiration
remains to be determined.)""",]},
'B0433' : {'ecocyc-rxns': {},'ucsd-rxns' : ['AGM4Pt2pp','AGM3Pt2pp','AGMt2pp',], 'protein-comments' : ["""(AmpG is a member of the major facilitator superfamily of transporters,
and together with AmpD, is essential for induction of the AmpC Β-lactamase
and is involved in the recycling of cell wall peptides
|CITS: [90120556] [94049112] [95291453] [96100441]|.
Mutants in ampG are unable to induce ampC and display greatly
increased cell wall turnover |CITS: [95009971]|.
AmpG is responsible for the transport of precursors of the anhMurNAc tripeptide into the cytoplasm
|CITS:[8878601]|. These precursors are the products of peptidoglycan degradation and include the
disaccharide GlcNAc-anhMurNAc as well as GlcNAc-anhMurNAc-oligopeptides (tri-, tetra-, and
pentapeptides). Transport is dependent on the proton motive force |CITS:[12426329]|.
Following uptake of these muropeptides, they are degraded, releasing the components which can
subsequently be used in cell wall synthesis |CITS: [95302966]|.
Experiments with β-lactamase fusions show AmpG contains two large cytoplasmic loops and 10
transmembrane segments |CITS:[15728916]|.
Cytosolic muramyl peptides probably induce expression of ampC by binding
to its regulator AmpR |CITS: [97302495]|.)""",]},
'B2045' : {'ecocyc-rxns': {},'ucsd-rxns' : ['GALKr',], 'protein-comments' : ["""(WcaK may be involved in colanic acid synthesis based on sequence its
presence in a putative colanic acid synthesis operon |CITS:[8759852]|.
WcaK may be responsible for adding the pyruvyl group to the E ring's
terminal galactosyl residue because it belongs to the polysaccharide
pyruvyl transferase family.)""",]},
'B0857' : {'ecocyc-rxns': {"""ABC-25-RXN""": """ATP + putrescine[periplasmic space] + H2O =ADP + phosphate + putrescine[cytosol] """,},'ucsd-rxns' : ['PTRCabcpp',], 'protein-comments' : ["""NIL""","""(The PotFGHI ATP-dependent putrescine transporter is a member of the ATP Binding Cassette (ABC)
Superfamily of transporters |CITS: [96381453]|. PotFGHI is similar in sequence and subunit composition to
the PotABCD putrescine/spermidine uptake system. Based on sequence similarity, PotG is the ATP-
binding component, PotH and Pot I are the membrane components, and PotF is the periplasmic binding
component of the ABC transporter. The PotF protein possesses a high binding affinity to putrescine
(Kd=2.0 μM) |CITS: [98316327]|. Site-directed mutagenesis have shown that PotF is the
putrescine-binding protein |CITS: [98316327]|, and gel filtration studies have show that in the presence of
1mM magnesium ion and 100mM potassium ion, PotF bound putrescine, but not spermidine, in a 1:1 ratio
|CITS: [93106992]|. A high resolution structure of PotF has been determined by x-ray crystallography
|CITS: [98316327]|. Knockout and complementation studies showed that the expression of all four proteins
was necessary for maximal putrescine transport activity |CITS: [93106992]|.)""",]},
'B2041' : {'ecocyc-rxns': {"""DTDPGLUCDEHYDRAT-RXN""": """dTDP-D-glucose = H2O + dTDP-4-dehydro-6-deoxy-D-glucose""",},'ucsd-rxns' : ['TDPGDH',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B2040' : {'ecocyc-rxns': {"""DTDPRHAMSYNTHMULTI-RXN""": """dTDP-4-dehydro-6-deoxy-D-glucose + NADH = dTDP-α-L-rhamnose + NAD+ + H+""","""DTDPDEHYRHAMREDUCT-RXN""": """NADP+ + dTDP-α-L-rhamnose = NADPH + dTDP-4-dehydro-6-deoxy-L-mannose""",},'ucsd-rxns' : ['TDPDRR',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B3543' : {'ecocyc-rxns': {"""ABC-8-RXN""": """ATP + a dipeptide[periplasmic space] + H2O =ADP + phosphate + a dipeptide[cytosol] """,},'ucsd-rxns' : ['ALAALAabcpp','CGLYabcpp','PROGLYabcpp',], 'protein-comments' : ["""NIL""","""(The DppABCDF dipeptide transport system is a member of the ATP-Binding Cassette (ABC)
Superfamily of transporters |CITS: [96381453]|. Based on sequence similarity, DppA is the substrate-binding
component, while DppB and DppC are the membrane components, and DppD and DppF are the
ATP-binding components of the ABC transporter. Mutations in dpp displayed resistance to the toxic
dipeptide Lys-aminoxyAla, and the loss of ability to utilize LeuTrp as a source of its required amino acids
|CITS: [85056880]|. Substrate specificity of DppA was studied in a filter binding assay in which column
fractions were monitored for binding activity towards radioactively labeled dipeptides and tripeptides. DppA
was observed to mediate the ATP-driven uptake of dipeptides and, to a lesser extent, tripeptides from the
periplasm |CITS: [20005603]|. DppABCDF is similar in sequence and subunit composition to the oligopeptide
uptake system OppABCDF, suggesting similar subunit functions. DppA?s unbound structure has been
resolved by x-ray crystallography to 2 angstroms, and shows two domains connected by two ?hinge? segments
|CITS: [9618375]|.
)""",]},
'B3542' : {'ecocyc-rxns': {"""ABC-8-RXN""": """ATP + a dipeptide[periplasmic space] + H2O =ADP + phosphate + a dipeptide[cytosol] """,},'ucsd-rxns' : ['ALAALAabcpp','CGLYabcpp','PROGLYabcpp',], 'protein-comments' : ["""NIL""","""(The DppABCDF dipeptide transport system is a member of the ATP-Binding Cassette (ABC)
Superfamily of transporters |CITS: [96381453]|. Based on sequence similarity, DppA is the substrate-binding
component, while DppB and DppC are the membrane components, and DppD and DppF are the
ATP-binding components of the ABC transporter. Mutations in dpp displayed resistance to the toxic
dipeptide Lys-aminoxyAla, and the loss of ability to utilize LeuTrp as a source of its required amino acids
|CITS: [85056880]|. Substrate specificity of DppA was studied in a filter binding assay in which column
fractions were monitored for binding activity towards radioactively labeled dipeptides and tripeptides. DppA
was observed to mediate the ATP-driven uptake of dipeptides and, to a lesser extent, tripeptides from the
periplasm |CITS: [20005603]|. DppABCDF is similar in sequence and subunit composition to the oligopeptide
uptake system OppABCDF, suggesting similar subunit functions. DppA?s unbound structure has been
resolved by x-ray crystallography to 2 angstroms, and shows two domains connected by two ?hinge? segments
|CITS: [9618375]|.
)""",]},
'B3541' : {'ecocyc-rxns': {"""ABC-8-RXN""": """ATP + a dipeptide[periplasmic space] + H2O =ADP + phosphate + a dipeptide[cytosol] """,},'ucsd-rxns' : ['ALAALAabcpp','CGLYabcpp','PROGLYabcpp',], 'protein-comments' : ["""NIL""","""(The DppABCDF dipeptide transport system is a member of the ATP-Binding Cassette (ABC)
Superfamily of transporters |CITS: [96381453]|. Based on sequence similarity, DppA is the substrate-binding
component, while DppB and DppC are the membrane components, and DppD and DppF are the
ATP-binding components of the ABC transporter. Mutations in dpp displayed resistance to the toxic
dipeptide Lys-aminoxyAla, and the loss of ability to utilize LeuTrp as a source of its required amino acids
|CITS: [85056880]|. Substrate specificity of DppA was studied in a filter binding assay in which column
fractions were monitored for binding activity towards radioactively labeled dipeptides and tripeptides. DppA
was observed to mediate the ATP-driven uptake of dipeptides and, to a lesser extent, tripeptides from the
periplasm |CITS: [20005603]|. DppABCDF is similar in sequence and subunit composition to the oligopeptide
uptake system OppABCDF, suggesting similar subunit functions. DppA?s unbound structure has been
resolved by x-ray crystallography to 2 angstroms, and shows two domains connected by two ?hinge? segments
|CITS: [9618375]|.
)""",]},
'B3540' : {'ecocyc-rxns': {"""ABC-8-RXN""": """ATP + a dipeptide[periplasmic space] + H2O =ADP + phosphate + a dipeptide[cytosol] """,},'ucsd-rxns' : ['ALAALAabcpp','CGLYabcpp','PROGLYabcpp',], 'protein-comments' : ["""NIL""","""(The DppABCDF dipeptide transport system is a member of the ATP-Binding Cassette (ABC)
Superfamily of transporters |CITS: [96381453]|. Based on sequence similarity, DppA is the substrate-binding
component, while DppB and DppC are the membrane components, and DppD and DppF are the
ATP-binding components of the ABC transporter. Mutations in dpp displayed resistance to the toxic
dipeptide Lys-aminoxyAla, and the loss of ability to utilize LeuTrp as a source of its required amino acids
|CITS: [85056880]|. Substrate specificity of DppA was studied in a filter binding assay in which column
fractions were monitored for binding activity towards radioactively labeled dipeptides and tripeptides. DppA
was observed to mediate the ATP-driven uptake of dipeptides and, to a lesser extent, tripeptides from the
periplasm |CITS: [20005603]|. DppABCDF is similar in sequence and subunit composition to the oligopeptide
uptake system OppABCDF, suggesting similar subunit functions. DppA?s unbound structure has been
resolved by x-ray crystallography to 2 angstroms, and shows two domains connected by two ?hinge? segments
|CITS: [9618375]|.
)""",]},
'B2720' : {'ecocyc-rxns': {"""FHLMULTI-RXN""": """formate = CO2 + H2""","""RXN0-3283""": """2 H+ + 2 e- -> H2""",},'ucsd-rxns' : ['FHL','HYD1pp',], 'protein-comments' : ["""(HycF is thought to encode a 4Fe-4S ferredoxin type protein, an intermediate electron carrier protein
|CITS: [90251163][92255260][92326636]|. The protein resembles one of the subunits of NADH:ubiquinone
oxidoreductase of the respiratory chain |CITS: [90251163][SAWERS04]|.)""","""NIL""","""(A report has described that formate oxidation in anaerobically grown E. coli is coupled to proton translocation
|CITS: [15848284]|.)""",]},
'B2721' : {'ecocyc-rxns': {"""FHLMULTI-RXN""": """formate = CO2 + H2""","""RXN0-3283""": """2 H+ + 2 e- -> H2""",},'ucsd-rxns' : ['FHL','HYD1pp',], 'protein-comments' : ["""(HycE is the large subunit of hydrogenase 3 |CITS: [90251163][92326636]|. The protein resembles one of the
subunits of NADH:ubiquinone oxidoreductase of the respiratory chain |CITS: [90251163][SAWERS04]|.
Maturation of HycE requires incorporation of nickel followed by processing after the Arg537 residue by the HycI
maturation endopeptidase |CITS: [8125094][7851435][8639025][10727938]|. Maturation has been reconstituted
in vitro and requires HypB, HypC, HypD, HypE, HypF, HycI and nickel, as it does in vivo
|CITS: [8756471]|. HypC interacts directly with pre-HycE and facilitates metal incorporation |CITS: [9485446]
[12441107]|; mutational studies of conserved cysteine residues have led to a model for nickel incorporation
|CITS: [10783387]|. After the incorporation of nickel, pre-HycE must dissociate from HypC to become a substrate for
the HycI maturation endopeptidase |CITS: [10812085]|.)""","""NIL""","""(A report has described that formate oxidation in anaerobically grown E. coli is coupled to proton translocation
|CITS: [15848284]|.)""",]},
'B2722' : {'ecocyc-rxns': {"""FHLMULTI-RXN""": """formate = CO2 + H2""","""RXN0-3283""": """2 H+ + 2 e- -> H2""",},'ucsd-rxns' : ['FHL','HYD1pp',], 'protein-comments' : ["""(HycD encodes an extremely hydrophobic protein with 8 predicted transmembrane domains. The protein
resembles one of the subunits of NADH:ubiquinone oxidoreductase of the respiratory chain |CITS: [90251163]
[SAWERS04]|.)""","""NIL""","""(A report has described that formate oxidation in anaerobically grown E. coli is coupled to proton translocation
|CITS: [15848284]|.)""",]},
'B2723' : {'ecocyc-rxns': {"""FHLMULTI-RXN""": """formate = CO2 + H2""","""RXN0-3283""": """2 H+ + 2 e- -> H2""",},'ucsd-rxns' : ['FHL','HYD1pp',], 'protein-comments' : ["""(HycC encodes an extremely hydrophobic protein with 12 to 16 predicted transmembrane domains. The protein
resembles one of the subunits of NADH:ubiquinone oxidoreductase of the respiratory chain |CITS: [90251163]
[SAWERS04]|.)""","""NIL""","""(A report has described that formate oxidation in anaerobically grown E. coli is coupled to proton translocation
|CITS: [15848284]|.)""",]},
'B3091' : {'ecocyc-rxns': {"""ALTRODEHYDRAT-RXN""": """D-altronate -> H2O + 2-dehydro-3-deoxy-D-gluconate""",},'ucsd-rxns' : ['ALTRH',], 'protein-comments' : ["""NIL""",]},
'B1198' : {'ecocyc-rxns': {"""2.7.1.121-RXN""": """dihydroxy-acetone + phosphoenolpyruvate -> dihydroxy-acetone-phosphate + pyruvate""",},'ucsd-rxns' : ['DHAPT',], 'protein-comments' : ["""(The M subunit is homologous to
certain components of PTS: to a domain of EI, to HPr, and to the AB domains of EII.)""","""(Dihydroxyacetone kinase, which is composed of three subunits: DhaK, DhaL, and DhaM, functions similarly to a
phosphotrasferase system (PTS) in that it utilizes phosphoenolpyruvate as a phosphoryl donor. It differs in not being
involved in transport. Other dihydroxyacetone kinases found in other bacteria, animals, and plants utilize ATP.
Two of the subunits, DhaK and DhaL, are homologous to the ATP-dependent dihydroxyacetone kinases. Another
subunit, DhaM is homologous to certain components of PTS: to a domain of EI, to HPr, and to the AB domains of EII.
The product of this reaction, dihydroxyacetone phosphate, is also formed by a flavin-dependent oxidation of
glycerol-3-phosphate. Dihydroxyacetone phosphate is further metabolized through the glycolytic pathway.)""",]},
'B1199' : {'ecocyc-rxns': {"""2.7.1.121-RXN""": """dihydroxy-acetone + phosphoenolpyruvate -> dihydroxy-acetone-phosphate + pyruvate""",},'ucsd-rxns' : ['DHAPT',], 'protein-comments' : ["""(The L subunit is similar to the C-terminal half of ATP-dependent dihydroxyacetone kinases of eukaryotes and other
bacteria.)""","""(Dihydroxyacetone kinase, which is composed of three subunits: DhaK, DhaL, and DhaM, functions similarly to a
phosphotrasferase system (PTS) in that it utilizes phosphoenolpyruvate as a phosphoryl donor. It differs in not being
involved in transport. Other dihydroxyacetone kinases found in other bacteria, animals, and plants utilize ATP.
Two of the subunits, DhaK and DhaL, are homologous to the ATP-dependent dihydroxyacetone kinases. Another
subunit, DhaM is homologous to certain components of PTS: to a domain of EI, to HPr, and to the AB domains of EII.
The product of this reaction, dihydroxyacetone phosphate, is also formed by a flavin-dependent oxidation of
glycerol-3-phosphate. Dihydroxyacetone phosphate is further metabolized through the glycolytic pathway.)""",]},
'B2901' : {'ecocyc-rxns': {"""6-PHOSPHO-BETA-GLUCOSIDASE-RXN""": """6-phospho-β-D-glucosyl-(1,4)-D-glucose + H2O -> β-D-glucose-6-phosphate + β-D-glucose""",},'ucsd-rxns' : ['AB6PGH',], 'protein-comments' : ["""(BglA is one of several 6-phospho-β-glucosidases in E. coli.
BglA is a 6-phospho-β-glucosidase |CITS: [4576407]|.
)""",]},
'B1192' : {'ecocyc-rxns': {"""RXN0-2061""": """UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminoheptanedioate-D-alanine + H2O -> L-alanine + UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminoheptanedioate""",},'ucsd-rxns' : ['UM4PCP','AM4PCP','4PCP','AGM4PCP',], 'protein-comments' : ["""(LdcA is an L,D-carboxypeptidase that has an essential function in murein (peptidoglycan) recycling/turnover
|CITS: [10428950]|.
An ldcA mutant exhibits defects in murein recycling, including decreased peptidoglycan cross-linking.
The mutation causes cell lysis at stationary phase |CITS: [10428950]|.
A dithiazoline inhibitor of LdcA has been identified |CITS: [16251288]|.
LdcA: "L,D-carboxypeptidase A" |CITS: [10428950]|.
)""",]},
'B1193' : {'ecocyc-rxns': {},'ucsd-rxns' : ['MLTGY3pp','MLTGY4pp','MLTGY1pp','MLTGY2pp',], 'protein-comments' : ["""(EmtA is a lytic endotransglycosylase which is expressed in Escherichia coli as a membrane-bound lipoprotein.
Overexpression of emtA results in the hydrolysis of glycan strands isolated from the murein (peptidoglycan)
sacculus, which serves as a bacterial exoskeleton |CITS:[9642199]|. It is believed that the emtA gene product,
like other murein hydrolases, is involved in cleavage of the net-like murein structure thereby allowing for cell enlargement
and division and also for localized opening of the peptidoglycan layer to allow the export of bulky compounds such as DNA,
toxins, flagella, and fimbrial proteins |CITS:[8824596]|, |CITS:[9642199]|.)""",]},
'B1190' : {'ecocyc-rxns': {"""ALARACECAT-RXN""": """L-alanine = D-alanine""",},'ucsd-rxns' : ['ALAR',], 'protein-comments' : ["""NIL""",]},
'B0613' : {'ecocyc-rxns': {"""RXN0-309""": """dephospho-CoA + ATP = 2'-(5''-triphosphoribosyl)-3'-dephospho-CoA + adenine""",},'ucsd-rxns' : ['TPRDCOAS',], 'protein-comments' : ["""NIL""",]},
'B1197' : {'ecocyc-rxns': {"""TREHALA-RXN""": """trehalose + H2O = 2 β-D-glucose""",},'ucsd-rxns' : ['TREHpp',], 'protein-comments' : ["""NIL""",]},
'B3172' : {'ecocyc-rxns': {"""ARGSUCCINSYN-RXN""": """L-aspartate + citrulline + ATP = L-arginino-succinate + diphosphate + AMP""",},'ucsd-rxns' : ['ARGSS',], 'protein-comments' : ["""(The subunit structure is not known.)""","""NIL""",]},
'B2675' : {'ecocyc-rxns': {"""RXN0-748""": """GDP + a reduced glutaredoxin 1 = dGDP + an oxidized glutaredoxin 1 + H2O""","""RXN0-747""": """ADP + a reduced glutaredoxin 1 = dADP + an oxidized glutaredoxin 1 + H2O""","""RXN0-722""": """UDP + a reduced glutaredoxin 1 = dUDP + an oxidized glutaredoxin 1 + H2O""","""RXN0-1""": """an acceptor + H2O + a 2'-deoxyribonucleoside diphosphate = a reduced acceptor + a ribonucleoside diphosphate""","""RIBONUCLEOSIDE-DIP-REDUCTII-RXN""": """CDP + a reduced glutaredoxin 1 = dCDP + an oxidized glutaredoxin 1 + H2O""",},'ucsd-rxns' : ['RNDR2b','RNDR2b','RNDR2b','RNDR2b','RNDR3b','RNDR3b','RNDR3b','RNDR3b','RNDR1b','RNDR1b','RNDR1b','RNDR1b','RNDR4b','RNDR4b','RNDR4b','RNDR4b',], 'protein-comments' : ["""(Expression of the nrdHIEF operon is increased by hydroxyurea |CITS: [8820648]| and oxidative stress
|CITS: [11278973]|. Expression is highest in minimal medium and in early log phase growth in complex medium;
deletion of Trx1 and Grx1 (trxA- grxA-) increases expression more than
100-fold |CITS: [11278973]|. nrdHIEF belongs to the Fur regulon |CITS: [11101675]|.
)""","""NIL""","""(The NrdE and NrdF proteins constitute a second ribonucleotide reductase (RDPR-II) in E. coli and
S. typhimurium. The enzyme has been studied in Salmonella. The Salmonella enzyme uses
dithiothreitol or reduced glutaredoxin as the electron donor instead of thioredoxin. The allosteric regulation of
RDPR-II also differs from the normally expressed RDPR-I enzyme |CITS: [95108064]|.
Review: |CITS: [15158709]|)""",]},
'B0855' : {'ecocyc-rxns': {"""ABC-25-RXN""": """ATP + putrescine[periplasmic space] + H2O =ADP + phosphate + putrescine[cytosol] """,},'ucsd-rxns' : ['PTRCabcpp',], 'protein-comments' : ["""NIL""","""(The PotFGHI ATP-dependent putrescine transporter is a member of the ATP Binding Cassette (ABC)
Superfamily of transporters |CITS: [96381453]|. PotFGHI is similar in sequence and subunit composition to
the PotABCD putrescine/spermidine uptake system. Based on sequence similarity, PotG is the ATP-
binding component, PotH and Pot I are the membrane components, and PotF is the periplasmic binding
component of the ABC transporter. The PotF protein possesses a high binding affinity to putrescine
(Kd=2.0 μM) |CITS: [98316327]|. Site-directed mutagenesis have shown that PotF is the
putrescine-binding protein |CITS: [98316327]|, and gel filtration studies have show that in the presence of
1mM magnesium ion and 100mM potassium ion, PotF bound putrescine, but not spermidine, in a 1:1 ratio
|CITS: [93106992]|. A high resolution structure of PotF has been determined by x-ray crystallography
|CITS: [98316327]|. Knockout and complementation studies showed that the expression of all four proteins
was necessary for maximal putrescine transport activity |CITS: [93106992]|.)""",]},
'B0182' : {'ecocyc-rxns': {"""LIPIDADISACCHARIDESYNTH-RXN""": """2,3-bis(3-hydroxymyristoyl)-β-D-glucosaminyl 1-phosphate + UDP-2,3-bis(3-hydroxymyristoyl)glucosamine = lipid A disaccharide + UDP""",},'ucsd-rxns' : ['LPADSS',], 'protein-comments' : ["""(Regulation has been described |CITS: [11544210]|. Transcription is induced by nalidixic acid, but not by mitomycin C, and induction does not require LexA |CITS: [11544210]|.)""",]},
'B1398' : {'ecocyc-rxns': {"""PHENYLACETATE--COA-LIGASE-RXN""": """phenylacetate + coenzyme A + ATP = phenylacetyl-CoA + AMP + diphosphate""",},'ucsd-rxns' : ['PACCOAL',], 'protein-comments' : ["""(PaaK is a phenylacetate-CoA ligase (shown in E. coli W) that acts at the first step in an aerobic pathway of phenylacetate degradation |CITS: [9748275]|. Additional steps in the phenylacetate degradation pathway have been predicted |CITS: [9748275], [12846838]|. The second step probably involves hydroxylation of phenylacetate-CoA by a complex comprising PaaA, PaaB, PaaC, PaaD, and PaaE |CITS: [9748275], [12846838]|. The compound 2-hydroxyphenylacetate (2-HPA) is a byproduct, but not a bona fide intermediate |CITS: [9748275]|, and several additional byproducts have been characterized in paaF, paaG, paaH, and paaZ mutants |CITS: [12846838]|. The third step, which includes opening of the ring, may be performed by PaaZ |CITS: [9748275]|, or by PaaZ, PaaG, and PaaJ |CITS: [12846838]|. PaaF and PaaH are predicted to form 3-ketoadipyl CoA, which is then subject to the predicted activity of PaaJ, resulting in production of acetyl-CoA and succinyl-CoA |CITS: [12846838]|. The oxidized end products of the pathway may feed into the Krebs cycle |CITS: [9748275]|.
PaaK of Azoarcus evansii has been characterized in detail |CITS: [10629172]|.
Regulation has been described (in E. coli W) |CITS: [9748275], [10766858]|.
Some, but not all, E. coli K-12 strains lack the ability to utilize phenylacetate; E. coli W and MG1655 exhibit utilization, though E. coli C does not exhibit utilization due to deletion of a large fragment that includes the paa region |CITS: [9748275]|.
)""",]},
'B2905' : {'ecocyc-rxns': {"""GCVMULTI-RXN""": """NAD+ + glycine + tetrahydrofolate = 5,10-methylene-THF + ammonia + CO2 + NADH""","""GCVT-RXN""": """H-protein-S-(aminomethyldihydrolipoyl)lysine + tetrahydrofolate = H-protein-(dihydrolipoyl)lysine + ammonia + 5,10-methylene-THF""",},'ucsd-rxns' : ['GLYCL',], 'protein-comments' : ["""NIL""","""(The glycine cleavage system is a multi-enzyme complex that
catalyzes the reversible oxidation of glycine and generates a C1 moiety. It is the second
major source of C1 units in the cell after serine hydroxymethyl
transferase.
One of the four
subunits, lipoamide dehydrogenase (E3), is shared with pyruvate
dehydrogenase and 2-oxoglutarate dehydrogenase.)""",]},
'B3893' : {'ecocyc-rxns': {"""FORMATEDEHYDROG-RXN""": """formate + menaquinone-8 = CO2 + menaquinol""",},'ucsd-rxns' : ['FDH4pp','FDH5pp',], 'protein-comments' : ["""(By similarity to the paralogous β subunit of formate dehydrogenase-N, FdnH, FdoH is thought to contain four
[4Fe-4S] clusters and one C-terminal transmembrane helix |CITS: [1650339][9852007]|. The topological orientation
of FdoH appears to be the reverse of the orientation of FdnH, with the [4Fe-4S] cluster-containing N-terminus
located in the cytoplasm |CITS: [9852007]|.
By analogy with FdnH, FdoH may serve as a conduit for electrons that are proposed to be transferred from the
formate oxidation site in FdoG to the menaquinone associated with the FdoI subunit of formate dehydrogenase-O.
)""","""(The proton motive force (PMF), composed of an electrochemical gradient and a concentration difference of protons
across the inner membrane, allows generation of the ubiquitous energy carrier ATP by ATP synthase. The PMF itself
can be generated by oxidative phosphorylation, using molecular oxygen as the terminal electron acceptor.
In addition to molecular oxygen, E. coli can use alternative terminal electron acceptors to generate the PMF.
Formate dehydrogenase-O is part of one such system. Expression of formate dehydrogenase-O is increased under
aerobic conditions; under anaerobic conditions, nitrate stimulates expression slightly |CITS: [8522521]|. The global
regulators H-NS and CRP may play a role in regulation of FDH-O expression |CITS: [8522521]|. The physiological
role of formate dehydrogenase-O may be the ability to rapidly adapt to anaerobiosis while levels of formate
dehydrogenase-N are still insufficient |CITS: [8522521]|. Formate dehydrogenase-O shares extensive sequence
similarity and immunological properties with the anaerobically expressed formate dehydrogenase-N
|CITS: [1504073][8522521]|.
)""",]},
'B3892' : {'ecocyc-rxns': {"""FORMATEDEHYDROG-RXN""": """formate + menaquinone-8 = CO2 + menaquinol""",},'ucsd-rxns' : ['FDH4pp','FDH5pp',], 'protein-comments' : ["""(By similarity to the paralogous γ subunit of formate dehydrogenase-N, FdnI, FdoI is the heme-containing
membrane subunit of formate dehydrogenase-O.
Both the N- and C-terminus of FdoI appear to be located in the cytoplasm |CITS: [9852007]|.
)""","""(The proton motive force (PMF), composed of an electrochemical gradient and a concentration difference of protons
across the inner membrane, allows generation of the ubiquitous energy carrier ATP by ATP synthase. The PMF itself
can be generated by oxidative phosphorylation, using molecular oxygen as the terminal electron acceptor.
In addition to molecular oxygen, E. coli can use alternative terminal electron acceptors to generate the PMF.
Formate dehydrogenase-O is part of one such system. Expression of formate dehydrogenase-O is increased under
aerobic conditions; under anaerobic conditions, nitrate stimulates expression slightly |CITS: [8522521]|. The global
regulators H-NS and CRP may play a role in regulation of FDH-O expression |CITS: [8522521]|. The physiological
role of formate dehydrogenase-O may be the ability to rapidly adapt to anaerobiosis while levels of formate
dehydrogenase-N are still insufficient |CITS: [8522521]|. Formate dehydrogenase-O shares extensive sequence
similarity and immunological properties with the anaerobically expressed formate dehydrogenase-N
|CITS: [1504073][8522521]|.
)""",]},
'B3894' : {'ecocyc-rxns': {"""FORMATEDEHYDROG-RXN""": """formate + menaquinone-8 = CO2 + menaquinol""",},'ucsd-rxns' : ['FDH4pp','FDH5pp',], 'protein-comments' : ["""(By similarity to the paralogous α subunit of formate dehydrogenase-N, FdnG, FdoG is thought to be the
catalytic subunit of formate dehydrogenase-O, containing the bis-molybdopterin guanine dinucleotide (MGD)
cofactor and selenocysteine |CITS: [1650339]|.
Unlike FdnG, FdoG appears to be located in the cytoplasm |CITS: [9852007]|.)""","""(The proton motive force (PMF), composed of an electrochemical gradient and a concentration difference of protons
across the inner membrane, allows generation of the ubiquitous energy carrier ATP by ATP synthase. The PMF itself
can be generated by oxidative phosphorylation, using molecular oxygen as the terminal electron acceptor.
In addition to molecular oxygen, E. coli can use alternative terminal electron acceptors to generate the PMF.
Formate dehydrogenase-O is part of one such system. Expression of formate dehydrogenase-O is increased under
aerobic conditions; under anaerobic conditions, nitrate stimulates expression slightly |CITS: [8522521]|. The global
regulators H-NS and CRP may play a role in regulation of FDH-O expression |CITS: [8522521]|. The physiological
role of formate dehydrogenase-O may be the ability to rapidly adapt to anaerobiosis while levels of formate
dehydrogenase-N are still insufficient |CITS: [8522521]|. Formate dehydrogenase-O shares extensive sequence
similarity and immunological properties with the anaerobically expressed formate dehydrogenase-N
|CITS: [1504073][8522521]|.
)""",]},
'B1126' : {'ecocyc-rxns': {"""ABC-25-RXN""": """ATP + putrescine[periplasmic space] + H2O =ADP + phosphate + putrescine[cytosol] ""","""ABC-24-RXN""": """ATP + spermidine[periplasmic space] + H2O =ADP + phosphate + spermidine[cytosol] """,},'ucsd-rxns' : ['PTRCabcpp','SPMDabcpp',], 'protein-comments' : ["""NIL""","""(PotABCD is an ATP-dependent polyamine transporter that is a member of the ATP-Binding
Cassette (ABC) Superfamily of transporters |CITS: [20053876]|. The transporter consists of a membrane
associated ATPase (PotA), two transmembrane proteins (PotB and PotC), and a periplasmic
substrate-binding protein (PotD) |CITS: [20053876]|. Knockout mutants in each of the four genes indicated
that they are all required for polyamine transport |CITS: [93374918] [20053876]|. PotA has been purified to homogeneity
and was shown to have magnesium and spermidine-dependent ATPase activity, with a Km
of 385 μM for ATP |CITS: [96029616] [20053876]|. Based on hydropathy analysis and sequence similarity, PotB and
PotC are the membrane components of the ABC transporter |CITS: [20053876]|. PotD is the periplasmic
substrate-binding protein that acts to recognize and facilitate the transport of the polyamines
|CITS: [20053876] [99315781]|. PotD preferentially binds spermidine, but will also bind putrescine with a lower affinity
(Km values of 0.1 μM and 1.5 μM for spermidine and putrescine, respectively |CITS: [20053876]|).
The dissociation constant for the binding of spermidine by PotD was found to be 3.2 μM
with an optimal spermidine concentration of 5-10 μM |CITS: [93374918]|. X-ray crystallography of
PotD showed that it has two domains with β-α -β topology, with four
acidic residues, used to recognize the positively charged nitrogen atoms of the spermidine
substrate, located in the central cleft between the two domains |CITS: [20053876] [99318982]|.
)""",]},
'B2540' : {'ecocyc-rxns': {"""HCAMULTI-RXN""": """3-phenylpropionate + NADH + O2 + H+ = cis-3-(carboxyethyl)-3,5-cyclohexadiene-1,2-diol + NAD+""",},'ucsd-rxns' : ['PPPNDO','CINNDO',], 'protein-comments' : ["""(HcaC encodes the ferredoxin component of the 3-phenylpropionate dioxygenase
system. It appears to be a 2Fe-2S type ferredoxin.
E. coli is able to utilize aromatic acids as carbon and
energy sources. A meta-cleavage pathway is used for the catabolism of
3-phenylpropionate. The
3-phenylpropionate dioxygenase system also includes a 3-phenylpropionate
dioxygenase and a ferredoxin reductase. |CITS: [98269008]|)""","""(The 3-phenylpropionate dioxygenase component is the product of the hcaA1 and
hcaA2 genes. HcaC codes for a ferredoxin and hcaD encodes a ferredoxin NAD+
reductase. |CITS: [98269008]|)""",]},
'B2541' : {'ecocyc-rxns': {"""PHENPRODIOLDEHYDROG-RXN""": """cis-3-(carboxyethyl)-3,5-cyclohexadiene-1,2-diol + NAD+ = 3-(2,3-dihydroxyphenyl)propionate + NADH""",},'ucsd-rxns' : ['DHCIND','DHPPD',], 'protein-comments' : ["""(The subunit structure
is unknown.)""",]},
'B2542' : {'ecocyc-rxns': {"""HCAMULTI-RXN""": """3-phenylpropionate + NADH + O2 + H+ = cis-3-(carboxyethyl)-3,5-cyclohexadiene-1,2-diol + NAD+""","""FERREDOXIN--NAD(+)-REDUCTASE-RXN""": """NAD+ + a reduced ferredoxin = NADH + an oxidized ferredoxin""",},'ucsd-rxns' : ['PPPNDO','CINNDO',], 'protein-comments' : ["""NIL""","""(The 3-phenylpropionate dioxygenase component is the product of the hcaA1 and
hcaA2 genes. HcaC codes for a ferredoxin and hcaD encodes a ferredoxin NAD+
reductase. |CITS: [98269008]|)""",]},
'B2143' : {'ecocyc-rxns': {"""CYTIDEAM2-RXN""": """H2O + cytidine -> ammonia + uridine""","""CYTIDEAM-RXN""": """H2O + deoxycytidine -> ammonia + deoxyuridine""",},'ucsd-rxns' : ['DCYTD','CYTD',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B2316' : {'ecocyc-rxns': {"""ACETYL-COA-CARBOXYLTRANSFER-RXN""": """ATP + acetyl-CoA + HCO3- + H+ = malonyl-CoA + phosphate + ADP""","""RXN0-5055""": """acetyl-CoA + carboxy-biotin-BCCP = malonyl-CoA + a biotin-BCCP (dimer)""",},'ucsd-rxns' : ['ACCOAC',], 'protein-comments' : ["""NIL""","""NIL""","""NIL""","""(The enzyme |FRAME:ACETYL-COA-CARBOXYLMULTI-CPLX| is one of the key enzymes in the
biosynthesis of fatty acids (see |FRAME: FASYN-INITIAL-PWY|).
The enzyme belongs to the family of enzymes that catalyze
the intermolecular transfer of carboxyl groups via the transient formation of a carboxyphosphate
intermediate covalently linked to a biotin prosthetic group |CITS: [15749055]|.
The E. coli enzyme complex is composed of two catalytic units and one carrier protein,
encoded by four different genes.
The catalytic units are |FRAME:BIOTIN-CARBOXYL-CPLX| (BC), a homodimer encoded by the
|FRAME: EG10276| gene, and |FRAME:ACETYL-COA-CARBOXYLMULTI-CPLX| (ACCT), an
α2β2 tetramer, encoded by the |FRAME:EG11647| and
|FRAME: EG10217| genes.
The carrier protein is the |FRAME:BCCP-CPLX| (BCCP), a homodimer encoded by the |FRAME:EG10275| gene.
The BCCP monomer is biotinylated by the enzyme |FRAME:BIOTINLIG-ENZRXN|.
Following dimerization of the biotinylated monomers, |FRAME:BIOTIN-CARBOXYL-CPLX| (BC) catalyzes the addition
of |FRAME: CARBON-DIOXIDE| to the carrier protein dimer, forming |FRAME:Carboxybiotin-BCCP| (carboxy-BCCP).
|FRAME:Carboxybiotin-BCCP|
in turn is the substrate for ACCT, which transfers the carboxy group to |FRAME:ACETYL-COA|,
resulting in the formation of |FRAME:MALONYL-COA| and the regeneration of |FRAME:BCCP-CPLX|.
Both biotinylation and carboxylation of the carrier protein require ATP, while the last step, transfer of the carboxy
group to |FRAME: ACETYL-COA|, does not |CITS: [15749055]|.)""",]},
'B0860' : {'ecocyc-rxns': {"""ABC-4-RXN""": """ATP + L-arginine[periplasmic space] + H2O =ADP + phosphate + L-arginine[cytosol] """,},'ucsd-rxns' : ['ARGabcpp',], 'protein-comments' : ["""NIL""","""(The ArtPMQJI arginine transporter is a member of the ATP Binding Cassette (ABC) transporter superfamily
|CITS: [98254124]|. ArtJ shows similarity to arginine-binding periplasmic protein components of other ABC
transporters. Expression studies show that ArtJ is localized to the periplasmic fractions of E. coli
and hybridization studies using radiolabeled arginine showed that part of the radioactivity co-eluted with
ArtJ, indicating that L-arginine is the natural substrate for ArtJ |CITS: [96111488]|. Furthermore, overexpression
of ArtJ resulted in stimulation of arginine uptake. In minimal medium, ArtJ was found in the periplasmic
extracts of E. coli but its presence was greatly diminished in high-arginine content medium
|CITS: [96111488]|. Sequence similarity, including a highly conserved ATP-binding consensus site, and
hydropathy analyses indicate that ArtP is highly homologous to the HisP ATP-binding protein of the
Histidine-LAO transporters (HisJQMP complexes) of S. typhimurium and E. coli . ArtQ
and ArtM are hydrophobic proteins and exhibit some homology to HisQ and HisM, membraneous
components of the Histidine-LAO ABC transport system, and to other ABC transporter integral membrane
proteins |CITS:[96111488]|. ArtQ and ArtM presumably function as integral membrane components and
couple the ATPase activity of ArtP to the transport of L-arginine across the inner membrane. ArtI exhibits
homology with a number of ABC transporter periplasmic binding proteins, but its substrate is not known
|CITS:[98254124]|.)""",]},
'B0863' : {'ecocyc-rxns': {"""ABC-4-RXN""": """ATP + L-arginine[periplasmic space] + H2O =ADP + phosphate + L-arginine[cytosol] """,},'ucsd-rxns' : ['ARGabcpp',], 'protein-comments' : ["""NIL""","""(The ArtPMQJI arginine transporter is a member of the ATP Binding Cassette (ABC) transporter superfamily
|CITS: [98254124]|. ArtJ shows similarity to arginine-binding periplasmic protein components of other ABC
transporters. Expression studies show that ArtJ is localized to the periplasmic fractions of E. coli
and hybridization studies using radiolabeled arginine showed that part of the radioactivity co-eluted with
ArtJ, indicating that L-arginine is the natural substrate for ArtJ |CITS: [96111488]|. Furthermore, overexpression
of ArtJ resulted in stimulation of arginine uptake. In minimal medium, ArtJ was found in the periplasmic
extracts of E. coli but its presence was greatly diminished in high-arginine content medium
|CITS: [96111488]|. Sequence similarity, including a highly conserved ATP-binding consensus site, and
hydropathy analyses indicate that ArtP is highly homologous to the HisP ATP-binding protein of the
Histidine-LAO transporters (HisJQMP complexes) of S. typhimurium and E. coli . ArtQ
and ArtM are hydrophobic proteins and exhibit some homology to HisQ and HisM, membraneous
components of the Histidine-LAO ABC transport system, and to other ABC transporter integral membrane
proteins |CITS:[96111488]|. ArtQ and ArtM presumably function as integral membrane components and
couple the ATPase activity of ArtP to the transport of L-arginine across the inner membrane. ArtI exhibits
homology with a number of ABC transporter periplasmic binding proteins, but its substrate is not known
|CITS:[98254124]|.)""",]},
'B3177' : {'ecocyc-rxns': {"""H2PTEROATESYNTH-RXN""": """p-aminobenzoate + 2-amino-4-hydroxy-6-hydroxymethyl-7,8-dihydropteridine diphosphate -> 7,8-dihydropteroate + diphosphate""",},'ucsd-rxns' : ['DHPS2',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B4120' : {'ecocyc-rxns': {"""TRANS-RXN-94B""": """Li+[periplasmic space] + melibiose[periplasmic space] =Li+[cytosol] + melibiose[cytosol] ""","""TRANS-RXN-94A""": """Na+[periplasmic space] + melibiose[periplasmic space] =Na+[cytosol] + melibiose[cytosol] ""","""TRANS-RXN-94""": """H+[periplasmic space] + melibiose[periplasmic space] =H+[cytosol] + melibiose[cytosol] """,},'ucsd-rxns' : ['MELIBt2pp',], 'protein-comments' : ["""(MelB is a melibiose-cation cotransport protein belonging to the Glycoside-Pentoside-Hexuronide:Cation
Symporter Family (GPH) |CITS: [94304911]|. Proteins in the GPH family facilitate sugar-cation symport
|CITS: [85207480]|. MelB has been purified, solubilized and reconstituted into liposomes and demonstrated to
mediate melibiose symport with sodium, lithium, or proton as the coupling ion |CITS: [84111656] [90241878]
[9023917]|. The effects of sodium ion, lithium ion, and proton on the sugar binding constants of MelB were
studied in de-energized membrane vesicles incubated in media containing various concentrations of the
co-transported cations |CITS: [9023917]|. It was observed that, in a similar fashion, sodium ions and lithium
ions activate sugar binding by selectively increasing the permease affinity for the co-transported sugar. This
suggests that the two monovalent cations have comparable activation strengths |CITS: [9023917]|. Hydropathy
analysis, proteolytic digestion, and PhoA fusions suggest a 12 transmembrane segment topology, with the N and C termini located on the cytoplasmic face of the membrane
|CITS:[99029991][8672452][9214297]|.
Two-dimensional crystallization of MelB permease was achieved, and a projection map at 8.0 A resolution
was derived by electron crystallography, suggesting an asymmetric protein unit hosting 12 potential
transmembrane alpha -helices that are distributed in two domains lining a central and curve-shaped
cleft. |CITS:[12110569]|.
Reviewed in |CITS:[11248194]|.
)""",]},
'B1441' : {'ecocyc-rxns': {},'ucsd-rxns' : ['PTRCabcpp','SPMDabcpp',], 'protein-comments' : ["""(ATP-binding component of ABC transporter)""","""(YdcS, YdcT, YdcU and YdcV are uncharacterized
members of the ABC superfamily of transporters
|CITS: [99091701]|. YdcS is the putative
periplasmic binding component, YdcT is the
putative ATP binding component, YdcU and YdcV
are the putative membrane spanning components.
Bases on sequence similarity they may function
together as an ATP-dependent spermidine/
putrecine transporter. The genes ydcS,
ydcT, ydcU, and ydcV are
probably located in a single operon.)""",]},
'B1442' : {'ecocyc-rxns': {},'ucsd-rxns' : ['PTRCabcpp','SPMDabcpp',], 'protein-comments' : ["""(membrane component of ABC transporter)""","""(YdcS, YdcT, YdcU and YdcV are uncharacterized
members of the ABC superfamily of transporters
|CITS: [99091701]|. YdcS is the putative
periplasmic binding component, YdcT is the
putative ATP binding component, YdcU and YdcV
are the putative membrane spanning components.
Bases on sequence similarity they may function
together as an ATP-dependent spermidine/
putrecine transporter. The genes ydcS,
ydcT, ydcU, and ydcV are
probably located in a single operon.)""",]},
'B4123' : {'ecocyc-rxns': {"""TRANS-RXN-106C""": """a C4-dicarboxylate[periplasmic space] + succinate[cytosol] =succinate[periplasmic space] + a C4-dicarboxylate[cytosol] ""","""TRANS-RXN-106B""": """a C4-dicarboxylate[periplasmic space] + malate[cytosol] =malate[periplasmic space] + a C4-dicarboxylate[cytosol] ""","""TRANS-RXN-106A""": """a C4-dicarboxylate[periplasmic space] + L-aspartate[cytosol] =L-aspartate[periplasmic space] + a C4-dicarboxylate[cytosol] ""","""TRANS-RXN-106""": """a C4-dicarboxylate[periplasmic space] + fumarate[cytosol] =fumarate[periplasmic space] + a C4-dicarboxylate[cytosol] """,},'ucsd-rxns' : ['ASPt2_3pp','MALt2_3pp','SUCFUMtpp','SUCCt2_3pp','FUMt2_3pp',], 'protein-comments' : ["""(The DcuB transporter is one of three transporters known to be
responsible for the uptake of C4-dicarboxylates such as fumarate under
anaerobic conditions. DcuA and DcuB are homologous transporters
which function as independent and mutually redundant C4-dicarboxylate
(aspartate, malate, fumarate and succinate) transporters. The third
anaerobic dicarboxylate transporter is DcuC. Mutations in either
dcuA or dcuB did not greatly affect anaerobic
growth on C4 dicarboxylates, but a double dcuA dcuB mutant
was severely impaired |CITS: [95050204]|. Whole cell transport
experiments have indicated that both DcuA and DcuB catalyse C4
dicarboxylate exchange, for instance fumarate uptake in exchange
for succinate with a Km for fumarate of approx 30 μM |CITS: [95050204]|.
dcuA is located downstream of aspA encoding aspartase and
dcuB is upstream of fumB encoding anaerobic fumarase implying
their physiological functions may be to catalyze aspartate:fumarate and
fumarate:malate exchange during the anaerobic utilization of aspartate and
fumarate, respectively |CITS: [95050204]|. However, their transport
specificities do not fully support this notion.
DcuA and DcuB are the prototype representatives of the Dcu family of
dicarboxylate transporters.
Expression of dcuA has been shown to be constitutive while
expression of dcuB is induced anaerobically by FNR and by
C-4 dicarboxylates |CITS: [99069334]|.
)""",]},
'B1444' : {'ecocyc-rxns': {"""AMINOBUTDEHYDROG-RXN""": """4-amino-butyraldehyde + NAD+ + H2O = 4-aminobutyrate + NADH""",},'ucsd-rxns' : ['ABUTD',], 'protein-comments' : ["""(γ-aminobutyraldehyde dehydrogenase is the second enzyme in a putrescine degradation pathway
|CITS: [3510672][16023116]|.
A crystal structure of YdcW has been solved at 2.1 A resolution; analysis of the active site configuration as well as
enzyme kinetics data suggested that YdcW is a medium-chain aldehyde dehydrogenase with a preference for linear
n-alkyl medium-chain aldehydes, using NAD as the cofactor |CITS: [15381418]|.)""","""NIL""",]},
'B3476' : {'ecocyc-rxns': {"""ABC-20-RXN""": """Ni2+[periplasmic space] + ATP + H2O =Ni2+[cytosol] + ADP + phosphate """,},'ucsd-rxns' : ['NI2uabcpp',], 'protein-comments' : ["""(NikA is the periplasmic binding component of the nickel ABC transporter in Escherichia coli. The crystal structure of protein in the presence and absence of nickel has been determined to 1.95 A and 1.85 A respectively |CITS:[12960164]|.)""","""(The NikABCDE ATP-dependent nickel (II) uptake system is a member of the ATP-Binding Cassette (ABC)
Superfamily of transporters |CITS: [96381453]|. The Nik system exhibits significant sequence similarity to
the components of other ABC transporters for dipeptides or oligopeptides |CITS: [95020649]|. Based on
sequence similarity, NikA is the periplasmic binding protein, NikB and NikC are the membrane components,
and NikD and NikE are the ATP-binding components of the ABC transporter. The nickel-binding
properties of the protein have been studied by monitoring the quenching of intrinsic protein fluorescence
|CITS: [95172074]|. NikA binds one atom of nickel per molecule of protein with a Kd of less
than 0.1 μM. The transporter's high specificity for nickel ion has also been demonstrated by
high-performance immobilized-metal-ion affinity chromatography |CITS:[95172074]|. The structure of NikA
has been determined to a resolution of 1.8 angstroms showing that it binds FeEDTA(H2O)
with very high affinity. It also binds the nickel ion associated with a metallophore which is at least similar
to EDTA |CITS:[16011372]|. Insertional mutation in the nik operon severely reduces nickel transport
ability |CITS:[95020649]|. Nickel is an important cofactor in a variety of enzymatic reactions in prokaryotes
|CITS:[20112624]|. However, nickel at high intracellular concentrations is toxic because it can catalyze the
formation of reactive forms of oxygen that can damage cellular constituents |CITS: [20112624]|. Because of
the toxicity of nickel, the synthesis of the Nik system is tightly controlled by nickel concentration. At high
nickel concentrations (0.3 mM) synthesis of Nik is completely repressed by the protein NikR
|CITS:[20112624]|. Expression of NikABCDE corresponds to expression of NiFe hydrogenases for which
nickel is a cofactor. Mutation and LacZ fusion experiments show that nitrate, via the activity of the NarLX
two-component system, represses expression of nikABCDE considerably. NikABCDE is
upregulated by FNR under anaerobic conditions |CITS:[16159764]|.
)""",]},
'B0688' : {'ecocyc-rxns': {"""PHOSPHOGLUCMUT-RXN""": """α-D-glucose 1-phosphate = α-D-glucose-6-phosphate""",},'ucsd-rxns' : ['PGMT',], 'protein-comments' : ["""NIL""",]},
'B0133' : {'ecocyc-rxns': {"""PANTOATE-BETA-ALANINE-LIG-RXN""": """β-alanine + L-pantoate + ATP = pantothenate + diphosphate + AMP""",},'ucsd-rxns' : ['PANTS',], 'protein-comments' : ["""NIL""","""(The subunit structure is not known definitively. In E. coli
B it appears to be a homotetramer. The E. coli K-12 may be a
homodimer.)""",]},
'B4129' : {'ecocyc-rxns': {"""LYSINE--TRNA-LIGASE-RXN""": """L-lysine + tRNAlys + ATP = L-lysyl-tRNAlys + diphosphate + AMP""",},'ucsd-rxns' : ['LYSTRS',], 'protein-comments' : ["""(The lysyl-tRNA synthetase LysU is a member of the family of aminoacyl tRNA synthetases, which interpret the genetic
code by covalently linking amino acids to their specific tRNA molecules. The reaction is driven by ATP hydrolysis.
LysU belongs to the Class II aminoacyl tRNA synthetases. E. coli contains both a constitutive and an
inducible lysyl tRNA synthetase; lysU encodes the inducible enzyme.
LysU may |CITS: [2188953]| or may not |CITS: [2001999]| be required for normal growth at elevated temperature.
lysU expression is induced by elevated temperature, anaerobiosis, and low pH |CITS: [2187401][1744045]
[1514820]|. LysU is negatively regulated by H-NS |CITS: [7961513]| and is a member of the Lrp (leucine-responsive
regulatory protein) regulon |CITS: [1346534][1555652][1569010][7678344]|. Cooperative binding of Lrp to the
lysU promoter region represses transcription |CITS: [8064854]|. Overexpression of lysU suppresses
the low temperature growth defect of a lysS null mutant |CITS: [1321323]|.
The enzyme is a homodimer |CITS: [7735833]|.
Crystal structures of LysU are presented |CITS: [7735833][10913247]|. Biochemical and computational molecular
dynamics studies of the reaction mechanism have been performed |CITS: [12787471]|.
Reviews: |CITS: [7934813][7576245]|)""","""NIL""",]},
'B0131' : {'ecocyc-rxns': {"""ASPDECARBOX-RXN""": """L-aspartate = β-alanine + CO2""",},'ucsd-rxns' : ['ASP1DC',], 'protein-comments' : ["""(The PanD proenzyme (π protein) is processed at the serine residue at position 25, resulting in two subunits,
α and β, which form a complex that is enzymatically active. Autocatalytic processing of purified enzyme
preparations occurs slowly at room temperature or 37 degrees C, and at a higher rate at elevated temperatures
|CITS: [9169598]|. How processing occurs in vivo remains unclear.
An S25A mutation eliminates self-cleavage of the π protein and eliminates enzymatic activity. A strain containing
this mutant form of PanD absolutely requires exogenous β-alanine for growth |CITS: [15033515]|.)""","""(The β subunit of aspartate 1-decarboxylase is the smaller N-terminal cleavage product of PanD
|CITS: [9169598]|.)""","""(The α subunit of aspartate 1-decarboxylase is the larger C-terminal cleavage product of PanD. It is further
processed to generate a pyruvoyl cofactor from the serine residue downstream of the cleavage site, Ser25, which is
now located at the N-terminus of the α subunit. On average, three out of four of the α subunits in the fully
processed enzyme contain the pyruvoyl cofactor |CITS: [9169598]|.)""","""(Aspartate 1-decarboxylase is responsible for the synthesis of β-alanine, which is needed in the biosynthesis
of panthothenate.
This enzyme is one of a small class of enzymes that use a covalently bound pyruvoyl prosthetic group.
The pyruvoyl group is thought to act analogously to pyridoxal phosphate
cofactor by forming a Schiff base with the amino group of the substrate and then serving as an electron
sink to facilitate the decarboxylation |CITS: [91208149]|.
Four of these enzymes, histidine decarboxylase (E.C. 4.1.1.22), |FRAME: PHOSPHASERDECARB-CPLX|,
|FRAME: CPLX0-2901|, and |FRAME: CPLX-6906| are decarboxylases forming important biological
amines. All of these enzymes are known to have the pyruvoyl prosthetic group attached via an amide
linkage to the amino terminus of the α subunit.
Two other enzymes in this group are are |FRAME: CPLX-782| and glycine reductase
(E.C. 1.21.4.2) |CITS: [10574985]|.
Pyruvoyl-containing enzymes are expressed as a zymogen which is processed post-translationally
by a self-maturation cleavage called serinolysis. In this process the pyruvoul group is formed from a
serine residue, splitting the presursor protein into two parts which become the α and β
subunits. In some cases additional subunits may be involved.)""","""(Aspartate 1-decarboxylase is responsible for the synthesis of β-alanine, which is needed in the biosynthesis
of panthothenate.
This enzyme is one of a small class of enzymes that use a covalently bound pyruvoyl prosthetic group.
The pyruvoyl group is thought to act analogously to pyridoxal phosphate
cofactor by forming a Schiff base with the amino group of the substrate and then serving as an electron
sink to facilitate the decarboxylation |CITS: [91208149]|.
Four of these enzymes, histidine decarboxylase (E.C. 4.1.1.22), |FRAME: PHOSPHASERDECARB-CPLX|,
|FRAME: CPLX0-2901|, and |FRAME: CPLX-6906| are decarboxylases forming important biological
amines. All of these enzymes are known to have the pyruvoyl prosthetic group attached via an amide
linkage to the amino terminus of the α subunit.
Two other enzymes in this group are are |FRAME: CPLX-782| and glycine reductase
(E.C. 1.21.4.2) |CITS: [10574985]|.
Pyruvoyl-containing enzymes are expressed as a zymogen which is processed post-translationally
by a self-maturation cleavage called serinolysis. In this process the pyruvoul group is formed from a
serine residue, splitting the presursor protein into two parts which become the α and β
subunits. In some cases additional subunits may be involved.)""",]},
'B4087' : {'ecocyc-rxns': {"""ABC-28-RXN""": """ATP + D-ribose[periplasmic space] + H2O =ADP + phosphate + D-ribose[cytosol] ""","""ABC-42-RXN""": """D-allose[periplasmic space] + ATP + H2O =D-allose[cytosol] + ADP + phosphate """,},'ucsd-rxns' : ['ALLabcpp','RIBabcpp',], 'protein-comments' : ["""NIL""","""(The AlsABC transporter belongs to the ATP-binding Cassette (ABC)
Superfamily |CITS: [94272333]|. It is responsible for the uptake of D-allose, an
all-cis hexose that can be used by E. coli as a sole carbon
source |CITS: [98062191]|. Deletion of the als genes resulted in an inability
to grow on D-allose |CITS: [98062191]|. AlsB is a periplasmic protein that binds
D-allose with a Kd of 0.33μM, as determined by
fluorescence spectroscopy |CITS: [98062191]|. Based on sequence similarity, AlsA
is the ATP-binding component, and AlsC is the membrane
component of the ABC transporter |CITS: [99165783]|. The AlsABC system also
transports ribose at low affinity |CITS: [98062191]|. Complementation analysis of
als mutants showed that the cloned als genes could
restore growth on ribose minimal media |CITS: [98062191]|. Analysis of
β-galactosidase transcriptional fusions suggest that AlsR is a
negative regulator of alsABC, and transcription of
alsR is regulated by allose |CITS: [98062191]|.)""",]},
'B4086' : {'ecocyc-rxns': {"""ABC-28-RXN""": """ATP + D-ribose[periplasmic space] + H2O =ADP + phosphate + D-ribose[cytosol] ""","""ABC-42-RXN""": """D-allose[periplasmic space] + ATP + H2O =D-allose[cytosol] + ADP + phosphate """,},'ucsd-rxns' : ['ALLabcpp','RIBabcpp',], 'protein-comments' : ["""NIL""","""(The AlsABC transporter belongs to the ATP-binding Cassette (ABC)
Superfamily |CITS: [94272333]|. It is responsible for the uptake of D-allose, an
all-cis hexose that can be used by E. coli as a sole carbon
source |CITS: [98062191]|. Deletion of the als genes resulted in an inability
to grow on D-allose |CITS: [98062191]|. AlsB is a periplasmic protein that binds
D-allose with a Kd of 0.33μM, as determined by
fluorescence spectroscopy |CITS: [98062191]|. Based on sequence similarity, AlsA
is the ATP-binding component, and AlsC is the membrane
component of the ABC transporter |CITS: [99165783]|. The AlsABC system also
transports ribose at low affinity |CITS: [98062191]|. Complementation analysis of
als mutants showed that the cloned als genes could
restore growth on ribose minimal media |CITS: [98062191]|. Analysis of
β-galactosidase transcriptional fusions suggest that AlsR is a
negative regulator of alsABC, and transcription of
alsR is regulated by allose |CITS: [98062191]|.)""",]},
'B4085' : {'ecocyc-rxns': {"""RXN0-304""": """D-allulose-6-phosphate = D-fructose-6-phosphate""",},'ucsd-rxns' : ['ALLULPE',], 'protein-comments' : ["""NIL""",]},
'B0134' : {'ecocyc-rxns': {"""3-CH3-2-OXOBUTANOATE-OH-CH3-XFER-RXN""": """H2O + 2-keto-isovalerate + 5,10-methylene-THF = 2-dehydropantoate + tetrahydrofolate""",},'ucsd-rxns' : ['MOHMT',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B0091' : {'ecocyc-rxns': {"""UDP-NACMUR-ALA-LIG-RXN""": """L-alanine + UDP-N-acetylmuramate + ATP = UDP-N-acetylmuramoyl-L-alanine + phosphate + ADP""",},'ucsd-rxns' : ['UAMAS',], 'protein-comments' : ["""NIL""",]},
'B2926' : {'ecocyc-rxns': {"""PHOSGLYPHOS-RXN""": """3-phosphoglycerate + ATP = 1,3-diphosphateglycerate + ADP""",},'ucsd-rxns' : ['PGK',], 'protein-comments' : ["""(Phosphoglycerate kinase is one of the proteins induced by anaerobiosis.
|CITS:[89306676]| The gene is transcribed from two promoters, one immediately
in front of an upstream gene coding for a 38-kDa polypeptide of
unknown function. The pgk gene was also found to show growth phase regulation. A
structural determinant for glycerate 3-P kinase is located near serA.
The map order is speB-pgk-serA-lysA-argA-eno-cysC.|CITS:[76195925]|
Pgk has similarity to an Edwardsiella ictaluri protein |CITS: [12542086]|.)""",]},
'B0109' : {'ecocyc-rxns': {"""QUINOPRIBOTRANS-RXN""": """CO2 + diphosphate + nicotinate nucleotide = 5-phosphoribosyl 1-pyrophosphate + quinolinate""",},'ucsd-rxns' : ['NNDPR',], 'protein-comments' : ["""(NadC catalyzes the third step in the biosynthesis of NAD from L-aspartate.
The nadC gene was cloned, and the NadC protein was overexpressed and purified to homogeneity |CITS: [8561507]|.
The protein appears as a dimer in Salmonella typhimurium |CITS: [8419294]|.)""","""NIL""",]},
'B1723' : {'ecocyc-rxns': {"""TAGAKIN-RXN""": """tagatose-6-phosphate + ATP = tagatose-1,6-bisphosphate + ADP""","""6PFRUCTPHOS-RXN""": """D-fructose-6-phosphate + ATP = ADP + fructose-1,6-bisphosphate""",},'ucsd-rxns' : ['PFK',], 'protein-comments' : ["""NIL""","""(This enzyme is an isozyme with phosphofructokinase-1. The
nucleotide sequences of the genes are not similar.|CITS: [85203917]|)""",]},
'B4039' : {'ecocyc-rxns': {"""CHORPYRLY-RXN""": """chorismate -> p-hydroxybenzoate + pyruvate""",},'ucsd-rxns' : ['CHRPL',], 'protein-comments' : ["""(The sdgG mutation, which suppresses a conditional mutation in dnaG (DNA primase), has been localized to either the ubiC, ubiA or yjbI gene |CITS: [9093842]|.)""",]},
'B1106' : {'ecocyc-rxns': {"""THIKIN-RXN""": """thiamine + ATP = thiamine-phosphate + ADP""",},'ucsd-rxns' : ['TMK',], 'protein-comments' : ["""(The thiK locus was mapped |CITS: [6284709]|, and the ycfN open reading frame has recently been identified as the
structural gene encoding thiamine kinase |CITS: [15150256]|.
Orthologs of thiK have so far only been found in the γ proteobacteria.)""",]},
'B1440' : {'ecocyc-rxns': {},'ucsd-rxns' : ['PTRCabcpp','SPMDabcpp',], 'protein-comments' : ["""(periplasmic binding protein of ABC transporter)""","""(YdcS, YdcT, YdcU and YdcV are uncharacterized
members of the ABC superfamily of transporters
|CITS: [99091701]|. YdcS is the putative
periplasmic binding component, YdcT is the
putative ATP binding component, YdcU and YdcV
are the putative membrane spanning components.
Bases on sequence similarity they may function
together as an ATP-dependent spermidine/
putrecine transporter. The genes ydcS,
ydcT, ydcU, and ydcV are
probably located in a single operon.)""",]},
'B0963' : {'ecocyc-rxns': {"""METHGLYSYN-RXN""": """dihydroxy-acetone-phosphate -> methylglyoxal + phosphate""",},'ucsd-rxns' : ['MGSA',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B2265' : {'ecocyc-rxns': {"""ISOCHORSYN-RXN""": """chorismate -> isochorismate""",},'ucsd-rxns' : ['ICHORS',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B2264' : {'ecocyc-rxns': {"""HYDGLUTSYN-RXN""": """propionyl-CoA + H2O + glyoxylate = 2-hydroxyglutarate + coenzyme A""","""SHCHCSYNTH-RXN""": """isochorismate + succinate-semialdehyde-thiamine PPi = 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate + thiamine diphosphate + pyruvate""","""2-OXOGLUT-DECARBOX-RXN""": """α-ketoglutarate + thiamine diphosphate = CO2 + succinate-semialdehyde-thiamine PPi""",},'ucsd-rxns' : ['SHCHCS2','OXGDC2',], 'protein-comments' : ["""(The menD gene codes for a bifunctional enzyme.)""",]},
'B3996' : {'ecocyc-rxns': {"""RXN0-4401""": """NADH + H2O -> NMNH + AMP""","""NADPYROPHOSPHAT-RXN""": """H2O + NAD+ = nicotinamide mononucleotide + AMP""",},'ucsd-rxns' : ['NADDP',], 'protein-comments' : ["""(NudC belongs to the family of "Nudix" hydrolases |CITS: [8810257]|. Unlike other members of this family, which have
nucleoside triphosphate pyrophosphohydrolase activity, it was shown to have NADH pyrophosphatase activity. The
enzyme has a preference for NADH, the reduced form of the cofactor, as a substrate; its
Km for NADH is 50-fold lower than its Km for NAD+ |CITS: [7829480]|.
The enzyme may be a homodimer in solution |CITS: [7829480]|.
Based on sequence similarity, NudC was predicted to be a NAD+ diphosphatase |CITS: [12952533]|.)""",]},
'B2521' : {'ecocyc-rxns': {"""MERCAPYSTRANS-RXN""": """hydrogen cyanide + 3-mercaptopyruvate -> pyruvate + thiocyanate""",},'ucsd-rxns' : ['MCPST',], 'protein-comments' : ["""(The sseA gene encodes a 3-mercaptopyruvate:cyanide sulfurtransferase (MST), a rhodanese-like enzyme
that, in contrast to rhodanese, uses 3-mercaptopyruvate as the preferred sulfur donor |CITS: [11445076]|. SseA can
use thiosulfate as the donor, but use of 3-mercaptopyruvate is favored |CITS: [11445076]|.
A crystal structure of SseA has been solved at 2.8 A resolution; the structure shows differences with the structure of
rhodanese enzymes, including a variation in the active site loop. The structure provides insight into the catalytic
mechanism of SseA |CITS: [12499560][14672665]|.
Overexpression enhances the serine sensitivity caused by serine-mediated inhibition of homoserine
dehydrogenase I activity during growth on some carbon sources and results in increased cellular rhodanese activity
|CITS: [7982894]|.
SseA: "serine sensitivity" |CITS: [7982894]|)""",]},
'B4122' : {'ecocyc-rxns': {"""FUMHYDR-RXN""": """malate = fumarate + H2O""",},'ucsd-rxns' : ['FUM',], 'protein-comments' : ["""(One of three isozymes in E. coli, fumarase B is a Class I fumarase. The FumB protein is 79% similar to the
FumA protein.)""","""NIL""",]},
'B2435' : {'ecocyc-rxns': {"""NACMURLALAAMI-RXN""": """EC# 3.5.1.28""",},'ucsd-rxns' : ['AGM3PApp','AGM4PApp',], 'protein-comments' : ["""(E. coli contains three N-acetylmuramyl-L-alanine amidases named AmiA, B, and C involved in cell division
by splitting the murein septum. They accomplish this by removing the peptide moiety from N-acetylmuramic acid,
removing crosslinks |CITS:[11454209]|.
AmiA and AmiC are transported to the periplasm by the twin-arginine protein transport (Tat) pathway
|CITS:[12787348][12787347]|. In all cells AmiA is dispersed evenly throughout the periplasm. It is predicted to have
a signal peptide from residues 1 to 34 which contains the Tat-targeting motif, an unknown domain from residues 35 to
117, and an amidase domain from residues 118 to 289 |CITS:[12787347]|.
Separation of daughter cells during division is reduced in amidase mutants, with the exception of amiB,
resulting in chaining of cells. Deletion of multiple amidases, including amiB, leads to increases in chain length
and relative number of chains formed. The triple amidase mutant is less sensitive to the combined activities of the
antibiotics aztreonam and bulgecin |CITS:[11454209]|.)""",]},
'B2508' : {'ecocyc-rxns': {"""IMP-DEHYDROG-RXN""": """H2O + NAD+ + inosine-5'-phosphate = NADH + xanthosine-5-phosphate""",},'ucsd-rxns' : ['IMPD',], 'protein-comments' : ["""NIL""","""(IMP dehydrogenase (IMPDH) is a homotetramer |CITS: [10545277]|.
IMPDH appears to bind single-stranded nucleic acids both in vivo and in vitro |CITS: [14766016]|.
)""",]},
'B1443' : {'ecocyc-rxns': {},'ucsd-rxns' : ['PTRCabcpp','SPMDabcpp',], 'protein-comments' : ["""(membrane component of ABC transporter)""","""(YdcS, YdcT, YdcU and YdcV are uncharacterized
members of the ABC superfamily of transporters
|CITS: [99091701]|. YdcS is the putative
periplasmic binding component, YdcT is the
putative ATP binding component, YdcU and YdcV
are the putative membrane spanning components.
Bases on sequence similarity they may function
together as an ATP-dependent spermidine/
putrecine transporter. The genes ydcS,
ydcT, ydcU, and ydcV are
probably located in a single operon.)""",]},
'B3213' : {'ecocyc-rxns': {"""GLUTAMATESYN-RXN""": """2 L-glutamate + NADP+ = L-glutamine + α-ketoglutarate + NADPH""",},'ucsd-rxns' : ['GLUSy',], 'protein-comments' : ["""(Glutamate synthase and other amidotransferases can utilize a
high level of ammonia in place of glutamine as nitrogen donor. The
ammonia dependent activity is a property of the small subunit. It
should be noted that the ammonia dependent reaction is the same
reaction as that catalyzed by glutamate dehydrogenase)""","""(The coli enzyme is composed of four dimers, each dimer
consisting of two different subunits. The gltBDF operon comprises
genes coding for the large (gltB) and small (gltD) glutamate synthase
subunits and a third downstream gene, gltF, the product of which is
involved in Ntr regulation |CITS:88115186|)""","""(Glutamate synthase has two functions, the synthesis of
glutamate and the removal of glutamine, the primary product of ammonia
assimilation during nitrogen-limited growth. The discovery of glutamate
synthase established a previously unknown pathway of glutamate
formation from ammonia; first ammonia is incorporated by glutamine
synthetase into glutamine,and then the amide of glutamine is
transferred to 2-ketoglutarate to form two molecules of glutamate.
The purified enzyme contains flavin (both flavin adenine dinucleotide
and flavin mononucleotide), iron, and labile sulfide.)""",]},
'B3212' : {'ecocyc-rxns': {"""GLUTAMATESYN-RXN""": """2 L-glutamate + NADP+ = L-glutamine + α-ketoglutarate + NADPH""",},'ucsd-rxns' : ['GLUSy',], 'protein-comments' : ["""(Glutaminase activity is a property of the larger subunit.)""","""(The coli enzyme is composed of four dimers, each dimer
consisting of two different subunits. The gltBDF operon comprises
genes coding for the large (gltB) and small (gltD) glutamate synthase
subunits and a third downstream gene, gltF, the product of which is
involved in Ntr regulation |CITS:88115186|)""","""(Glutamate synthase has two functions, the synthesis of
glutamate and the removal of glutamine, the primary product of ammonia
assimilation during nitrogen-limited growth. The discovery of glutamate
synthase established a previously unknown pathway of glutamate
formation from ammonia; first ammonia is incorporated by glutamine
synthetase into glutamine,and then the amide of glutamine is
transferred to 2-ketoglutarate to form two molecules of glutamate.
The purified enzyme contains flavin (both flavin adenine dinucleotide
and flavin mononucleotide), iron, and labile sulfide.)""",]},
'B2344' : {'ecocyc-rxns': {"""RXN0-1802""": """a fatty acid[extracellular space] =a fatty acid[periplasmic space] """,},'ucsd-rxns' : ['HDCEAtexi','HDCAtexi','OCDCEAtexi','TTDCEAtexi','DDCAtexi','OCDCAtexi','TTDCAtexi',], 'protein-comments' : ["""(FadL is an outer membrane protein involved with the uptake of long-chain fatty acids.
|CITS:[8340375]| Proteolysis studies suggest that the amino terminal contains a portion
required for bacteriophage T2 binding and the carboxy terminal contains the sequence
required for long chain fatty acid transport. |CITS:[10845710]| Mutational analyses have
isolated the amino acid residues and domains involved in long-chain fatty acid specificity
and transport.
Neural network prediction suggested that the pore consists of 20 antiparallel
β-strands |CITS:[10845710]|. The crystal structure has been solved at 2.6 and 2.8
angstrom resolutions which show that FadL in fact forms a 14-stranded antiparallel
β barrel. The amino terminus forms a small "hatch" domain which plugs the barrel
on the extracellular side |CITS:[15178802]|. FadL has been found as a dimer in the
outer membrane |CITS:[16079137]|.
)""",]},
'B3831' : {'ecocyc-rxns': {"""URPHOS-RXN""": """phosphate + uridine = ribose-1-phosphate + uracil""",},'ucsd-rxns' : ['PYNP2r',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B2342' : {'ecocyc-rxns': {"""KETOACYLCOATHIOL-RXN""": """an acyl-CoA + acetyl-CoA = a 3-ketoacyl-CoA + coenzyme A""",},'ucsd-rxns' : ['KAT8','KAT1','KAT2','KAT3','KAT4','KAT5','KAT6','KAT7',], 'protein-comments' : ["""(During anaerobic beta-oxidation of fatty acids FadI, FadJ, and FadK serve functions parallel to those of FadA, FadB, and FadD in the aerobic pathway |CITS: [12535077]|.
FadJ and FadI exhibit partial functional redundancy with FadA and FadB under aerobic conditions and the two complexes are proposed to increase efficiency of the process by favoring substrates of different chain length |CITS: [12535077]|.
A strain producing FadJ and FadI from a plasmid exhibits thiolase activity with beta-ketyoacyl-CoAs of 6 to 12 carbon units but not with acetoacetyl-CoA |CITS: [12270828]|. FadJ and FadI copurify over a gel filtration column |CITS: [12270828]|.
Regulation has been described |CITS: [12535077]|. FadR represses transcription of yfcYX in the presence of oxygen |CITS: [12535077]|.)""","""NIL""","""(During anaerobic beta-oxidation of fatty acids FadI, FadJ, and FadK serve functions parallel to those of FadA, FadB, and FadD in the aerobic pathway |CITS: [12535077]|.)""",]},
'B1109' : {'ecocyc-rxns': {"""R170-RXN""": """NADH + Cu2+ = NAD+ + Cu+""","""NADH-DEHYDROG-A-RXN""": """ubiquinone-8 + NADH = ubiquinol-8 + NAD+""",},'ucsd-rxns' : ['NADH10','NADH5','NADH9',], 'protein-comments' : ["""(There are two distinct NADH dehydrogenases in E. coli. NADH dehydrogenase I (NDH-1) is encoded by the
nuo genes, and NADH dehydrogenase II (NDH-2) is encoded byndh. In contrast to NDH-1, NDH-2
utilizes NADH exclusively, and electron flow from NADH to ubiquinone-1 does not generate an electrochemical
gradient |CITS: [93259946]|. NDH-2 links the major catabolic and energy-producing pathways in the cell |CITS: [81184511]|.
NDH-2 also has cupric reductase activity |CITS: [99441207]|. The enzyme contains a thiolate-bound Cu(I) ion, and
a putative copper binding site has been identified |CITS: [12176061]|.
NDH-2 has remote similarity to the SCOP-family of FAD/NAD-linked reductases. Based on this similarity, a
structural model of NDH-2 has been proposed |CITS: [15581635]|.)""",]},
'B2341' : {'ecocyc-rxns': {"""KETOACYLCOATHIOL-RXN""": """an acyl-CoA + acetyl-CoA = a 3-ketoacyl-CoA + coenzyme A""","""ENOYL-COA-HYDRAT-RXN""": """H2O + a trans-2-enoyl-CoA = an L-3-hydroxyacyl-CoA""","""OHBUTYRYL-COA-EPIM-RXN""": """a D-3-hydroxyacyl-CoA = an L-3-hydroxyacyl-CoA""","""ENOYL-COA-DELTA-ISOM-RXN""": """a cis-3-enoyl-CoA = a trans-2-enoyl-CoA""","""OHACYL-COA-DEHYDROG-RXN""": """NAD+ + an L-3-hydroxyacyl-CoA = NADH + a 3-ketoacyl-CoA""",},'ucsd-rxns' : ['HACD3i','HACD8i','HACD4i','HACD5i','HACD6i','HACD7i','HACD1i','ECOAH8','ECOAH6','ECOAH7','ECOAH4','ECOAH5','ECOAH2','ECOAH3','ECOAH1','HACD2i',], 'protein-comments' : ["""(During anaerobic beta-oxidation of fatty acids FadI, FadJ, and FadK serve functions parallel to those of FadA, FadB, and FadD in the aerobic pathway |CITS: [12535077]|.
FadJ has 34% identity to FadB and, in a fadB mutant background, FadJ is essential for processing of long-chain fatty acids to medium-chain polyhydroxyalkanoates (PHAMCL) |CITS: [12270828]|. Overproduced protein exhibits enoyl-CoA hydratase and 3-hydroxyacyl-CoA dehydrogenase activity |CITS: [12270828]|.
A strain producing FadJ and FadI from a plasmid exhibits thiolase activity with beta-ketyoacyl-CoAs of 6 to 12 carbon units but not with acetoacetyl-CoA |CITS: [12270828]|. FadJ and YfcY copurify over a gel filtration column |CITS: [12270828]|.
Conservation of enoyl-CoA hydratase, 3-hydroxyacyl-CoA epimerase, and 3-hydroxyacyl-CoA dehydrogenase active site residues is observed |CITS: [12270828]|.
FadJ and FadI exhibit partial functional redundancy with FadA and FadB under aerobic conditions and the two complexes are proposed to increase efficiency of the process by favoring substrates of different chain length |CITS: [12535077]|.
Regulation has been described |CITS: [12535077]|. FadR represses transcription of yfcYX in the presence of oxygen |CITS: [12535077]|.
Transcription of fadJ is induced upon biofilm formation compared to planktonic growth in both exponential and
stationary phase. Induction of expression was found to be independent of the presence of the F plasmid
|CITS: [14731270]|.
A fadJ mutant is impaired in biofilm formation |CITS: [14731270]|.)""","""NIL""","""(During anaerobic beta-oxidation of fatty acids FadI, FadJ, and FadK serve functions parallel to those of FadA, FadB, and FadD in the aerobic pathway |CITS: [12535077]|.)""",]},
'B1246' : {'ecocyc-rxns': {"""ABC-22-RXN""": """ATP + a peptide[periplasmic space] + H2O =ADP + phosphate + a peptide[cytosol] """,},'ucsd-rxns' : ['4PEPTabcpp','3PEPTabcpp',], 'protein-comments' : ["""NIL""","""(OppABCDF is an ATP-dependent oligopeptide transporter that is a
member of the ATP-Binding Cassette (ABC) Superfamily of transporters |CITS:[1738314]|.
OppABCDF has not been investigated in detail in E. coli,
but the orthologous system in Salmonella typhimurium has been
extensively characterized. Binding affinity and competition assays have
shown that OppABCDF will transport oligopeptides up to five amino acids
in length, but has no affinity for free amino acids |CITS:[3536860],[8801122]|.
The system has been observed to function in oligopeptide uptake, as
well as recycling of cell wall peptides |CITS:[2821267]|. Based on
sequence similarity, OppB and OppC are the membrane components
of the ABC transporter, and OppD and OppF are the ATP-binding
components of the ABC transporter |CITS:[8801122],[1738314]|.
OppA is the periplasmic substrate-binding component, however MppA
can replace OppA as a periplasmic-binding component of the transporter
when it binds murein tripeptides |CITS:[9495761]|. MppA was shown to be
required for murein tripeptide transport in a diaminoimelic acid-requiring
strain |CITS:[9495761]|. Insertion mutation of the oppF gene has
shown that OppF is required for Opp transporter function |CITS:[2821267]|.
In addition, Insertional mutants of each of the opp genes were
constructed, and the opp-minus strains were unable to utilize the
peptide Pro-Gly-Gly, normally transported by the wild-type transporter |CITS:[2821267]|.
Expression of oppABCD increased after long-term adaptation
to growth in complex medium with acetate or propionate |CITS:[12620868]|.
Expression of mppA decreased after long-term adaptation to growth
in complex medium with acetate or propionate |CITS:[12620868]|.
Expression of mppA was shown to be activated by cyclic AMP
receptor protein |CITS:[15520470]|.
)""","""(OppABCDF is an ATP-dependent oligopeptide transporter that is a member of the ATP-Binding Cassette
(ABC) Superfamily of transporters |CITS: [92149312]|. OppABCDF has not been investigated in detail in
E. coli, but the orthologous system in Salmonella typhimurium has been extensively
characterized. Binding affinity and competition assays have shown that OppABCDF will transport
oligopeptides up to five amino acids in length, but has no affinity for free amino acids |CITS: [87056967]
[8801122]|. The system has been observed to function in oligopeptide uptake, as well as recycling of cell
wall peptides |CITS: [88011222]|. Based on sequence similarity, OppB and OppC are the membrane
components of the ABC transporter, and OppD and OppF are the ATP-binding components of the ABC
transporter |CITS: [8801122][92149312]|. OppA is the periplasmic substrate-binding component that binds
oligopeptides with a Kd of approximately 1E-6 |CITS: [94261830]|. Insertion mutant of the
oppF gene has shown that OppF is required for Opp transporter function |CITS: [88011222]|. In
addition, Insertional mutants of each of the opp genes were constructed, and the opp-minus
strains were unable to utilize the peptide Pro-Gly-Gly, normally transported by the wild-type transporter
|CITS: [88011222]|.
OppA has been crystallized and its structure resolved to 2.3 A resolution showing OppA to be a bilobal,
principally beta-stranded, three-domain protein |CITS:[15299334]|.
Targeting of OppA to the Sec-translocase for transport across the inner membrane
is SecB-dependent |CITS:[16352602]|.)""",]},
'B1247' : {'ecocyc-rxns': {"""ABC-22-RXN""": """ATP + a peptide[periplasmic space] + H2O =ADP + phosphate + a peptide[cytosol] """,},'ucsd-rxns' : ['4PEPTabcpp','3PEPTabcpp',], 'protein-comments' : ["""NIL""","""(OppABCDF is an ATP-dependent oligopeptide transporter that is a
member of the ATP-Binding Cassette (ABC) Superfamily of transporters |CITS:[1738314]|.
OppABCDF has not been investigated in detail in E. coli,
but the orthologous system in Salmonella typhimurium has been
extensively characterized. Binding affinity and competition assays have
shown that OppABCDF will transport oligopeptides up to five amino acids
in length, but has no affinity for free amino acids |CITS:[3536860],[8801122]|.
The system has been observed to function in oligopeptide uptake, as
well as recycling of cell wall peptides |CITS:[2821267]|. Based on
sequence similarity, OppB and OppC are the membrane components
of the ABC transporter, and OppD and OppF are the ATP-binding
components of the ABC transporter |CITS:[8801122],[1738314]|.
OppA is the periplasmic substrate-binding component, however MppA
can replace OppA as a periplasmic-binding component of the transporter
when it binds murein tripeptides |CITS:[9495761]|. MppA was shown to be
required for murein tripeptide transport in a diaminoimelic acid-requiring
strain |CITS:[9495761]|. Insertion mutation of the oppF gene has
shown that OppF is required for Opp transporter function |CITS:[2821267]|.
In addition, Insertional mutants of each of the opp genes were
constructed, and the opp-minus strains were unable to utilize the
peptide Pro-Gly-Gly, normally transported by the wild-type transporter |CITS:[2821267]|.
Expression of oppABCD increased after long-term adaptation
to growth in complex medium with acetate or propionate |CITS:[12620868]|.
Expression of mppA decreased after long-term adaptation to growth
in complex medium with acetate or propionate |CITS:[12620868]|.
Expression of mppA was shown to be activated by cyclic AMP
receptor protein |CITS:[15520470]|.
)""","""(OppABCDF is an ATP-dependent oligopeptide transporter that is a member of the ATP-Binding Cassette
(ABC) Superfamily of transporters |CITS: [92149312]|. OppABCDF has not been investigated in detail in
E. coli, but the orthologous system in Salmonella typhimurium has been extensively
characterized. Binding affinity and competition assays have shown that OppABCDF will transport
oligopeptides up to five amino acids in length, but has no affinity for free amino acids |CITS: [87056967]
[8801122]|. The system has been observed to function in oligopeptide uptake, as well as recycling of cell
wall peptides |CITS: [88011222]|. Based on sequence similarity, OppB and OppC are the membrane
components of the ABC transporter, and OppD and OppF are the ATP-binding components of the ABC
transporter |CITS: [8801122][92149312]|. OppA is the periplasmic substrate-binding component that binds
oligopeptides with a Kd of approximately 1E-6 |CITS: [94261830]|. Insertion mutant of the
oppF gene has shown that OppF is required for Opp transporter function |CITS: [88011222]|. In
addition, Insertional mutants of each of the opp genes were constructed, and the opp-minus
strains were unable to utilize the peptide Pro-Gly-Gly, normally transported by the wild-type transporter
|CITS: [88011222]|.
OppA has been crystallized and its structure resolved to 2.3 A resolution showing OppA to be a bilobal,
principally beta-stranded, three-domain protein |CITS:[15299334]|.
Targeting of OppA to the Sec-translocase for transport across the inner membrane
is SecB-dependent |CITS:[16352602]|.)""",]},
'B1244' : {'ecocyc-rxns': {"""ABC-22-RXN""": """ATP + a peptide[periplasmic space] + H2O =ADP + phosphate + a peptide[cytosol] """,},'ucsd-rxns' : ['4PEPTabcpp','3PEPTabcpp',], 'protein-comments' : ["""(membrane component of ABC transporter)""","""(OppABCDF is an ATP-dependent oligopeptide transporter that is a
member of the ATP-Binding Cassette (ABC) Superfamily of transporters |CITS:[1738314]|.
OppABCDF has not been investigated in detail in E. coli,
but the orthologous system in Salmonella typhimurium has been
extensively characterized. Binding affinity and competition assays have
shown that OppABCDF will transport oligopeptides up to five amino acids
in length, but has no affinity for free amino acids |CITS:[3536860],[8801122]|.
The system has been observed to function in oligopeptide uptake, as
well as recycling of cell wall peptides |CITS:[2821267]|. Based on
sequence similarity, OppB and OppC are the membrane components
of the ABC transporter, and OppD and OppF are the ATP-binding
components of the ABC transporter |CITS:[8801122],[1738314]|.
OppA is the periplasmic substrate-binding component, however MppA
can replace OppA as a periplasmic-binding component of the transporter
when it binds murein tripeptides |CITS:[9495761]|. MppA was shown to be
required for murein tripeptide transport in a diaminoimelic acid-requiring
strain |CITS:[9495761]|. Insertion mutation of the oppF gene has
shown that OppF is required for Opp transporter function |CITS:[2821267]|.
In addition, Insertional mutants of each of the opp genes were
constructed, and the opp-minus strains were unable to utilize the
peptide Pro-Gly-Gly, normally transported by the wild-type transporter |CITS:[2821267]|.
Expression of oppABCD increased after long-term adaptation
to growth in complex medium with acetate or propionate |CITS:[12620868]|.
Expression of mppA decreased after long-term adaptation to growth
in complex medium with acetate or propionate |CITS:[12620868]|.
Expression of mppA was shown to be activated by cyclic AMP
receptor protein |CITS:[15520470]|.
)""","""(OppABCDF is an ATP-dependent oligopeptide transporter that is a member of the ATP-Binding Cassette
(ABC) Superfamily of transporters |CITS: [92149312]|. OppABCDF has not been investigated in detail in
E. coli, but the orthologous system in Salmonella typhimurium has been extensively
characterized. Binding affinity and competition assays have shown that OppABCDF will transport
oligopeptides up to five amino acids in length, but has no affinity for free amino acids |CITS: [87056967]
[8801122]|. The system has been observed to function in oligopeptide uptake, as well as recycling of cell
wall peptides |CITS: [88011222]|. Based on sequence similarity, OppB and OppC are the membrane
components of the ABC transporter, and OppD and OppF are the ATP-binding components of the ABC
transporter |CITS: [8801122][92149312]|. OppA is the periplasmic substrate-binding component that binds
oligopeptides with a Kd of approximately 1E-6 |CITS: [94261830]|. Insertion mutant of the
oppF gene has shown that OppF is required for Opp transporter function |CITS: [88011222]|. In
addition, Insertional mutants of each of the opp genes were constructed, and the opp-minus
strains were unable to utilize the peptide Pro-Gly-Gly, normally transported by the wild-type transporter
|CITS: [88011222]|.
OppA has been crystallized and its structure resolved to 2.3 A resolution showing OppA to be a bilobal,
principally beta-stranded, three-domain protein |CITS:[15299334]|.
Targeting of OppA to the Sec-translocase for transport across the inner membrane
is SecB-dependent |CITS:[16352602]|.)""",]},
'B0004' : {'ecocyc-rxns': {"""THRESYN-RXN""": """O-phospho-L-homoserine + H2O = phosphate + L-threonine""",},'ucsd-rxns' : ['THRS','4HTHRS',], 'protein-comments' : ["""(The three proteins of threonine biosynthesis, ThrA, ThrB and ThrC, may have descended from a common ancestor.
|CITS: [77077184] [87080286] [81150470]|)""",]},
'B3198' : {'ecocyc-rxns': {"""KDO-8PPHOSPHAT-RXN""": """3-deoxy-D-manno-octulosonate 8-P + H2O = 3-deoxy-D-manno-octulosonate + phosphate""",},'ucsd-rxns' : ['KDOPP',], 'protein-comments' : ["""(3-deoxy-D-manno-octulosonate 8-phosphate phosphatase is specific for the hydrolysis of
3-deoxy-D-manno-octulosonate 8-phosphate. The product of this reaction is a unique eight-carbon keto
sugar sugar that is an integral part of lipopolysaccharide, forming a direct link between lipid A and the growing
polysaccharide chain. The enzyme was initially purified from E. coli B |CITS: [80182062]|.
YrbI belongs to the family of HAD-like hydrolases and is a tetramer in solution |CITS: [12639950]|.
The reaction kinetics and optimal conditions have been characterized using recombinant enzyme |CITS: [12639950]|.
The enzyme exhibits tight substrate specificity and shows a requirement for divalent cation |CITS: [12639950]|.)""","""NIL""",]},
'B1243' : {'ecocyc-rxns': {"""ABC-22-RXN""": """ATP + a peptide[periplasmic space] + H2O =ADP + phosphate + a peptide[cytosol] """,},'ucsd-rxns' : ['4PEPTabcpp',], 'protein-comments' : ["""NIL""","""(OppABCDF is an ATP-dependent oligopeptide transporter that is a member of the ATP-Binding Cassette
(ABC) Superfamily of transporters |CITS: [92149312]|. OppABCDF has not been investigated in detail in
E. coli, but the orthologous system in Salmonella typhimurium has been extensively
characterized. Binding affinity and competition assays have shown that OppABCDF will transport
oligopeptides up to five amino acids in length, but has no affinity for free amino acids |CITS: [87056967]
[8801122]|. The system has been observed to function in oligopeptide uptake, as well as recycling of cell
wall peptides |CITS: [88011222]|. Based on sequence similarity, OppB and OppC are the membrane
components of the ABC transporter, and OppD and OppF are the ATP-binding components of the ABC
transporter |CITS: [8801122][92149312]|. OppA is the periplasmic substrate-binding component that binds
oligopeptides with a Kd of approximately 1E-6 |CITS: [94261830]|. Insertion mutant of the
oppF gene has shown that OppF is required for Opp transporter function |CITS: [88011222]|. In
addition, Insertional mutants of each of the opp genes were constructed, and the opp-minus
strains were unable to utilize the peptide Pro-Gly-Gly, normally transported by the wild-type transporter
|CITS: [88011222]|.
OppA has been crystallized and its structure resolved to 2.3 A resolution showing OppA to be a bilobal,
principally beta-stranded, three-domain protein |CITS:[15299334]|.
Targeting of OppA to the Sec-translocase for transport across the inner membrane
is SecB-dependent |CITS:[16352602]|.)""",]},
'B2942' : {'ecocyc-rxns': {"""S-ADENMETSYN-RXN""": """ATP + L-methionine + H2O = phosphate + diphosphate + S-adenosyl-L-methionine""",},'ucsd-rxns' : ['METAT',], 'protein-comments' : ["""(S-adenosylmethionine synthetase binds two divalent cations per subunit |CITS: [81117279]|.
The enzyme has been crystallized.
A novel catalytic mechanism for SAM has been proposed |CITS: [14967023]|.
metK is essential for growth in E. coli |CITS: [11952912]|; lack of S-adenosylmethionine synthetase
(SAM) activity causes a defect in cell division |CITS: [9658005]|.
Regulation has been described |CITS: [14727089][9658005]|. Transcription is induced upon biofilm formation
|CITS: [14727089]|.)""","""NIL""",]},
'B2943' : {'ecocyc-rxns': {"""TRANS-RXN-21""": """H+[periplasmic space] + β-D-galactose[periplasmic space] =H+[cytosol] + β-D-galactose[cytosol] """,},'ucsd-rxns' : ['GALt2pp','GLCt2pp',], 'protein-comments' : ["""(GalP is one of two, along with MglABC, major routes for galactose transport into E. coli 2-deoxy-
D-galactose is a specific substrate for GalP but not for MglABC and GalP operates by a sugar-proton
symport mechanism while MglABC does not |CITS: [77157180]|. Mutation studies |CITS: [83161013]|
demonstrated that insertions in the galP gene resulted in a mutant strain resistant to
2-deoxygalactose and defective in uptake of radiolabelled 2-deoxyglucose. The GalP protein has been
overproduced and purified and reconstituted as a galactose transporter |CITS: [20288932]| and has been
shown to share a high level of sequence similarity with other proton-linked systems for L-arabinose (AraE,
64% identity) and for D-xylose (XylE, 34% identity) in E.coli |CITS:[87115869]|. Equilibrium binding
studies |CITS: [91217048]| indicate that cytochalasin B, which is a potent inhibitor of passive glucose
transporters in mammals, is bound with high-affinity by membranes of an E. coli strain constitutive for GalP.
The same studies indicate that this binding is inhibited by the presence of substrates for GalP in order of
their effectiveness as substrates and/ or inhibitors of the GalP transporter. GalP is a member of the Major
Facilitator Superfamily (MFS) of transporters |CITS: [98190790]|.)""",]},
'B2827' : {'ecocyc-rxns': {"""THYMIDYLATESYN-RXN""": """dUMP + 5,10-methylene-THF = dTMP + 7,8-dihydrofolate""",},'ucsd-rxns' : ['TMDS',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B4115' : {'ecocyc-rxns': {"""RXN0-2162""": """L-arginine[periplasmic space] + agmatine[cytosol] =L-arginine[cytosol] + agmatine[periplasmic space] """,},'ucsd-rxns' : ['ARGAGMt7pp',], 'protein-comments' : ["""(To survive in extremely acidic environments, E. coli has evolved three acid resistance strategies. One of them is dependent upon external arginine.
This system employs the AdiA decarboxylase and the AdiC Arginine:Agmatine antiporter to exchange extracellular Arginine
for the intracellular by-product of decarboxylation, Agmatine |CITS: [12867448]| . The proton consuming decarboxylase reaction counteracts
acidifcation in a strongly acidic environment. Deletion mutation and complementation studies |CITS:[12867448]| indicate that AdiC is the
arginine/agmatine antiporter responsible for maintaining arginine-dependent acid resistance.)""",]},
'B1363' : {'ecocyc-rxns': {"""TRANS-RXN-3""": """H+[periplasmic space] + K+[periplasmic space] =H+[cytosol] + K+[cytosol] """,},'ucsd-rxns' : ['Kt2pp',], 'protein-comments' : ["""(TrkG is a potassium ion transporter, closely related to the TrkH
potassium ion transporter. Inactivation of either trkG or
trkH genes affects the kinetics of potassium uptake
|CITS: [95204366]|. Both TrkG and TrkH appear to be low affinity
transporters for potassium (Km of 1-6 mM). Both TrkG and TrkH
appear to function in conjunction with TrkA, a peripheral membrane
binding protein that binds NAD+ and is essential for TrkG/H activity
|CITS: [89380255] [94018648]|. TrkE, an ATP binding protein, additionally
is required for TrkH activity and affects the kinetics of TrkG activity
|CITS: [91100357]|. Both TrkA and TrkE probably play regulatory roles.
Interactions between TrkG and TrkH remain to be clarified. TrkG and
TrkH are members of the Trk family of potassium ion transporters and
probably function as potassium ion/proton symporters.
The trkG gene is probably a foreign gene which was inserted
with a rac prophage |CITS: [95204366]|.)""",]},
'B2536' : {'ecocyc-rxns': {},'ucsd-rxns' : ['PPPNt2rpp',], 'protein-comments' : ["""(HcaT is a member of the major facilitator superfamily (MFS) of transporters |CITS: [98190790]|.
HcaT is a putative 3-phenylpropionate transporter. The hcaT gene is
located immediately downstream of the hcaR gene, whose product regulates
expression of the hcaA-D operon responsible for catabolism of
3-phenylpropionic acid |CITS: [98269008]|.
Membrane topology predictions using experimentally determined C terminus
locations indicate that HcaT has 12 transmembrane helices and the C-terminus is
located in the cytoplasm |CITS:[15044727]|.)""",]},
'B0452' : {'ecocyc-rxns': {"""THIOESTER-RXN""": """an acyl-CoA + H2O -> a fatty acid + coenzyme A""",},'ucsd-rxns' : ['FACOAE180','FACOAE100','FACOAE120','FACOAE141','FACOAE140','FACOAE161','FACOAE160','FACOAE181','FACOAE60','FACOAE80',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B2533' : {'ecocyc-rxns': {"""MYO-INOSITOL-1(OR-4)-MONOPHOSPHATASE-RXN""": """H2O + D-myo-inositol (3)-monophosphate = phosphate + myo-inositol""",},'ucsd-rxns' : ['MI1PP',], 'protein-comments' : ["""NIL""",]},
'B1249' : {'ecocyc-rxns': {"""CARDIOLIPSYN-RXN""": """2 an L-1-phosphatidyl-glycerol -> cardiolipin + glycerol""",},'ucsd-rxns' : ['CLPNS140pp','CLPNS180pp','CLPNS181pp','CLPNS141pp','CLPNS160pp','CLPNS161pp','CLPNS120pp',], 'protein-comments' : ["""NIL""",]},
'B4407' : {'ecocyc-rxns': {},'ucsd-rxns' : ['THZPSN',], 'protein-comments' : ["""(ThiS is the sulfur source for the thiazole moiety in thiamin
biosynthesis. In a reaction catalyzed by the ThiF protein, ThiS is
adenylated, yielding ThiS-COAMP. Sulfur is transferred to ThiS-COAMP
from cysteine in a reaction also catalyzed by ThiF and the ThiI protein, yielding
ThiS-COSH. |CITS: [99311269] [98298179]|)""","""(ThiS is the sulfur source for the thiazole moiety in thiamin
biosynthesis. In a reaction catalyzed by the ThiF protein, ThiS is
adenylated, yielding ThiS-COAMP. Sulfur is transferred to ThiS-COAMP
from cysteine in a reaction also catalyzed by ThiF and the ThiI protein, yielding
ThiS-COSH. In a reaction combining deoxy-D-xylulose-P, tyrosine and
ThiS-COSH the thiazole moiety is synthesized. |CITS: [99311269] [98298179]|)""","""(ThiS is the sulfur source for the thiazole moiety in thiamin
biosynthesis. In a reaction catalyzed by the ThiF protein, ThiS is
adenylated, yielding ThiS-COAMP. Sulfur is transferred to ThiS-COAMP
from cysteine in a reaction also catalyzed by ThiF and the ThiI protein, yielding
ThiS-COSH. |CITS: [99311269] [98298179]|)""",]},
'B4154' : {'ecocyc-rxns': {"""R601-RXN""": """fumarate + menaquinol + 2 H+ -> succinate + menaquinone-8""",},'ucsd-rxns' : ['FRD2','FRD3',], 'protein-comments' : ["""(FrdA is one of two catalytic subunits in the four subunit enzyme. This subunit contains the FAD cofactor.
This protein has similarity to the SdhA subunit of succinate dehydrogenase |CITS: [6383359]|. A 2.2 Å crystal
structure of L-aspartate oxidase suggests that an unusual tertiary structure is shared by L-aspartate oxidase, the
SdhA subunit of succinate dehydrogenase, and the FrdA subunit of fumarate reductase |CITS: [10425677]|.)""","""(The reaction catalysed by fumarate reductase allows fumarate to serve as a terminal electron acceptor
when E. coli is growing under anaerobic conditions. The electron donor for
this reaction is reduced menaquinone. It contributes to generating a proton gradient in a scalar mechanism by
utilitzing two protons from the cytoplasm.
Fumarate reductase is composed of 4 subunits and two domains. The catalytic domain consists of two subunits: one
with a covalently-bound flavin cofactor and the fumarate binding site; the other contains 3 iron-sulfur clusters. This
catalytic domain is attached to the cytoplasmic side of the cytoplasmic membrane by the anchor domain, which
consists of two subunits that interact with quinone and contain heme b556 |CITS: [11803023]|. The enzyme has two
quinol-binding sites, Qp and Qd, indicating their being proximal or distal to the site of fumarate reduction. It is not
clear whether both of the two quinol-binding sites are functionally relevant |CITS: [11850430]|. The amino acid
residues involved in the interaction with quinones have been identified |CITS: [8419359]|.
Fumarate reductase is made under anaerobic conditions with glucose or glycerol
as carbon source. The covalent attachment of FAD to the enzyme (A subunit apoprotein) is
stimulated by citrate, isocitrate, succinate and fumarate, acting possibly
as allosteric effectors. The enzyme has been crystallized |CITS: [11850430]|. Fumarate reductase is
closely related to succinate dehydrogenase and is regulated by the products of fnr and ntr genes.
|CITS: [89276374] [99301923]|)""",]},
'B1850' : {'ecocyc-rxns': {"""OXALODECARB-RXN""": """oxaloacetate = pyruvate + CO2""","""KDPGALDOL-RXN""": """2-keto-3-deoxy-6-phospho-gluconate = D-glyceraldehyde-3-phosphate + pyruvate""","""4OH2OXOGLUTARALDOL-RXN""": """D-4-hydroxy-2-keto-glutarate = glyoxylate + pyruvate""",},'ucsd-rxns' : ['EDA','OAADC',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B4151' : {'ecocyc-rxns': {"""R601-RXN""": """fumarate + menaquinol + 2 H+ -> succinate + menaquinone-8""",},'ucsd-rxns' : ['FRD2','FRD3',], 'protein-comments' : ["""(This is one of two membrane proteins in the four subunit enzyme.
The FrdC and FrdD subunits bind the two menaquinone molecules
involved in the electron transfer reactions of the enzyme. |CITS: [99301923]|
Despite similar function, hydrophobicity, and protein size, the FrdC and FrdD
subunits of fumarate reductase do not share significant sequence identity
with the corresponding membrane-binding subunits of succinate dehydrogenase, SdhC and SdhD |CITS: [6383359]|.)""","""(The reaction catalysed by fumarate reductase allows fumarate to serve as a terminal electron acceptor
when E. coli is growing under anaerobic conditions. The electron donor for
this reaction is reduced menaquinone. It contributes to generating a proton gradient in a scalar mechanism by
utilitzing two protons from the cytoplasm.
Fumarate reductase is composed of 4 subunits and two domains. The catalytic domain consists of two subunits: one
with a covalently-bound flavin cofactor and the fumarate binding site; the other contains 3 iron-sulfur clusters. This
catalytic domain is attached to the cytoplasmic side of the cytoplasmic membrane by the anchor domain, which
consists of two subunits that interact with quinone and contain heme b556 |CITS: [11803023]|. The enzyme has two
quinol-binding sites, Qp and Qd, indicating their being proximal or distal to the site of fumarate reduction. It is not
clear whether both of the two quinol-binding sites are functionally relevant |CITS: [11850430]|. The amino acid
residues involved in the interaction with quinones have been identified |CITS: [8419359]|.
Fumarate reductase is made under anaerobic conditions with glucose or glycerol
as carbon source. The covalent attachment of FAD to the enzyme (A subunit apoprotein) is
stimulated by citrate, isocitrate, succinate and fumarate, acting possibly
as allosteric effectors. The enzyme has been crystallized |CITS: [11850430]|. Fumarate reductase is
closely related to succinate dehydrogenase and is regulated by the products of fnr and ntr genes.
|CITS: [89276374] [99301923]|)""",]},
'B4019' : {'ecocyc-rxns': {"""HOMOCYSMETB12-RXN""": """L-homocysteine + 5-methyl-THF = L-methionine + tetrahydrofolate""",},'ucsd-rxns' : ['METS',], 'protein-comments' : ["""(X-ray crystallography has been done |CITS: [92277660]|;
the peptide binding cobalamin has been isolated |CITS: [89340482]|)""",]},
'B4153' : {'ecocyc-rxns': {"""R601-RXN""": """fumarate + menaquinol + 2 H+ -> succinate + menaquinone-8""",},'ucsd-rxns' : ['FRD2','FRD3',], 'protein-comments' : ["""(This is one of two catalytic subunits of the four subunit enzyme.
This subunit contains three iron-sulfur clusters: a 4Fe-4S, a 3Fe-4S
and a 2Fe-2S.
This subunit has 38% identity to the succinate dehydrogenase iron-sulfur
cluster subunit, SdhB |CITS: [6388571]|.)""","""(The reaction catalysed by fumarate reductase allows fumarate to serve as a terminal electron acceptor
when E. coli is growing under anaerobic conditions. The electron donor for
this reaction is reduced menaquinone. It contributes to generating a proton gradient in a scalar mechanism by
utilitzing two protons from the cytoplasm.
Fumarate reductase is composed of 4 subunits and two domains. The catalytic domain consists of two subunits: one
with a covalently-bound flavin cofactor and the fumarate binding site; the other contains 3 iron-sulfur clusters. This
catalytic domain is attached to the cytoplasmic side of the cytoplasmic membrane by the anchor domain, which
consists of two subunits that interact with quinone and contain heme b556 |CITS: [11803023]|. The enzyme has two
quinol-binding sites, Qp and Qd, indicating their being proximal or distal to the site of fumarate reduction. It is not
clear whether both of the two quinol-binding sites are functionally relevant |CITS: [11850430]|. The amino acid
residues involved in the interaction with quinones have been identified |CITS: [8419359]|.
Fumarate reductase is made under anaerobic conditions with glucose or glycerol
as carbon source. The covalent attachment of FAD to the enzyme (A subunit apoprotein) is
stimulated by citrate, isocitrate, succinate and fumarate, acting possibly
as allosteric effectors. The enzyme has been crystallized |CITS: [11850430]|. Fumarate reductase is
closely related to succinate dehydrogenase and is regulated by the products of fnr and ntr genes.
|CITS: [89276374] [99301923]|)""",]},
'B4152' : {'ecocyc-rxns': {"""R601-RXN""": """fumarate + menaquinol + 2 H+ -> succinate + menaquinone-8""",},'ucsd-rxns' : ['FRD2','FRD3',], 'protein-comments' : ["""(This is one of two membrane proteins in the four subunit enzyme.
The FrdC and FrdD subunits bind the two menaquinone molecules
involved in the electron transfer reactions of the enzyme. |CITS: [99301923]|
Despite similar function, hydrophobicity, and protein size, the FrdC and FrdD
subunits of fumarate reductase do not share significant sequence identity
with the corresponding membrane-binding subunits of succinate dehydrogenase, SdhC and SdhD |CITS: [6383359]|.)""","""(The reaction catalysed by fumarate reductase allows fumarate to serve as a terminal electron acceptor
when E. coli is growing under anaerobic conditions. The electron donor for
this reaction is reduced menaquinone. It contributes to generating a proton gradient in a scalar mechanism by
utilitzing two protons from the cytoplasm.
Fumarate reductase is composed of 4 subunits and two domains. The catalytic domain consists of two subunits: one
with a covalently-bound flavin cofactor and the fumarate binding site; the other contains 3 iron-sulfur clusters. This
catalytic domain is attached to the cytoplasmic side of the cytoplasmic membrane by the anchor domain, which
consists of two subunits that interact with quinone and contain heme b556 |CITS: [11803023]|. The enzyme has two
quinol-binding sites, Qp and Qd, indicating their being proximal or distal to the site of fumarate reduction. It is not
clear whether both of the two quinol-binding sites are functionally relevant |CITS: [11850430]|. The amino acid
residues involved in the interaction with quinones have been identified |CITS: [8419359]|.
Fumarate reductase is made under anaerobic conditions with glucose or glycerol
as carbon source. The covalent attachment of FAD to the enzyme (A subunit apoprotein) is
stimulated by citrate, isocitrate, succinate and fumarate, acting possibly
as allosteric effectors. The enzyme has been crystallized |CITS: [11850430]|. Fumarate reductase is
closely related to succinate dehydrogenase and is regulated by the products of fnr and ntr genes.
|CITS: [89276374] [99301923]|)""",]},
'B4014' : {'ecocyc-rxns': {"""MALSYN-RXN""": """acetyl-CoA + H2O + glyoxylate = malate + coenzyme A""",},'ucsd-rxns' : ['MALS',], 'protein-comments' : ["""NIL""",]},
'B3803' : {'ecocyc-rxns': {},'ucsd-rxns' : ['UPP3MT',], 'protein-comments' : ["""(The HemX protein was suggested to be a uroporphyrinogen III methylase |CITS: [3062586]|. However, the function
of the protein has not been experimentally determined.
HemX exists as a homooligomer in the inner membrane |CITS: [16079137]|.)""",]},
'B1779' : {'ecocyc-rxns': {"""GAPOXNPHOSPHN-RXN""": """D-glyceraldehyde-3-phosphate + phosphate + NAD+ = 1,3-diphosphateglycerate + NADH""",},'ucsd-rxns' : ['GAPD',], 'protein-comments' : ["""(E. coli is unusual in having two glyceraldehyde-3-phosphate dehydrogenases. The protein GAPDH-A has a
sequence that is more similar to eukaryotic sequences than it is to the thermophilic bacterial
enzymes and prokaryotic enzymes in general |CITS:[91087241][85257641]|. GapA is
required for glycolysis, while Epd (GapB) is not |CITS: [9260967]|. GapA and Epd may be involved in production of
pyridoxal 5'-phosphate (PLP) |CITS: [9696782]|.
A gapA mutant exhibits a growth defect and also exhibits increased aggregation and lysis phenotypes that are
rescued by high-salt media |CITS: [9260967]|.
Regulation has been described |CITS: [12672900]|. The regulation of the fkpA, gapA, and hslT
genes is affected by evolution under conditions of chronic heat stress |CITS: [12672900]|.)""","""NIL""",]},
'B3806' : {'ecocyc-rxns': {"""ADENYLATECYC-RXN""": """ATP = cyclic-AMP + diphosphate""",},'ucsd-rxns' : ['ADNCYC',], 'protein-comments' : ["""NIL""",]},
'B2296' : {'ecocyc-rxns': {"""PROPKIN-RXN""": """ATP + propionate = ADP + propionyl-P""","""ACETATEKIN-RXN""": """acetate + ATP = acetylphosphate + ADP""",},'ucsd-rxns' : ['ACKr',], 'protein-comments' : ["""(Regulation has been described |CITS: [11350954]|. Transcription is induced by the CreBC two-component system by minimal media growth conditions |CITS: [11350954]|.
)""",]},
'B3804' : {'ecocyc-rxns': {"""UROGENIIISYN-RXN""": """hydroxymethylbilane = H2O + uroporphyrinogen-III""",},'ucsd-rxns' : ['UPP3S',], 'protein-comments' : ["""NIL""",]},
'B3805' : {'ecocyc-rxns': {"""OHMETHYLBILANESYN-RXN""": """H2O + 4 porphobilinogen = 4 ammonia + hydroxymethylbilane""",},'ucsd-rxns' : ['HMBS',], 'protein-comments' : ["""NIL""",]},
'B2297' : {'ecocyc-rxns': {"""PHOSACETYLTRANS-RXN""": """phosphate + acetyl-CoA = acetylphosphate + coenzyme A""","""PTAALT-RXN""": """propionyl-CoA + phosphate = propionyl-P + coenzyme A""",},'ucsd-rxns' : ['PTAr','PTA2',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B1855' : {'ecocyc-rxns': {"""MYRPALMTRAN-RXN""": """KDO2-(palmitoleoyl)-lipid IVA + myristoyl-ACP = KDO2-lipid A, cold adapted + acyl carrier protein""","""MYRISTOYLACYLTRAN-RXN""": """KDO2-(lauroyl)-lipid IVA + myristoyl-ACP = KDO2-lipid A + acyl carrier protein""",},'ucsd-rxns' : ['EDTXS4','EDTXS2',], 'protein-comments' : ["""NIL""",]},
'B1854' : {'ecocyc-rxns': {"""PEPDEPHOS-RXN""": """pyruvate + ATP = ADP + phosphoenolpyruvate""",},'ucsd-rxns' : ['PYK',], 'protein-comments' : ["""(There are 2 genes, pykA and pykF, for 2 isozymes)""","""NIL""",]},
'B2539' : {'ecocyc-rxns': {"""HCAMULTI-RXN""": """3-phenylpropionate + NADH + O2 + H+ = cis-3-(carboxyethyl)-3,5-cyclohexadiene-1,2-diol + NAD+""",},'ucsd-rxns' : ['PPPNDO','CINNDO',], 'protein-comments' : ["""NIL""","""NIL""","""(The 3-phenylpropionate dioxygenase component is the product of the hcaA1 and
hcaA2 genes. HcaC codes for a ferredoxin and hcaD encodes a ferredoxin NAD+
reductase. |CITS: [98269008]|)""",]},
'B2291' : {'ecocyc-rxns': {"""RXN0-3741""": """a deoxyribonucleoside 5'-monophosphate + H2O -> a deoxyribonucleoside + phosphate""",},'ucsd-rxns' : ['NTD12','NTD8','NTD6','NTD5','NTD3','NTD1',], 'protein-comments' : ["""(YfbR has phosphatase activity with deoxyribonucleoside 5'-monophosphates and does not hydrolyze ribonucleotides
or deoxyribonucloside 3'-monophosphates |CITS: [15489502]|. Nucleotidase activity of YfbR was discovered in a
high-throughput screen of purified proteins |CITS: [15808744]|.
)""",]},
'B0915' : {'ecocyc-rxns': {"""TETRAACYLDISACC4KIN-RXN""": """lipid A disaccharide + ATP = lipid IVA + ADP""",},'ucsd-rxns' : ['TDSK',], 'protein-comments' : ["""NIL""",]},
'B0446' : {'ecocyc-rxns': {"""RXN0-3543""": """4-amino-2-methyl-5-hydroxymethylpyrimidine pyrophosphate -> 4-amino-2-methyl-5-hydroxymethylpyrimidine phosphate + phosphate""",},'ucsd-rxns' : ['2MAHMP',], 'protein-comments' : ["""(Overexpression of Cof from a multicopy plasmid leads to resistance to the HMP
(4-amino-2-methyl-5-hydroxymethylpyrimidine) analog bacimethrin (MeO-HMP). The enzyme is involved in the
hydrolysis of HMP-PP, an intermediate in thiamin biosynthesis |CITS: [15292217]|.)""",]},
'B0910' : {'ecocyc-rxns': {"""CMPKI-RXN""": """CMP + ATP = CDP + ADP""",},'ucsd-rxns' : ['UMPK','CYTK1','CYTK2',], 'protein-comments' : ["""NIL""",]},
'B0459' : {'ecocyc-rxns': {"""MALTACETYLTRAN-RXN""": """maltose + acetyl-CoA = acetylmaltose + coenzyme A""",},'ucsd-rxns' : ['GLCATr','MALTATr',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B4084' : {'ecocyc-rxns': {"""ALLOSE-KINASE-RXN""": """D-allose + ATP -> D-allose-6-phosphate + ADP""",},'ucsd-rxns' : ['ALLK',], 'protein-comments' : ["""(The alsK gene encodes a putative D-allose kinase. AlsK is not required for utilization of a D-allose carbon
source |CITS: [9401019][10559180]|, and expression of alsK appears to be unaffected by allose
|CITS: [10559180]|.
Overexpression of alsK rescues the auxotrophic phenotype of a glucokinase mutant; the enzyme can
phosphorylate D-glucose with a kcat/Km value that is 100000-fold lower than its
kcat/Km for D-allose |CITS: [16086580]|.
Als: "D-allose" |CITS: [9401019]|.)""",]},
'B0918' : {'ecocyc-rxns': {"""CPM-KDOSYNTH-RXN""": """3-deoxy-D-manno-octulosonate + CTP = CMP-3-deoxy-D-manno-octulosonate + diphosphate""",},'ucsd-rxns' : ['KDOCT2',], 'protein-comments' : ["""NIL""",]},
'B2688' : {'ecocyc-rxns': {"""GLUTCYSLIG-RXN""": """L-cysteine + L-glutamate + ATP = L-γ-glutamylcysteine + phosphate + ADP""",},'ucsd-rxns' : ['GLUCYS',], 'protein-comments' : ["""NIL""",]},
'B0485' : {'ecocyc-rxns': {"""GLUTAMIN-RXN""": """L-glutamine + H2O = L-glutamate + ammonia""",},'ucsd-rxns' : ['GLUN',], 'protein-comments' : ["""(Based on sequence similarity, YbaS is predicted to be a glutaminase |CITS: [12952533]|.
)""",]},
'B3449' : {'ecocyc-rxns': {"""GLYCPDIESTER-RXN""": """H2O + a glycerophosphodiester -> an alcohol + sn-glycerol-3-phosphate""",},'ucsd-rxns' : ['GPDDA2','GPDDA4','GPDDA5','GPDDA1','GPDDA3',], 'protein-comments' : ["""NIL""",]},
'B3367' : {'ecocyc-rxns': {"""TRANS-RXN-137""": """H+[periplasmic space] + nitrite[periplasmic space] =H+[cytosol] + nitrite[cytosol] """,},'ucsd-rxns' : ['NO2t2rpp',], 'protein-comments' : ["""(NirC is a putative nitrite transporter which is a member of the FNT family
of formate and nitrite transporters |CITS: [99184734]|. The nirC
gene is located in the nir operon which codes for a NADH-dependent
nitrite reductase |CITS: [90345936]|. NirC may function to import nitrite
as a substrate for this enzyme complex. The nir operon is anaerobically
expressed and is repressed by oxygen |CITS: [93062014]|.)""",]},
'B3366' : {'ecocyc-rxns': {"""NITRITREDUCT-RXN""": """3 NAD(P)+ + NH(4)OH + H2O -> 3 NAD(P)H + nitrite""",},'ucsd-rxns' : ['NTRIR2x',], 'protein-comments' : ["""(The nirD gene encodes the small subunit of the nitrite reductase.
|CITS: [90345936] [93062014]|)""","""NIL""",]},
'B3365' : {'ecocyc-rxns': {"""NITRITREDUCT-RXN""": """3 NAD(P)+ + NH(4)OH + H2O -> 3 NAD(P)H + nitrite""",},'ucsd-rxns' : ['NTRIR2x',], 'protein-comments' : ["""NIL""","""NIL""","""NIL""",]},
'B3368' : {'ecocyc-rxns': {"""UROPORIIIMETHYLTRANSA-RXN""": """2 S-adenosyl-L-methionine + uroporphyrinogen-III = 2 S-adenosyl-L-homocysteine + precorrin-2""","""DIMETHUROPORDEHYDROG-RXN""": """precorrin-2 + NAD+ = sirohydrochlorin + NADH""","""SIROHEME-FERROCHELAT-RXN""": """sirohydrochlorin + Fe2+ = 2 H+ + siroheme""",},'ucsd-rxns' : ['UPP3MT','SHCHF','SHCHD2',], 'protein-comments' : ["""(The E. coli cysG gene encodes a trifunctional enzyme responsible for the complete transformation of
uroporphyrinogen III into siroheme |CITS: [7945210][8243665]|. The first reaction consists of two SAM-dependent
methylations of uroporphyrinogen III to yield dihydrosirohydrochlorin (precorrin-2), a key intermediate
|CITS: [2407234]|. The second reaction consists of a pyridine dinucleotide-dependent dehydrogenation converting
dihydrosirohydrochlorin into sirohydrochlorin |CITS: [2407558]|. The third and final reaction is the ferrochelation of
sirohydrochlorin, which yields siroheme |CITS: [8243665]|.
The enzyme consists of two separable domains. The C-terminal domain has uroporphyrinogen III methylase activity,
but not dehydrogenase or ferrochelatase activity |CITS: [7945210]|. Certain mutants in conserved amino acid
residues in the C-terminal domain affect SAM binding |CITS: [9461500]|. SAM may be covalently linked to CysG;
a multistep transmethylation mechanism has been proposed |CITS: [8573073]|. Deletion of the N-terminal NAD
binding site and mutation of certain amino acid residues affect the dehydrogenase and ferrochelatase activities, but
not the methylase activity |CITS: [9461500]|. The two domains can function independently |CITS: [9461500]|.
)""","""NIL""",]},
'B3447' : {'ecocyc-rxns': {"""GAMMA-GLUTAMYLTRANSFERASE-RXN""": """an amino acid + (5-L-glutamyl)-L-peptide = (5-L-glutamyl)-L-amino acid + a peptide""",},'ucsd-rxns' : ['GTHRDHpp',], 'protein-comments' : ["""(The ggt gene encodes gamma-glutamyltranspeptidase |CITS: [2892489]|.
Enzyme activity has been characterized |CITS: [2877974], [1981661], [8720138], [10869181], [12418234]|. Residue T391 is the catalytic amino acid |CITS: [10869181]|.
Ggt is periplasmic |CITS: [2877974], [2877975], [2892489]|. Ggt is subject to post-translational processing/cleavage |CITS: [2570061], [12207027]| into two subunits of 39.207 and 20.015 kDa |CITS: [8720138]|. The post-translational processing is required for wild-type enzyme activity |CITS: [1360205], [8537328], [8720138]|.
A crystal structure of the enzyme is presented at 3 A resolution |CITS: [8864839]|.
A ggt mutant exhibits a defect in gamma-glutamyltranspeptidase activity |CITS: [2887543]|. A mutant exhibits increased glutathione efflux, compared to wild type |CITS: [2887543]|, and increased resistance to osmotic stress |CITS: [11703177]|. A mutant does not exhibit apparent auxotrophies or cold sensitivity |CITS: [2887543]|.
Regulation has been described |CITS: [2877974], [2877975], [9028034]|.)""",]},
'B0040' : {'ecocyc-rxns': {"""TRANS-RXN-100""": """γ-butyrobetaine[cytosol] + L-carnitine[periplasmic space] =γ-butyrobetaine[periplasmic space] + L-carnitine[cytosol] """,},'ucsd-rxns' : ['CRNt7pp','CRNt8pp',], 'protein-comments' : ["""(CaiT is a carnitine transporter belonging to the Betaine, Carnitine, Chromium Transport (BCCT)
Family |CITS: [98241519]|. It operates as an antiporter, exchanging L- or D- carnitine
or the carnitine utilization products crotonobetaine or γ-butyrobetaine for exogenous
L-carnitine |CITS: [12163501]|.
E. coli uses two operons, the caiTABCDE operon and the fixABCX operon,
for anaerobic carnitine metabolism. Transcriptional studies of lacZ fusion showed that both
operons are coexpressed during anaerobic growth in the presence of carnitine, they respond to common
environmental stimuli, and are modulated positively by the same general regulators, CRP and FNR, and
negatively by H-NS |CITS: [98241519]|.)""",]},
'B0312' : {'ecocyc-rxns': {"""BADH-RXN""": """betaine aldehyde + NAD+ + H2O -> glycine betaine + NADH""",},'ucsd-rxns' : ['BETALDHx','BETALDHy',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B1858' : {'ecocyc-rxns': {"""ABC-63-RXN""": """Zn2+[periplasmic space] + H2O + ATP =Zn2+[cytosol] + ADP + phosphate """,},'ucsd-rxns' : ['ZNabcpp',], 'protein-comments' : ["""(ATP-binding component of ABC transporter)""","""(ZnuABC is a high-affinity zinc uptake system that is a member
of the ATP Binding Cassette (ABC) Superfamily |CITS: [96381453]|.
znuA encodes the periplasmic zinc-binding component
of the transporter, while znuB encodes the membrane
component, and znuC encodes the ATPase subunit.
Complementation analysis of znu mutants showed that
transport of zinc (II) ion was restored in the presence of
znuABC cloned on a low-copy-number vector |CITS: [98343803]|.
The three components of ZnuABC also show high nucleotide
sequence similarity to the corresponding components of the
AdcABC zinc transporter of S. pneumoniae as well as
subunits of other ABC metal ion transporters. The high-affinity
transport of zinc ion by ZnuABC is inhibited by arsenate,
suggesting that ZnuABC-mediated transport is energized by
ATP hydrolysis |CITS: [98343803]|. Analysis of LacZ fusions indicated that
expression of znuA and znuB was regulated by
the protein Zur, which has amino acid sequence similarity to
the iron regulator Fur |CITS: [98343803]|. znuA and znuBC
are transcribed divergently |CITS: [98343803]|.)""",]},
'B0336' : {'ecocyc-rxns': {"""TRANS-RXN-116""": """H+[periplasmic space] + cytosine[periplasmic space] =H+[cytosol] + cytosine[cytosol] """,},'ucsd-rxns' : ['CSNt2pp',], 'protein-comments' : ["""(CodB is a cytosine transporter which probably functions as a
cytosine/proton symporter. Whole cell transport assays have shown
that the cloned codB gene can complement mutants with
cytosine transport defects which had mapped to a locus near the
codA gene |CITS: [92349961]|. The codB gene is
located in a cytosine-inducible operon with the codA gene
encoding cytosine deaminase |CITS: [96102281] [92349961]|.
Consistent with this, CodB belongs to the NCS1 family of purine
and pyrimidine transporters |CITS: [99184734]|. Analysis of alkaline
phosphatase and β-galactosidase fusions has suggested that CodB
consists of twelve TMS |CITS: [96081504]|.
Imported cytosine can be metabolised via hydrolytic deamination by
CodA to yield uracil and ammonia.)""",]},
'B0099' : {'ecocyc-rxns': {"""RXN0-385""": """dGTP + H2O = dGMP + diphosphate""",},'ucsd-rxns' : ['NTPP2','NTPP1','DNTPPA',], 'protein-comments' : ["""(dGTP pyrophosphohydrolase (MutT) can catalyze the hydrolysis of
all eight canonical nucleotides, but it shows a marked
preference for dGTP. It requires two divalent
cations for activity. MutT also prevents A:T to C:G transversions
during DNA replication |CITS: [91225007] [94124521] [20411488]
[88243762]|.)""",]},
'B0908' : {'ecocyc-rxns': {"""2.5.1.19-RXN""": """shikimate-3-phosphate + phosphoenolpyruvate = 5-enolpyruvyl-shikimate-3-phosphate + phosphate""",},'ucsd-rxns' : ['PSCVT',], 'protein-comments' : ["""(3-D structure has been studied |CITS:[PNAS88-5046-91]|)""",]},
'B3930' : {'ecocyc-rxns': {"""DMK-RXN""": """octaprenyl diphosphate + 1,4-dihydroxy-2-naphthoate = demethylmenaquinone-8 + diphosphate + CO2""",},'ucsd-rxns' : ['DHNAOT4',], 'protein-comments' : ["""(Membrane topology predictions using experimentally determined C terminus
locations indicate that MenA has 9 transmembrane helices and the C-terminus is
located in the periplasm |CITS:[15044727]|.)""",]},
'B0314' : {'ecocyc-rxns': {"""TRANS-RXN-99""": """H+[periplasmic space] + choline[periplasmic space] =H+[cytosol] + choline[cytosol] """,},'ucsd-rxns' : ['CHLt2pp',], 'protein-comments' : ["""(BetT is a proton-motive-force-driven choline transporter that belongs to the Betaine
Carnitine Choline Transport (BCCT) family of proteins. Deletion mutants of betT
displayed essentially no choline uptake activity, but could be complemented with a
betT-encoding plasmid, restoring rapid choline uptake |CITS: [92065800]|. Choline uptake
activity was completely inhibited by the protonophore carbonylcyanide
p-trifluoromethoxyphenyl hydrazone, suggesting that choline transport by BetT is
driven by the proton-motive force |CITS: [92065800]|. Choline is used to synthesize glycine
betaine, which is used by E. coli to overcome growth inhibition caused by
osmotic stress |CITS: [89124888]|. The betTIAB genes are expressed only under aerobic
conditions, and are induced by osmotic stress |CITS: [92065800]|. Analysis of betT-lacZ
fusions showed that betT transcription increased 7-10 fold in response to
increases in medium osmolarity. The presence of choline further increases this response
|CITS: [89033906]|.)""",]},
'B0238' : {'ecocyc-rxns': {"""XANPRIBOSYLTRAN-RXN""": """xanthosine-5-phosphate + diphosphate = 5-phosphoribosyl 1-pyrophosphate + xanthine""","""GUANPRIBOSYLTRAN-RXN""": """guanine + 5-phosphoribosyl 1-pyrophosphate -> diphosphate + GMP""","""HYPXPRIBOSYLTRAN-RXN""": """hypoxanthine + 5-phosphoribosyl 1-pyrophosphate = diphosphate + inosine-5'-phosphate""",},'ucsd-rxns' : ['GUAPRT','XPPT','HXPRT',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B2747' : {'ecocyc-rxns': {"""2.7.7.60-RXN""": """2-C-methyl-D-erythritol-4-phosphate + CTP = 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol + diphosphate""",},'ucsd-rxns' : ['MEPCT',], 'protein-comments' : ["""(IspD is an essential protein that acts in the mevalonate-independent pathway of isopentenyl diphosphate
biosynthesis |CITS: [Kuzuyama00][11115399]|. The homodimeric |CITS: [10518523][11427897]| enzyme catalyzes
production of 4-diphosphocytidyl-2-C-methylerythritol from 2-C-methylerythritol 4-phosphate and CTP
|CITS: [10518523]|.
A mutant does not grow in complex media |CITS: [11361082]|. EMS-induced point mutants identifying residues
essential for catalytic activity have been isolated |CITS: [12859972]|. Site-directed mutagenesis of IspD and kinetic
analysis of point mutants has been performed |CITS: [15379557]|.
Crystal structures of the enzyme, enzyme-CTP-Mg2+ complex, and enzyme-Mg2+
complex are presented, and these structures are informative with respect to the mechanism of catalysis
|CITS: [11427897][12595740][16021622]|.
Related proteins are widespread among bacterial pathogens, indicating potential utility as an antibiotic drug target
|CITS: [11361082]|. Some organisms produce bifunctional proteins with domains with similarity to the IspD and IspF
proteins, which are separate polypeptides in E. coli |CITS: [10518523]|.
)""","""NIL""",]},
'B0805' : {'ecocyc-rxns': {"""RXN0-1721""": """ferric dihydroxybenzoylserine[extracellular space] =ferric dihydroxybenzoylserine[periplasmic space] """,},'ucsd-rxns' : ['FE3DHBZStonex',], 'protein-comments' : ["""(B0805 is a putative outer membrane porin. Sequence similarity suggests that it is a member of the Outer
Membrane Receptor (OMR) family. It is believed to facilitate the uptake of the siderophore dihydroxybenzoylserine
|CITS: [2139424]| . It also serves as the receptor for microcins E492, M, and H47 |CITS: [12949180]| . Beta lactams can also
enter via Fiu |CITS: [2407721]| .)""",]},
'B3939' : {'ecocyc-rxns': {"""METBALT-RXN""": """2-oxobutanoate + succinate + ammonia = O-succinyl-L-homoserine + H2O""","""O-SUCCHOMOSERLYASE-RXN""": """L-cysteine + O-succinyl-L-homoserine = succinate + cystathionine""",},'ucsd-rxns' : ['SHSL1',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B4230' : {'ecocyc-rxns': {},'ucsd-rxns' : ['RIBabcpp',], 'protein-comments' : ["""(membrane component of ABC transporter)""","""(YtfR, YtfS, YjfF, YtfT, and YtfQ are uncharacterized members
of the ABC superfamily of transporters |CITS: [99091701]|.
YtfR and YtfS are the putative ATP-binding components.
YjfF and YtfT are the putative membrane components.
YtfQ is the putative binding protein. Based on sequence
similarity they probably function together as an ATP-dependant
sugar transporter. The genes ytfR, ytfS, yjfF,
ytfT, and ytfQ probably constitute a single operon.)""",]},
'B2019' : {'ecocyc-rxns': {"""ATPPHOSPHORIBOSYLTRANS-RXN""": """phosphoribosyl-ATP + diphosphate = ATP + 5-phosphoribosyl 1-pyrophosphate""",},'ucsd-rxns' : ['ATPPRT',], 'protein-comments' : ["""NIL""","""(Each subunit of the hisG protein hexamer contains one
allosteric site for histidine binding, which does not seem to overlap
the subunit's active site.)""",]},
'B3725' : {'ecocyc-rxns': {"""ABC-27-RXN""": """ATP + phosphate[periplasmic space] + H2O =ADP + phosphate[cytosol] + phosphate[cytosol] """,},'ucsd-rxns' : ['PIuabcpp',], 'protein-comments' : ["""NIL""","""(PstABCS is an ATP-dependent phosphate uptake system that is a member of the ATP-Binding Cassette
(ABC) Superfamily of transporters |CITS: [96381453]|. PstABCS is responsible for inorganic phosphate (Pi)
uptake under Pi starvation conditions. Inorganic phosphate is an essential component in cellular function
since phosphorylation of nucleic acids, lipids, sugars, and proteins are important for gene regulation and
signaling |CITS: [91054431]|. Based on sequence similarity, PstA and PstC are the membrane components
of the ABC transporter, while PstS is the periplasmic phosphate binding protein |CITS: [91054431]|, and
PstB is the ATP-binding component of the ABC transporter |CITS: [91054431]|. Whole cell transport
assay indicates that the Pst system has a Km of 0.20 μM |CITS: [82030542]|. Transcription
of the Pst system is induced by Pi starvation, as opposed to the Pit phosphate transport system that is
expressed regardless of Pi level |CITS: [91054431]|.)""",]},
'B1651' : {'ecocyc-rxns': {"""GLYOXI-RXN""": """S-lactoyl-glutathione = methylglyoxal + glutathione""",},'ucsd-rxns' : ['LGTHL',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B2762' : {'ecocyc-rxns': {"""PAPSREDGLUT-RXN""": """a reduced glutaredoxin 1 + 3'-phosphoadenylyl-sulfate = an oxidized glutaredoxin 1 + H+ + sulfite + adenosine-3',5'-bisphosphate""","""1.8.4.8-RXN""": """adenosine-3',5'-bisphosphate + sulfite + a thioredoxin disulfide = 3'-phosphoadenylyl-sulfate + a reduced thioredoxin""",},'ucsd-rxns' : ['PAPSR','PAPSR','PAPSR2','PAPSR2','PAPSR2','PAPSR2',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B2763' : {'ecocyc-rxns': {"""FMNREDUCT-RXN""": """FMNH2 + NAD(P)+ = FMN + NAD(P)H + H+""","""SULFITE-REDUCT-RXN""": """3 H2O + 3 NADP+ + hydrogen sulfide = 3 NADPH + sulfite""",},'ucsd-rxns' : ['FLVR','FMNRx2','SULR','FADRx2',], 'protein-comments' : ["""(Contains one siroheme and one 4-Fe-4S iron-sulfur center per
chain. The heme is an octacarboxylic iron-tetrahydroporphyrin.
|CITS: [74127023] [74127024] [74127025]|)""","""NIL""",]},
'B2764' : {'ecocyc-rxns': {"""FMNREDUCT-RXN""": """FMNH2 + NAD(P)+ = FMN + NAD(P)H + H+""","""SULFITE-REDUCT-RXN""": """3 H2O + 3 NADP+ + hydrogen sulfide = 3 NADPH + sulfite""",},'ucsd-rxns' : ['FLVR','FMNRx2','SULR','FADRx2',], 'protein-comments' : ["""(The subunit binds one FMN and one FAD per chain.)""","""NIL""",]},
'B1654' : {'ecocyc-rxns': {},'ucsd-rxns' : ['RNDR2b','RNDR3b','RNDR1b','GRXR','PAPSR2','RNDR4b',], 'protein-comments' : ["""(Grx4 belongs to the family of monothiol glutaredoxins. Oxidized Grx4 can be reduced by the thioredoxin system or
glutaredoxin 1. Grx4 is not active in the standard glutaredoxin assay |CITS: [15833738]|.
Grx4 is an abundant protein that is upregulated during stationary phase; the increased expression is dependent on
ppGpp |CITS: [15833738]|.
A grxD null mutant could not be obtained |CITS: [15833738]|. grxD has previously been reported to be
essential for aerobic growth in rich media |CITS: [13129938]|.
A solution structure of the reduced form of Grx4 has been determined |CITS: [15840565]|)""",]},
'B1656' : {'ecocyc-rxns': {"""SUPEROX-DISMUT-RXN""": """2 H+ + 2 O2- = H2O2 + O2""",},'ucsd-rxns' : ['SPODM',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B1714' : {'ecocyc-rxns': {"""PHENYLALANINE--TRNA-LIGASE-RXN""": """tRNAphe + L-phenylalanine + ATP -> L-phenylalanyl-tRNAphe + diphosphate + AMP""",},'ucsd-rxns' : ['PHETRS',], 'protein-comments' : ["""(The α subunit of PheRS contains the phenylalanine binding site |CITS: [1104359][7043240]| within the
conserved motif 2 and motif 3 of the protein |CITS: [1942071][1959653]|. It interacts with the 3'-adenosine of
tRNAPhe |CITS: [2823880]|.
Isolated α subunits exist primarily as dimers |CITS: [1915899]|.
)""","""(Phenylalanyl-tRNA synthetase (PheRS) is a member of the family of aminoacyl-tRNA synthetases, which interpret the
genetic code by covalently linking amino acids to their specific tRNA molecules. The reaction is driven by ATP
hydrolysis. PheRS belongs to the Class II aminoacyl tRNA synthetases, which share three regions of homology
|CITS: [2203971][1852601]|.
PheRS is a tetramer consisting of two α and two β subunits. Both subunits are required for catalytic
activity |CITS: [4603142][6360212]|. Two molecules of tRNAPhe bind to one PheRS complex
|CITS: [6337625]|, and both binding sites are active sites |CITS: [170267][793866]|. Binding is not dependent on
Mg2+ |CITS: [1100384]|.
The reaction mechanism of PheRS includes the formation of an aminoacyl adenylate intermediate, which then serves
as the animo acid donor in the aminoacyl-tRNA synthetase reaction |CITS: [320199]|. Binding of
tRNAPhe to PheRS induces a conformational change in the tRNA |CITS: [383142]| as well as in PheRS
|CITS: [7011376]|. Aminoacylation is limited by the kinetics of a conformational change of the
PheRS-Phe-tRNAPhe complex |CITS: [7046786][7046787]|. PheRS can aminoacylate a synthetic
substrate with a deoxyribose backbone (tDNA) |CITS: [2455342]|.
Specificity determinants within tRNAPhe that are important for recognition by PheRS and for attenuation
have been identified
|CITS: [776674][365576][3894009][3311746][2643111][2231729][2023934][1420156][7687542][8082771][8089840]|.
A synthetically constructed tRNAPhe(AAA) is not a good substrate for PheRS |CITS: [1370814]|.
Specificity determinants and residues within PheRS that are important for catalytic activity have been investigated
|CITS: [2823880]|. The Ala294 residue of the α subunit is involved in binding phenylalanine and influences
amino acid specificity by determining of the size of the binding pocket |CITS: [8003476]|.
A proofreading mechanism hydrolyzes a PheRS-tyrosine adenylate complex and Tyr-tRNAPhe
|CITS: [8003476][15526031]|. The editing site localizes to the B3/B4 domain of the β subunit |CITS: [15526031]|.
PheRS of E. coli B contains a proofreading activity which deacylates misacylated Ile-tRNAPhe
|CITS: [4558664][6222761]|.
Expression of pheST is derepressed by an attenuation mechanism when the level of aminoacylated
tRNAPhe is low |CITS: [6317865][6317866][6426518][3126825]| and by high levels of PheRS
|CITS: [3158742]|.
Review: |CITS: [10966471]|
)""",]},
'B0158' : {'ecocyc-rxns': {"""RXN0-2121""": """cob(I)alamin[extracellular space] =cob(I)alamin[cytosol] ""","""ABC-5-RXN""": """ATP + cob(I)alamin[periplasmic space] + H2O =ADP + phosphate + cob(I)alamin[cytosol] """,},'ucsd-rxns' : ['CBL1abcpp','CBIuabcpp','ADOCBLabcpp',], 'protein-comments' : ["""(BtuF is the periplasmic vitamin B12 binding protein that delivers cobalamin to the ABC transporter BtuCD.
Two surface glutamates from BtuF may interact with arginine residues on the periplasmic surface of BtuCD. |CITS: [12475936]|
The crystal structures of Escherichia coli BtuF have been determined in the apo state at 3.0 A resolution and with vitamin B12
bound at 2.0 A resolution |CITS:[12468528]|.)""","""(BtuCDF is a vitamin B12 transport system that is a member of the ATP-Binding Cassette
(ABC) Superfamily of transporters |CITS: [96381453]|. Based on sequence similarity, BtuD is the ATP-binding
component, BtuC is the integral membrane component, and BtuF is the periplasmic substrate-binding
component of the ABC transporter |CITS: [12475936]| . Transposon insertions in the btuCand regions
conferred a deficiency in vitamin B12 utilization and transport |CITS: [86304183]|. However, there are
indications that BtuE (residing within the operon) is not required for transport. Transposon insertions in btuE were not
complemented by plasmids carrying btuE alone, whereas insertions in btuC and
btuD were effectively complemented by plasmids carrying the corresponding functional gene |CITS: [86304183] [89364713]|.
btuE mutants were also shown to have little effect on vitamin B12 binding and
transport and did not affect the utilization of vitamin B12 or other cobalamins for
methionine biosynthesis |CITS: [89364713]|.
The crystal structure of the Escherichia coli BtuCD protein has been resolved to 3.2 angstrom resolution |CITS:[12004122]|.)""","""NIL""",]},
'B3503' : {'ecocyc-rxns': {"""RXN-982""": """arsenate + a reduced glutaredoxin 2 = arsenite + an oxidized glutaredoxin 2""",},'ucsd-rxns' : ['ASR',], 'protein-comments' : ["""(Based on sequence similarity with
the R773-plasmid encoded arsenite resistance operon, ArsB is a transporter and ArsC is an arsenate reductase |CITS: [95164532]|.
The chromosomally encoded operon, however is lacking arsA, which encodes a putative ATP-binding protein. Deletion mutants of the chromosomal arsRBC
operon exhibit 10-20 times more sensitivity to arsenite and 5-10 times more selectivity to antimonite and arsenate than the parent strain. Expression of the
cloned arsRBC conferred increased arsenite resistance compared with wild-type |CITS: [95164532]|
)""",]},
'B3502' : {'ecocyc-rxns': {"""TRANS-RXN-7""": """ATP + arsenate[cytosol] + H2O =ADP + phosphate + arsenate[periplasmic space] """,},'ucsd-rxns' : ['ASO3t8pp',], 'protein-comments' : ["""(Based on sequence similarity with
the R773-plasmid encoded arsenite resistance operon, ArsB is a transporter and ArsC is an arsenate reductase |CITS: [95164532]|.
The chromosomally encoded operon, however, is lacking arsA, which encodes a putative ATP-binding protein. Deletion mutants of the chromosomal arsRBC
operon exhibit 10-20 times more sensitivity to arsenite and 5-10 times more selectivity to antimonite and arsenate than the parent strain. Expression of the
cloned arsRBC conferred increased arsenite resistance compared with wild-type |CITS: [95164532]|
)""","""NIL""",]},
'B3500' : {'ecocyc-rxns': {"""GLUTATHIONE-REDUCT-NADPH-RXN""": """2 glutathione + NADP+ -> glutathione disulfide + NADPH + H+""",},'ucsd-rxns' : ['GTHOr',], 'protein-comments' : ["""(Passes electrons between NADPH and glutathione.)""","""NIL""",]},
'B1096' : {'ecocyc-rxns': {"""PABSYNMULTI-RXN""": """L-glutamine + chorismate = p-aminobenzoate + L-glutamate + pyruvate""","""ADCLY-RXN""": """4-amino-4-deoxychorismate = p-aminobenzoate + pyruvate""",},'ucsd-rxns' : ['ADCL',], 'protein-comments' : ["""NIL""","""NIL""","""NIL""",]},
'B1095' : {'ecocyc-rxns': {"""3-OXOACYL-ACP-SYNTH-BASE-RXN""": """acetyl-ACP + malonyl-ACP -> an acyl carrier protein + an acetoacetyl-ACP + CO2""","""3-OXOACYL-ACP-SYNTH-RXN""": """an acyl-ACP + malonyl-ACP -> acyl carrier protein + a β-ketoacyl-ACP + CO2""",},'ucsd-rxns' : ['KAS14','3OAS100','3OAS120','3OAS80','3OAS180','3OAS181','3OAS60','3OAS140','3OAS160',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B1094' : {'ecocyc-rxns': {},'ucsd-rxns' : ['UAGAAT','AACPS8','AACPS9','AACPS4','AACPS5','AACPS6','AACPS7','AACPS1','AACPS2','AACPS3','MCOATA','ACOATA',], 'protein-comments' : ["""(Acyl carrier protein (ACP) plays an important role in fatty
acid biosynthesis. It carries fatty acid chains via a thioester
linkage to a phosphopantetheine prosthetic group as the chains are
elongated. There is also evidence that it has a function in the
biosynthesis of membrane-derived oligosaccharides. Therefore ACP and
its acyl forms interact with at least 12 different E. coli enzymes.
|CITS: [92210530] [89050961] [88296479]| ACP is the most abundant
protein in E. coli, with about 1.5E6 molecules per cell. |CITS: [Mathews&vanHolde]| ACP contains a
phosphopantetheine moiety (as does CoA) as the reactive unit, attached
to the ACP protein through a serine. The holo-ACP synthase enzyme
(encoded by the acpS gene) transfers the 4-phosphopantetheine
moeity of CoA to the apo-ACP to form holo-ACP, which is the active
form of the carrier in lipid synthesis |CITS: [68313114] [81215492]|.)""","""(Lipoate synthase catalyzes the step of lipoic acid biosynthesis at which sulfur is inserted into octanoyl-ACP to form the lipoate moiety |CITS: [8444795], [11106496]|. Lipoate modification (by lipoyl-protein ligases LipB or LplA) of complex subunits is important for function of pyruvate dehydrogenase |CITS: [814874], [6794598], [8444795]|, alpha-ketoglutarate dehydrogenase |CITS: [814874], [6794598], [8444795]|, and the glycine cleavage system |CITS: [1655709], [8444795]|.)""","""(Lipoate synthase catalyzes the step of lipoic acid biosynthesis at which sulfur is inserted into octanoyl-ACP to form the lipoate moiety |CITS: [8444795], [11106496]|. Lipoate synthase is a LipA homodimer with two (4Fe-4S) iron-sulfur clusters per protein dimer under anaerobic conditions, and these clusters are oxidized to the (2Fe-2S) state in air |CITS: [10747808], [10403368]|. The enzyme uses octanoyl-ACP, but not octanoic acid, as substrate and also uses S-adenosyl methionine |CITS: [11106496]|.)""","""NIL""","""NIL""","""NIL""","""NIL""","""NIL""","""NIL""","""NIL""","""NIL""","""NIL""","""NIL""","""NIL""","""NIL""","""NIL""","""NIL""","""NIL""","""NIL""","""(The holo-ACP synthase enzyme (encoded by acpS) transfers the 4-phosphopantetheine
moiety of CoA to the apo-ACP to form holo-ACP, which is the active
form of the carrier in lipid synthesis |CITS: [68313114] [81215492]|.)""",]},
'B1093' : {'ecocyc-rxns': {"""RXN0-2142""": """β-keto-cis-Δ5-dodecenoyl-ACP + NADPH = β-hydroxy-cis-Δ5-dodecenoyl-ACP + NADP+""","""3-OXOACYL-ACP-REDUCT-RXN""": """a D-3-hydroxy-acyl-ACP + NADP+ = NADPH + a β-ketoacyl-ACP""",},'ucsd-rxns' : ['3OAR60','3OAR80','3OAR100','3OAR121','3OAR120','3OAR141','3OAR140','3OAR161','3OAR160','3OAR40','3OAR181','3OAR180',], 'protein-comments' : ["""(Cotranscribed with acpP. |CITS: [92210530]|)""",]},
'B3581' : {'ecocyc-rxns': {"""RXN0-705""": """3-keto-L-gulonate 6-phosphate = L-xylulose-5-phosphate + CO2""",},'ucsd-rxns' : ['KG6PDC',], 'protein-comments' : ["""NIL""",]},
'B1091' : {'ecocyc-rxns': {"""3-OXOACYL-ACP-COA-SYNTHIII-RXN""": """acetyl-CoA + malonyl-ACP -> an acetoacetyl-ACP + coenzyme A + CO2""","""ACP-S-ACETYLTRANSFER-RXN""": """acyl carrier protein + acetyl-CoA = acetyl-ACP + coenzyme A""",},'ucsd-rxns' : ['KAS15','ACOATA',], 'protein-comments' : ["""(The polypeptide catalyzes two distinct reactions.)""","""NIL""",]},
'B3779' : {'ecocyc-rxns': {"""PPPGPPHYDRO-RXN""": """H2O + guanosine 3'-diphosphate 5'-triphosphate = phosphate + guanosine 5'-diphosphate,3'-diphosphate""",},'ucsd-rxns' : ['GTPDPDP',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B2497' : {'ecocyc-rxns': {"""TRANS-RXN-132""": """H+[periplasmic space] + uracil[periplasmic space] =H+[cytosol] + uracil[cytosol] """,},'ucsd-rxns' : ['URAt2pp',], 'protein-comments' : ["""(UraA is a probable high affinity uracil transporter, responsible for
the uptake of uracil. A uraA transposon mutant was defective
for uracil uptake at low concentrations, but not high concentrations,
and did not affect cytosine uptake |CITS: [95238271]|. The cloned
uraA gene was able to complement this uracil uptake defect.
UraA is a member of the NCS2 family of nucleobase:cation symporters
and probably functions as a uracil/proton symport system.
Analysis of a uraA-galK fusion suggested that the uraA
gene forms part of a pyrimidine-inducible operon with the upp
gene encoding phosphoribosyltransferase |CITS: [95238271]|.
Imported uracil is metabolised via the pyrimidine salvage pathways.)""",]},
'B4301' : {'ecocyc-rxns': {},'ucsd-rxns' : ['RPE',], 'protein-comments' : ["""(No information about this protein was found by a literature search conducted on September 19, 2005.)""",]},
'B0260' : {'ecocyc-rxns': {},'ucsd-rxns' : ['MMETt2pp',], 'protein-comments' : ["""(MmuP belongs to the APC superfamily of amino acid transporters and is a putative S-methylmethionine transporter
|CITS: [9882684]|.
A mutant with a non-polar in-frame deletion in mmuP is unable to utilize S-methylmethionine as a source of
methionine in a metE metH mutant background |CITS: [9882684]|.
mmuP : "S-methylmethionine utilization" |CITS: [9882684]|)""",]},
'B2168' : {'ecocyc-rxns': {"""1PFRUCTPHOSN-RXN""": """ATP + fructose-1-phosphate -> ADP + fructose-1,6-bisphosphate""",},'ucsd-rxns' : ['FRUK',], 'protein-comments' : ["""NIL""","""(fruK had significant sequence similarities to the minor form
of 6-phosphofructokinase(pfkB) but not the major form
6-phosphofructokinase(pfkA) |CITS: [91164390]|)""",]},
'B1098' : {'ecocyc-rxns': {"""DTMPKI-RXN""": """dTMP + ATP = dTDP + ADP""",},'ucsd-rxns' : ['DTMPK',], 'protein-comments' : ["""(Thymidylate kinase is essential for growth |CITS: [16461678]|.)""",]},
'B0650' : {'ecocyc-rxns': {},'ucsd-rxns' : ['NTP1',], 'protein-comments' : ["""(HscC (Hsc62) is an E. coli-specific member of the Hsc66 subfamily |CITS: [10574456]| of Hsp70-family
chaperones |CITS: [9735342][12054669]|. Hsc62 exhibits ATPase activity |CITS: [9735342]|, but does not show
chaperone activity toward a denatured protein substrate |CITS: [12183460]|. Hsc62 associates with σ70 and
negatively regulates σ70 activity |CITS: [12059959]|. It is the ATPase domain of Hsc62 that is essential for its
activity towards σ70 |CITS: [14734171]|.
The substrate specificity, substrate binding, and kinetics of ATPase activity have been compared between Hsc62
and DnaK |CITS: [12183460]|. Hsc62 ATPase activity shows a lower optimal temperature than that of Hsc66 and
DnaK, and this ATPase activity is not activated by DnaJ, in contrast to the activation by DnaJ of Hsc66 and DnaK
|CITS: [9735342]|. Hsc62 ATPase activity is activated by the DnaJ-like Hsc56 protein |CITS: [12054669][12183460]|,
whereas the ATPase activity of DnaK or Hsc66 is not activated by Hsc56 |CITS: [12054669]|. Reports differ as to
whether |CITS: [12054669]| or not |CITS: [12183460]| Hsc62 ATPase activity is affected by the GrpE nucleotide
exchange factor.
Overproduction of Hsc62 results in growth inhibition |CITS: [12059959]|. Deletion of Hsc62 also results in growth
inhibition, but this effect wanes after some cell cycles |CITS: [12183460]|. An hscC null mutant exhibits
decreased resistance to Cd2+ stress or to UV light, compared to wild type |CITS: [12183460]|. Hsc62
production does not suppress the phenotypes of a dnaK null mutant |CITS: [12054669][12183460]|. A
dnaK hscA hscC triple null mutant is viable |CITS: [12183460]|. Hsc62 has similarity to DnaK and Hsc66
|CITS: [9735342]|.)""",]},
'B0789' : {'ecocyc-rxns': {"""CARDIOLIPSYN-RXN""": """2 an L-1-phosphatidyl-glycerol -> cardiolipin + glycerol""",},'ucsd-rxns' : ['CLPNS140pp','CLPNS180pp','CLPNS181pp','CLPNS141pp','CLPNS160pp','CLPNS161pp','CLPNS120pp',], 'protein-comments' : ["""NIL""",]},
'B3749' : {'ecocyc-rxns': {"""ABC-28-RXN""": """ATP + D-ribose[periplasmic space] + H2O =ADP + phosphate + D-ribose[cytosol] """,},'ucsd-rxns' : ['RIBabcpp',], 'protein-comments' : ["""NIL""","""(RbsABC is an ATP-dependent ribose transporter that is a member of the ATP-Binding Cassette (ABC)
Superfamily of transporters |CITS: [99121048]|. Based on sequence similarity, RbsA is the ATP-binding
constituent, RbsB is the periplasmic substrate-binding protein, and RbsC form the transmembrane
constituent of the transporter |CITS: [99121048]|. Mutations in each of the components eliminated transport
of ribose at external concentration of 1 μM, indicating that the components make up a transport system
that is responsible for high-affinity ribose transport. However, these mutants are able to grow normally on
high concentrations of the sugar, suggesting that there is at least a second, low-affinity transport system for
ribose in E. coli |CITS: [84212237]|. Hydrophobicity analysis has shown that RbsC contains six
transmembrane helices, while alkaline phosphatase fusions and the use of inside-out vesicles with proteolysis
have shown that the C and N termini are both on the cytoplasmic side of the membrane.)""",]},
'B1291' : {'ecocyc-rxns': {"""ABC-29-RXN""": """ATP + a peptide[periplasmic space] + H2O =ADP + phosphate + a peptide[cytosol] """,},'ucsd-rxns' : ['Kt2pp','Kt2pp',], 'protein-comments' : ["""NIL""","""(SapABCDF (Sensitive to antimicrobial peptides) is a member of the ATP Binding Cassette (ABC) transporter
superfamily |CITS:[98254124]|. Disruption of the sap gene results in increased susceptibility to
endogenous antimicrobial peptides, such as protamine, mellitin, defensins and human neutrophil granules.
This suggests that the SapABCDF system may be involved in uptake of these peptides as part of a defense
degradation system |CITS:[94038887]|. Based on sequence similarity and hydrophobicity analysis, SapA is
the putative periplasmic binding protein, SapB and SapC are both transmembrane domains and SapD
and SapF are the ATP-binding proteins of the complex. Supporting this hypothesis, SapABCD are homologs
of the Salmonella typhimurium SapABCD proteins which are required for virulence and resistance to
antimicrobial peptides melittin and protamine |CITS: [94038887]| and the Sap proteins show sequence
similarity with other ABC peptide uptake systems. SapD has been implicated in an additional role in
conferring ATP dependence to the K+ uptake proteins TrkG and TrkH which are not related
to the ABC superfamily |CITS: [21557159]|. ATP binding to SapD has also been shown to be sufficient for
restoring K+ uptake in E. coli via its two Trk potassium transporters |CITS: [21557159]|.
Furthermore the previously described trkE locus |CITS: [94038887]| maps inside the
sapABCDF operon.)""",]},
'B4288' : {'ecocyc-rxns': {"""RXN0-2261""": """ferric dicitrate[extracellular space] =ferric dicitrate[cytosol] ""","""ABC-9-RXN""": """ATP + ferric dicitrate[periplasmic space] + H2O =ADP + phosphate + ferric dicitrate[cytosol] """,},'ucsd-rxns' : ['FE3DCITabcpp',], 'protein-comments' : ["""(FecD is one of two (along with FecC) integral membrane protein components of the iron dicitrate ABC transporter.)""","""(FecBCDE is an ATP Binding Cassette (ABC) citrate-dependent iron (III) transport system. Sequence
homology and hydropathy analyses indicate that FecB is the periplasmic binding protein, FecC and FecD
are integral membrane proteins and FecE is the ATP-binding protein |CITS: [88227855]|. Mutation and
induction studies indicate that exogenous ferric citrate induces the expression of fec transport genes
through a signaling mechanism which does not require ferric citrate to enter the cytoplasm |CITS: [82004187]|.
|CITS:[81116964]|, or to cross the outer membrane into the periplasmic space |CITS: [95246736]|. Rather,
induction of fec transport genes is a function of FecA-ferric citrate binding and is coupled through
the TonB, ExbB and ExbD proteins independent of their role in uptake |CITS:[95246736]|.)""","""NIL""",]},
'B1605' : {'ecocyc-rxns': {},'ucsd-rxns' : ['ARGORNt7pp',], 'protein-comments' : ["""(ArcD is an uncharacterised member of the APC family of
amino acid transporters. ArcD is highly similar to the
Pseudomonas aeruginosa ArcD arginine/ornithine
antiporter and probably has a similar function.)""",]},
'B0822' : {'ecocyc-rxns': {"""SUGAR-PHOSPHATASE-RXN""": """H2O + a sugar phosphate = a sugar + phosphate""",},'ucsd-rxns' : ['R5PP','G3PT','MN6PP','G6PP','F6PP',], 'protein-comments' : ["""(YbiV is a type II HAD phosphatase with sugar phosphatase activity |CITS: [15657928]|. Phosphatase activity of YbiV
was also discovered in a high-throughput screen of purified proteins |CITS: [15808744]|.
Crystal structures of YbiV have been solved, and a catalytic mechanism was suggested |CITS: [15657928]|.
)""",]},
'B0825' : {'ecocyc-rxns': {"""RXN0-313""": """D-fructose-6-phosphate = dihydroxy-acetone + D-glyceraldehyde-3-phosphate""",},'ucsd-rxns' : ['F6PA',], 'protein-comments' : ["""NIL""","""(The enzyme is made up of either 10 or 12 subunits.
|CITS: [21179155]|)""",]},
'B3061' : {'ecocyc-rxns': {"""LTARTDEHYDRA-RXN""": """tartrate = oxaloacetate + H2O""",},'ucsd-rxns' : ['TARTD',], 'protein-comments' : ["""(The ttdA gene encodes the alpha subunit of the L-tartrate dehydratase enzyme |CITS: [8371115]| and is expressed
in exponentially growing cells |CITS: [3297921]|.)""","""NIL""","""(E.coli is capable of degrading tartrate under aerobic or anaerobic conditions. L-tartrate dehydratase is induced
during anaerobic growth on glycerol plus L- and meso-tartrates |CITS: [8371115]|.)""",]},
'B1297' : {'ecocyc-rxns': {"""RXN0-3901""": """putrescine + L-glutamate + ATP = γ-glutamyl-L-putrescine + ADP + phosphate""",},'ucsd-rxns' : ['GLNS','GGPTRCS',], 'protein-comments' : ["""(PuuA was identified as the γ-glutamylputrescine synthetase in a putrescine utilization pathway.
The function of genes in the puu gene cluster was initially inferred by similarity with the ipuABCDEGFH
operon in Pseudomonas sp. |CITS: [15590624]|)""",]},
'B3063' : {'ecocyc-rxns': {"""TRANS-RXN-127""": """tartrate[periplasmic space] + succinate[cytosol] =tartrate[cytosol] + succinate[periplasmic space] """,},'ucsd-rxns' : ['TARTRt7pp',], 'protein-comments' : ["""(YgjE is a putative tartrate/succinate antiporter belonging to the
DASS family of di- and tri-carboxylic acid transporters. The ygjE
is located in a probable operon with the ttdAB genes encoding
L-tartrate dehydratase. In an analogous manner to CitT |CITS: [98361905]|,
YgjE probably allows the uptake of tartrate in exchange for succinate,
the end product of tartrate fermentation.)""",]},
'B0829' : {'ecocyc-rxns': {"""RXN0-11""": """glutathione[periplasmic space] + ATP + H2O =glutathione[cytoplasm] + ADP + phosphate """,},'ucsd-rxns' : ['GTHRDabcpp',], 'protein-comments' : ["""(ATP-binding component of glutathione ABC transporter)""","""(The GsiABCD glutathione transporter is a member of the ATP Binding Cassette (ABC) superfamily
of transporters. Based on sequence similarity, GsiA is predicted to be the ATP-binding component, GsiB
is predicted to be the periplasmic binding component, and GsiC and GsiD are predicted to be inner
membrane components. Mutation of any component impairs the ability of E. coli to transport the
glutathione molecule into the cell. Expression of the cloned genes in their respective mutants restores their
ability to transport glutathione. Transport by the glutathione ABC transporter is one of two known
mechanisms for salvage of glutathione excreted from the cell. The other involves hydrolysis of glutathione
by γ-glutamyl transpeptidase in the periplasm to yield glutamic acid and cysteinylglycine which
can be taken back into the cell |CITS:[16109926]|.)""",]},
'B1298' : {'ecocyc-rxns': {"""RXN0-3942""": """γ-glutamyl-γ-aminobutyrate + H2O = 4-aminobutyrate + L-glutamate""",},'ucsd-rxns' : ['GGGABAH',], 'protein-comments' : ["""(PuuD was identified as the γ-glutamyl-γ-aminobutyrate hydrolase in a putrescine utilization pathway.
The function of genes in the puu gene cluster was initially inferred by similarity with the ipuABCDEGFH
operon in Pseudomonas sp. |CITS: [15590624]|
PuuD is highly expressed in early stationary phase; expression of puuD is induced by growth on putrescine as
the sole source of nitrogen |CITS: [15590624][16499623]|. Addition of succinate or NH4Cl to the medium
reduces PuuD expression |CITS: [16499623]|.
A strain carrying a mutation in puuD can not grow on putrescine as the sole source of nitrogen and
accumulates γ-glutamyl-γ-aminobutyrate |CITS: [16499623]|.)""","""NIL""",]},
'B4287' : {'ecocyc-rxns': {"""RXN0-2261""": """ferric dicitrate[extracellular space] =ferric dicitrate[cytosol] ""","""ABC-9-RXN""": """ATP + ferric dicitrate[periplasmic space] + H2O =ADP + phosphate + ferric dicitrate[cytosol] """,},'ucsd-rxns' : ['FE3DCITabcpp',], 'protein-comments' : ["""(ATP binding component of the iron dicitrate ABC transporter)""","""(FecBCDE is an ATP Binding Cassette (ABC) citrate-dependent iron (III) transport system. Sequence
homology and hydropathy analyses indicate that FecB is the periplasmic binding protein, FecC and FecD
are integral membrane proteins and FecE is the ATP-binding protein |CITS: [88227855]|. Mutation and
induction studies indicate that exogenous ferric citrate induces the expression of fec transport genes
through a signaling mechanism which does not require ferric citrate to enter the cytoplasm |CITS: [82004187]|.
|CITS:[81116964]|, or to cross the outer membrane into the periplasmic space |CITS: [95246736]|. Rather,
induction of fec transport genes is a function of FecA-ferric citrate binding and is coupled through
the TonB, ExbB and ExbD proteins independent of their role in uptake |CITS:[95246736]|.)""","""NIL""",]},
'B0514' : {'ecocyc-rxns': {"""GLY3KIN-RXN""": """glycerate + ATP = 3-phosphoglycerate + ADP""",},'ucsd-rxns' : ['GLYCK',], 'protein-comments' : ["""NIL""",]},
'B1484' : {'ecocyc-rxns': {},'ucsd-rxns' : ['ALAALAabcpp',], 'protein-comments' : ["""(ATP-binding component of ABC transporter)""","""(YddO, YddP, YddQ, YddR and YddS are uncharacterized
members of the ABC superfamily of transporters |CITS: [99091701]|.
YddO and YddP are the putative ATP-binding proteins.
YddQ and YddR are the putative membrane components.
YddS is the putativeperiplasmic binding protein.
Based on sequence similarity, these proteins probably
function together as an ATP-dependent peptide transporter.
The genes yddO, yddP, yddQ, yddR,
and yddS are probably located within a single
operon.)""",]},
'B1485' : {'ecocyc-rxns': {},'ucsd-rxns' : ['ALAALAabcpp',], 'protein-comments' : ["""(membrane component of ABC transporter
Protein topology in the inner membrane has been determined |CITS: [11867724]|.)""","""(YddO, YddP, YddQ, YddR and YddS are uncharacterized
members of the ABC superfamily of transporters |CITS: [99091701]|.
YddO and YddP are the putative ATP-binding proteins.
YddQ and YddR are the putative membrane components.
YddS is the putativeperiplasmic binding protein.
Based on sequence similarity, these proteins probably
function together as an ATP-dependent peptide transporter.
The genes yddO, yddP, yddQ, yddR,
and yddS are probably located within a single
operon.)""",]},
'B1486' : {'ecocyc-rxns': {},'ucsd-rxns' : ['ALAALAabcpp',], 'protein-comments' : ["""(membrane component of ABC transporter)""","""(YddO, YddP, YddQ, YddR and YddS are uncharacterized
members of the ABC superfamily of transporters |CITS: [99091701]|.
YddO and YddP are the putative ATP-binding proteins.
YddQ and YddR are the putative membrane components.
YddS is the putativeperiplasmic binding protein.
Based on sequence similarity, these proteins probably
function together as an ATP-dependent peptide transporter.
The genes yddO, yddP, yddQ, yddR,
and yddS are probably located within a single
operon.)""",]},
'B1487' : {'ecocyc-rxns': {},'ucsd-rxns' : ['ALAALAabcpp',], 'protein-comments' : ["""(periplasmic binding component of ABC transporter)""","""(YddO, YddP, YddQ, YddR and YddS are uncharacterized
members of the ABC superfamily of transporters |CITS: [99091701]|.
YddO and YddP are the putative ATP-binding proteins.
YddQ and YddR are the putative membrane components.
YddS is the putativeperiplasmic binding protein.
Based on sequence similarity, these proteins probably
function together as an ATP-dependent peptide transporter.
The genes yddO, yddP, yddQ, yddR,
and yddS are probably located within a single
operon.)""",]},
'B1849' : {'ecocyc-rxns': {"""GARTRANSFORMYL2-RXN""": """5-phospho-ribosyl-glycineamide + formate + ATP = phosphate + 5'-phosphoribosyl-N-formylglycineamide + ADP""","""ACETATEKIN-RXN""": """acetate + ATP = acetylphosphate + ADP""",},'ucsd-rxns' : ['GART','ACKr',], 'protein-comments' : ["""NIL""",]},
'B0179' : {'ecocyc-rxns': {"""UDPHYDROXYMYRGLUCOSAMNACETYLTRANS-RXN""": """UDP-3-O-(3-hydroxymyristoyl)glucosamine + (R)-3-hydroxymyristoyl-ACP = UDP-2,3-bis(3-hydroxymyristoyl)glucosamine + acyl carrier protein""",},'ucsd-rxns' : ['U23GAAT',], 'protein-comments' : ["""NIL""",]},
'B1483' : {'ecocyc-rxns': {},'ucsd-rxns' : ['ALAALAabcpp',], 'protein-comments' : ["""(ATP-binding component of ABC transporter)""","""(YddO, YddP, YddQ, YddR and YddS are uncharacterized
members of the ABC superfamily of transporters |CITS: [99091701]|.
YddO and YddP are the putative ATP-binding proteins.
YddQ and YddR are the putative membrane components.
YddS is the putativeperiplasmic binding protein.
Based on sequence similarity, these proteins probably
function together as an ATP-dependent peptide transporter.
The genes yddO, yddP, yddQ, yddR,
and yddS are probably located within a single
operon.)""",]},
'B0175' : {'ecocyc-rxns': {"""CDPDIGLYSYN-RXN""": """CTP + an L-phosphatidate = diphosphate + a CDP-diacylglycerol""",},'ucsd-rxns' : ['DASYN180','DASYN181','DASYN160','DASYN161','DASYN140','DASYN141','DASYN120',], 'protein-comments' : ["""NIL""",]},
'B0174' : {'ecocyc-rxns': {"""UPPSYN-RXN""": """a cis,trans-polyisoprenyln-PP + Δ3-isopentenyl-PP = diphosphate + cis,trans-polyisoprenyln+1-PP""","""DECAPCISTRANSFER-RXN""": """di-trans,poly-cis-decaprenyl diphosphate + Δ3-isopentenyl-PP = diphosphate + di-trans,poly-cis-undecaprenyl diphosphate""",},'ucsd-rxns' : ['UDCPDPS',], 'protein-comments' : ["""(Crystal structures of UppS have been solved, revealing a possible reaction mechanism |CITS: [11581264][12756244]
[15044730]|. Substrate specificity has been studied |CITS: [15447632]|.)""","""NIL""",]},
'B1488' : {'ecocyc-rxns': {"""3.4.17.14-RXN""": """EC# 3.4.17.14""",},'ucsd-rxns' : ['ALAALAD',], 'protein-comments' : ["""(VanX is a D-Ala-D-Ala dipeptidase, which catalyzes hydrolysis of the D-alanyl-D-alanine dipeptide required for wild-type peptidoglycan biosynthesis |CITS: [9751644]|. VanX activity has been characterized |CITS: [9751644]|.
VanX-related proteins are involved in the production of a variant peptidoglycan that results in resistance of pathogenic bacteria to the antibiotic vancomycin; see |CITS: [10500118]|. VanX may act in murein recycling |CITS: [9751644]|. VanX allows D-Ala-D-Ala to be utilized as a carbon source, which may have significance with respect to survival at stationary phase |CITS: [9751644]|.
Regulation has been described |CITS: [9751644]|. The vanX gene has sequences indicative of RpoS regulation |CITS: [9751644]|.
Review: |CITS: [10500118]|.)""",]},
'B0679' : {'ecocyc-rxns': {"""TRANS-RXN-167""": """phosphoenolpyruvate + N-acetyl-D-glucosamine[periplasmic space] =N-acetyl-D-glucosamine-6-phosphate[cytosol] + pyruvate """,},'ucsd-rxns' : ['ACGAptspp',], 'protein-comments' : ["""(contains PTS Enzyme IIA, IIB and IIC domains)""","""(NagE, the N-acetylglucosamine PTS permease, belongs to the functional
superfamily of the phosphoenolpyruvate (PEP)-dependent, sugar
transporting phosphotransferase system (PTS). The PTS transports
and simultaneously phosphorylates its sugar substrates in a process
called group translocation. NagE takes up exogenous N-acetylglucosamine,
releasing the phosphate ester into the cell cytoplasm in preparation
for metabolism, primarily via glycolysis |CITS: [94066914]|.
NagE, the Enzyme IINag complex, possesses
three domains in a single polypeptide chain with the domain order
IIC-IIB-IIA |CITS: [89050950]|. It is homologous to PtsG/Crr (the glucose-specific
PTS Enzyme II) which has been reported to possess 8 transmembrane
α-helical segments in its IIC domain.
The IIB and IIA domains are localized to the cytoplasmic side
of the membrane. The overall PTS-mediated phosphoryl transfer
reaction, requiring the two general energy coupling proteins of
the PTS, Enzyme I and HPr, as well as the three domains of the
Enzyme II complex is:
PEP--> Enzyme
I(his~~P) --> HPr(his~~P)
--> IIA(his~~P)
--> IIB(cys~~P)
-(IIC)-> N-acetylglucosamine-6-P.
NagE transports N-acetylglucosamine with low micromolar affinity.
It can also transport antibiotics such as streptozotocin.
The monocistronic nagE operon and the nagBACD operon
comprise part of the nag regulon and are transcribed from
divergent promoters. The nagBACD operon encodes (a) glucosamine-P
deaminase (NagB), (b) N-acetylglucosamine-6-P deacetylase (NagA),
(c) the nag regulon transcriptional regulator (NagC) and
(d) a gene of unknown function which is, however, homologous to
functionally characterized phosphatases (NagD) |CITS: [89343637]|. NagC together
with the cyclic AMP-cyclic AMP receptor protein (CRP) complex
controls expression of the nag regulon |CITS: [92114782] [95311313]|.)""",]},
'B0171' : {'ecocyc-rxns': {"""UMPKI-RXN""": """ATP + UMP = ADP + UDP""",},'ucsd-rxns' : ['UMPK','URIDK2r',], 'protein-comments' : ["""(Expression of uridylate kinase is essential for growth of E. coli |CITS: [8190075]|. Temperature-sensitive and
site-directed mutants in pyrH have been studied to reveal residues essential for thermodynamic stability,
catalysis and allosteric regulation |CITS: [15256558][9457846]|.
Uridylate kinase is subject to complex regulatory control by GTP and UTP. The enzyme is dually localized; it is
cytosolic and close to the membranes |CITS: [99121021] [95226394]|.
PyrH plays a role in the transcriptional regulation of the carAB operon |CITS: [9677289]|.
Crystal structures of PyrH bound to the substrate and product of the reaction have been solved. UTP was found to
act as a competitive inhibitor |CITS: [15857829]|.)""","""NIL""",]},
'B3591' : {'ecocyc-rxns': {"""2.9.1.1-RXN""": """selenophosphate + L-seryl-tRNAsec = phosphate + H2O + L-selenocysteinyl-tRNAsec""",},'ucsd-rxns' : ['SELCYSS',], 'protein-comments' : ["""(Selenocysteine synthase is encoded by the selA gene |CITS: [2007584]|. Selenocysteine synthase contains
10 SelA subunits arranged in two rings |CITS: [1474891]|; the complex exhibits a molecular weight of approximately
600 kDa |CITS: [2007584]|. Pyridoxal 5-phosphate is present at a stoichiometry of one per monomer
|CITS: [2007584]|. The seryl-tRNA(Sec UCA) substrate is present at a stoichiometry of one per two monomers
|CITS: [2007585]|. The reaction mechanism is described |CITS: [2007585]|.
A selA or selD mutant exhibits a defect in selenocysteine formation, whereas a selB mutant does
not |CITS: [2524495]|.
Cloning, sequencing, and protein purification is described |CITS: [2007584]|. Extracts of cells overproducing SelA
and SelD exhibit in vitro production of selenocysteinyl-tRNA(Ser)(UCA) from seryl-tRNA(UCA)
|CITS: [2405383]|.
Regulation has been described |CITS: [1650339]|.
Review: |CITS: [12098758]|.)""","""NIL""",]},
'B3619' : {'ecocyc-rxns': {"""5.1.3.20-RXN""": """ADP-D-glycero-D-manno-heptose = ADP-L-glycero-D-manno-heptose""",},'ucsd-rxns' : ['AGMHE',], 'protein-comments' : ["""(The hldD gene encodes ADP-L-glycero-D-mannoheptose-6-epimerase, the last enzyme in the pathway for
synthesis of the ADP-heptose precursor of core LPS |CITS: [11751812]|. The enzyme is glycosylated
|CITS: [7929099]|. It was initially thought to contain NAD+ as a cofactor |CITS: [7929099]|, but the cofactor found in
the crystal structure was NADP+ |CITS: [10896473]|. Subsequent studies showed that the enzyme has a preference
of NADP+ over NAD+ |CITS: [11313358]|.
A crystal structure of HldD has been solved at 2 A resolution |CITS: [10896473]|. The enzyme was initially thought to
form a homohexamer |CITS: [7929099]|, but appears as a homopentamer in the crystal structure |CITS: [10896473]|.
An hldD null mutant strain is unable to grow above 42 degrees C and has a mucoid phenotype
|CITS: [1656498]|. An hldD mutant is supersensitive to novobiocin and other hydrophobic drugs, and its
lipopolysaccharide contains the stereoisomer D-glycero-D-manno-heptose rather than
L-glycero-D-manno-heptose |CITS: [383699][6337148]|. An hldD::cat mutation results in
induction of mucoidy and increased expression of gabT, which is likely due to increased expression of RpoS
|CITS: [15576807]|.
hldD expression increases under high temperature conditions and is regulated by the alternative sigma factor
sigma 32 |CITS: [1656498][1861974]|.)""","""NIL""",]},
'B2235' : {'ecocyc-rxns': {"""RXN0-1""": """an acceptor + H2O + a 2'-deoxyribonucleoside diphosphate = a reduced acceptor + a ribonucleoside diphosphate""","""RIBONUCLEOSIDE-DIP-REDUCTI-RXN""": """a thioredoxin disulfide + H2O + a 2'-deoxyribonucleoside diphosphate = a reduced thioredoxin + a ribonucleoside diphosphate""","""CDPREDUCT-RXN""": """dCDP + a thioredoxin disulfide + H2O = CDP + a reduced thioredoxin""","""UDPREDUCT-RXN""": """dUDP + a thioredoxin disulfide + H2O = UDP + a reduced thioredoxin""","""ADPREDUCT-RXN""": """dADP + a thioredoxin disulfide + H2O = ADP + a reduced thioredoxin""","""GDPREDUCT-RXN""": """dGDP + a thioredoxin disulfide + H2O = GDP + a reduced thioredoxin""",},'ucsd-rxns' : ['RNDR4','RNDR4','RNDR3','RNDR3','RNDR2','RNDR2','RNDR1','RNDR1',], 'protein-comments' : ["""(The B2 protein of ribonucleoside-diphosphate reductase contains the tyrosyl radical-dinuclear iron
center, which is thought to initiate catalysis by long-range electron
transfer. |CITS: [93003133] [73218477]|
NrdA and/or NrdB are required for growth of a nrdD or nrdG null mutant under microaerophilic conditions
|CITS: [8954104]|.
Review: |CITS: [15158709]|)""","""NIL""","""NIL""",]},
'B2711' : {'ecocyc-rxns': {"""RXN0-2721""": """NADH + oxidized flavorubredoxin + 2 nitric oxide = NAD+ + reduced flavorubredoxin + nitrous oxide + H2O""",},'ucsd-rxns' : ['NHFRBO',], 'protein-comments' : ["""(NorW encodes the reductase enzyme which can convert oxidized flavorubredoxin to its reduced form
|CITS: [12529359][11751865][12101220]|.
Regulation has been described |CITS: [12529359]|.)""",]},
'B0778' : {'ecocyc-rxns': {"""DETHIOBIOTIN-SYN-RXN""": """CO2 + 7,8-diaminononanoate + ATP = dethiobiotin + phosphate + ADP""",},'ucsd-rxns' : ['DBTS',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B4381' : {'ecocyc-rxns': {"""DEOXYRIBOSE-P-ALD-RXN""": """deoxyribose-5-phosphate = acetaldehyde + D-glyceraldehyde-3-phosphate""",},'ucsd-rxns' : ['DRPA',], 'protein-comments' : ["""(The purified enzyme may exist as both a monomer and a dimer.
In Tris/HCl containing EDTA the enzyme exists as a monomer and as a
dimer in phosphate buffer. |CITS: [83003651]|)""",]},
'B0775' : {'ecocyc-rxns': {"""2.8.1.6-RXN""": """dethiobiotin + 2 S-adenosyl-L-methionine + sulfur donor -> biotin + 2 5'-deoxyadenosine + 2 L-methionine""",},'ucsd-rxns' : ['BTS4',], 'protein-comments' : ["""(Biotin synthase catalyzes the final reaction of biotin biosynthesis by inserting a sulfur atom between C6 and C9 of
dethiobiotin in a S-adenosylmethoinine (SAM)-dependent reaction. It has not been possible to reconstitute
a catalytic reaction in vitro, and considerable uncertainty regarding the reaction mechanism, cofactor
requirements, and the source of the sulfur atom still remains |CITS: [15850974]|.
BioB belongs to the family of "radical SAM" enzymes |CITS: [15581586]|. The enzyme purifies as a homodimer
|CITS: [8142361]|. It contains two distinct iron-sulfur binding sites; one carries a [2Fe-2S] cluster, and the other a
[4Fe-4S] cluster that binds SAM and facilitates its reductive cleavage to generate a 5'-deoxyadenosyl radical
which activates dethiobiotin |CITS: [11834738][12614166][14704425][14967042]|. One of the reaction products,
5'-deoxyadenosine, inhibits BioB function |CITS: [15911379]|.
A crystal structure of biotin synthase has been solved at 3.4 Å resolution |CITS: [14704425]|. Reaction mechanisms
involving either the [2Fe-2S] cluster |CITS: [9862460][11444982]| or the cofactor PLP |CITS: [12119030][12482614]|
have been proposed; however, the crystal structure of BioB |CITS: [14704425]| and the cofactor composition of the
enzyme |CITS: [14967041]| do not support involvement of PLP.
Consistent with a proposed role as the sulfur donor, degradation of the [2Fe-2S] cluster is observed during turnover
of the enzyme |CITS: [14967042]|. The enzyme does not appear to be able to function catalytically in vitro
|CITS: [15610037]|; BioB is catalytically active in vivo, but it is thought that reconstitution of the [2Fe-2S]
cluster makes the enzyme susceptible to proteolytic degradation |CITS: [15850983]|.
Reviews: |CITS: [15581586][16042606]|)""","""NIL""",]},
'B0774' : {'ecocyc-rxns': {"""DAPASYN-RXN""": """S-adenosyl-L-methionine + 8-amino-7-oxononanoate = S-adenosyl-4-methylthio-2-oxobutanoate + 7,8-diaminononanoate""",},'ucsd-rxns' : ['AMAOTr',], 'protein-comments' : ["""(The BioA protein functions as the 7.8-diaminopelargonic acid synthase enzyme in the biotin biosynthesis pathway.
Regulation of the bio operon by transcription by attenuation has been described |CITS: [2466544]|.)""","""NIL""",]},
'B0776' : {'ecocyc-rxns': {"""7KAPSYN-RXN""": """L-alanine + pimelyl-CoA = CO2 + coenzyme A + 8-amino-7-oxononanoate""",},'ucsd-rxns' : ['AOXSr',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B2719' : {'ecocyc-rxns': {"""FHLMULTI-RXN""": """formate = CO2 + H2""","""RXN0-3283""": """2 H+ + 2 e- -> H2""",},'ucsd-rxns' : ['FHL','HYD1pp',], 'protein-comments' : ["""(HycG has similarity to small subunits of hydrogenases |CITS: [92326636]| and resembles one of the subunits of
NADH:ubiquinone oxidoreductase of the respiratory chain |CITS: [90251163][SAWERS04]|.)""","""NIL""","""(A report has described that formate oxidation in anaerobically grown E. coli is coupled to proton translocation
|CITS: [15848284]|.)""",]},
'B3616' : {'ecocyc-rxns': {"""THREODEHYD-RXN""": """L-threonine + NAD+ = 2-amino-3-oxobutanoate + NADH""",},'ucsd-rxns' : ['THRD',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B1992' : {'ecocyc-rxns': {"""COBALAMIN5PSYN-RXN""": """adenosylcobinamide-GDP + α-ribazole-5'-P = adenosylcobalamin-5'-phosphate + GMP""","""COBALAMINSYN-RXN""": """adenosylcobinamide-GDP + α-ribazole = coenzyme B12 + GMP""",},'ucsd-rxns' : ['ADOCBLS',], 'protein-comments' : ["""(The cobS gene product is associated with a large complex of
proteins. |CITS: [SwissProt]|)""",]},
'B1993' : {'ecocyc-rxns': {"""COBINPGUANYLYLTRANS-RXN""": """adenosylcobinamide-P + GTP = adenosylcobinamide-GDP + diphosphate""","""COBINAMIDEKIN-RXN""": """adenosylcobinamide + ATP = adenosylcobinamide-P + ADP""",},'ucsd-rxns' : ['ADOCBIK','ACBIPGT',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B4268' : {'ecocyc-rxns': {"""GLUCONOKIN-RXN""": """ATP + gluconate = ADP + 6-phospho-D-gluconate""",},'ucsd-rxns' : ['GNK',], 'protein-comments' : ["""(The subunit structure is unknown, however gluconokinase I
is known to be a homotrimer. |CITS: [94285041]|)""",]},
'B0957' : {'ecocyc-rxns': {},'ucsd-rxns' : ['H2Otex',], 'protein-comments' : ["""(OmpA is a member of the OmpA-OmpF Porin (OOP) family. OmpA is believed to be a nonspecific diffusion channel,
allowing various small solutes to cross the outer membrane. |CITS: [1370823]| It is also believed to serve several other
functions including, as a phage receptor |CITS: [330500]| , as a mediator of F-factor dependent conjugation |CITS: [323051]|,
and in shape stabilization of the bacterium. It is 325 amino acids long and is one of the most abundant proteins in the
outer membrane of E. coli. Structural data at 1.65 angstroms reveals that OmpA consists of an eight-stranded
all-next-neighbor antiparallel beta-barrel. There is some debate asto whether OmpA is truly a channel having both open
and closed conformation |CITS: [7517935]| , or whether the observed porin activity is artifactual.
OmpA was found as a dimer in the outer membrane |CITS:[16079137]|.
Targeting of OmpA to the Sec-translocase for transport across the inner membrane
is SecB-dependent |CITS:[16352602]|.)""",]},
'B0061' : {'ecocyc-rxns': {"""RIBULPEPIM-RXN""": """L-ribulose-5-phosphate = D-xylulose-5-phosphate""",},'ucsd-rxns' : ['RBP4E',], 'protein-comments' : ["""(The nucleotide sequences of the araD genes from E. coli B/r and K-12 were 97% identical. |CITS: [91067495]|
The protein has been crystallized. |CITS: [69029406]|)""","""NIL""",]},
'B0575' : {'ecocyc-rxns': {"""TRANS-RXN-90""": """H+[periplasmic space] =H+[cytosol] """,},'ucsd-rxns' : ['CUt3','AGt3',], 'protein-comments' : ["""(YbdE is a member of the Resistance-Nodulation-Cell Division (RND) Transporter Superfamily and is
involved in the detoxification of silver ions in E. coli. An in-frame chromosomal deletion mutant of
ybdE yielded a silver-sensitive E. coli mutant strain which did not differ in its copper
resistance from its isogenic parent |CITS: [21178899]|. The ybdE gene is located in the
ylcBCD-ybdE operon, where ybdE is preceded by a gene encoding a membrane fusion
protein, ylcD, and a gene encoding a putative outer-membrane associated protein, ylcB |CITS:
[21178899]|. YbdE, YlcD, and YlcB probably interact to mediate silver extrusion, possibly by a
proton-dependent mechanism. Northern hybridization, RT-PCR, and primer extension analyses showed that
ylcBCD-ybdE mRNA is induced by the presence of silver ion |CITS: [21178899]|. Since the
ylcBCD-ybdE operon provides only a low level of silver resistance in E. coli, it is an open
question whether silver is the sole or main substrate of the efflux system.
The cusABFCRS gene cluster has similarity to a gene cluster contained on a silver resistance plasmid from a clinical Salmonella isolate |CITS: [12829274]|.
Agr: Ag(I) resistance |CITS: [12829274]|.)""","""(The Copper transporting efflux system, CusCFBA, is one of at least three systems involved in copper resistance.
CusB is a member of the membrane fusion protein (MFP) family. CusC is the outer membrane factor which forms a channel in the outer membrane.
CusA is the resistance-nodulation-division (RND) permease. CusF is the periplasmic copper binding protein.
The CusCFBA complex may translocate copper from the cytoplasm to the extracellular enviornment across both the inner and outer membrane. Alternatively, the Cus complex
may capture copper in the periplasm and export it outside. Evidence that supports the alternative claim includes the
periplasmic localization of the copper binding protein, CusF, and the assumption that copper access to the RND protein, CusA, may be possible from the cytoplasm as well as the periplasm. |CITS: [12374972]|
)""",]},
'B3390' : {'ecocyc-rxns': {"""SHIKIMATE-KINASE-RXN""": """shikimate + ATP = shikimate-3-phosphate + ADP""",},'ucsd-rxns' : ['SHKK',], 'protein-comments' : ["""NIL""",]},
'B4015' : {'ecocyc-rxns': {"""ISOCIT-CLEAV-RXN""": """isocitrate = glyoxylate + succinate""",},'ucsd-rxns' : ['ICL',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B3396' : {'ecocyc-rxns': {},'ucsd-rxns' : ['MCTP2App','MCTP1App','MCTP1Bpp','MPTG','MPTG2',], 'protein-comments' : ["""(PBP1A is the product of the mrcA gene |CITS:[3882429]|. PBP1A is a bifunctional, inner membrane enzyme
catalyzing the transglycosylation and transpeptidation of murein (peptidoglycan) precursors in the formation of the
murein sacculus |CITS:[9529891]|. The amino terminus contains a signal sequence |CITS:[3882429]|. PBP1A is able
to dimerize without disulfide bonds, but doesn't form a complex with PBP1B |CITS:[12057973]|. Either PBP1A or
PBP1B (the other major bifunctional enzyme in murein synthesis with a different penicillin-binding affinity) is required
for cell elongation because a PBP1A-PBP1B double mutation is lethal |CITS:[1103132][341159][345275][2993822]|.
Experiments have been performed involving inhibition or mutation of PBP1A alone or coupled with inhibition or
mutation of other proteins involved in cell division and murein metabolism |CITS:[7007327][2211517][2066344][10383966]|.)""",]},
'B2307' : {'ecocyc-rxns': {"""ABC-14-RXN""": """ATP + L-histidine[periplasmic space] + H2O =ADP + phosphate + L-histidine[cytosol] ""","""ABC-37-RXN""": """ATP + L-ornithine[periplasmic space] + H2O =ADP + phosphate + L-ornithine[cytosol] ""","""ABC-4-RXN""": """ATP + L-arginine[periplasmic space] + H2O =ADP + phosphate + L-arginine[cytosol] ""","""ABC-3-RXN""": """L-lysine[periplasmic space] + ATP + H2O =L-lysine[cytosol] + ADP + phosphate """,},'ucsd-rxns' : ['ORNabcpp','LYSabcpp','HISabcpp','ARGabcpp',], 'protein-comments' : ["""NIL""","""(Functions with HisMQP.)""","""(HisPMQJ is an ATP-dependent histidine transport system that is a member of the ATP-Binding
Cassette (ABC) Superfamily of transporters |CITS: [96381453]|. Based on sequence similarity, HisJ is the
periplasmic histidine-binding protein, HisQ and HisM are the integral membrane components, and HisP is
the ATP-binding component of the ABC transport complex |CITS: [98188231]|. Although the transport
properties of the His complex in E. coli have not yet been characterized, extensive investigations on
the orthologous proteins in Salmonella typhimurium have been reported. The His complex of
Salmonella typhimurium was purified and reconstituted into ATP-encapsulated proteoliposomes,
and histidine transport activity was observed |CITS: [97150838]|. His-mediated transport activity is
completely dependent on the presence of all four protein components and on the internal ATP concentration,
with apparent Km of 8 mM for ATP |CITS: [97150838] [89386658]|. The transport activity is
also affected by pH, temperature, and salt concentration |CITS: [97150838]|. Transport is irreversible and
accumulation reaches a plateau at which point transport ceases |CITS: [97150838]|. The transport complex is
inhibited by ADP and by high concentrations of internal histidine |CITS: [97150838]|.)""",]},
'B2308' : {'ecocyc-rxns': {"""ABC-14-RXN""": """ATP + L-histidine[periplasmic space] + H2O =ADP + phosphate + L-histidine[cytosol] ""","""ABC-37-RXN""": """ATP + L-ornithine[periplasmic space] + H2O =ADP + phosphate + L-ornithine[cytosol] ""","""ABC-4-RXN""": """ATP + L-arginine[periplasmic space] + H2O =ADP + phosphate + L-arginine[cytosol] ""","""ABC-3-RXN""": """L-lysine[periplasmic space] + ATP + H2O =L-lysine[cytosol] + ADP + phosphate """,},'ucsd-rxns' : ['ORNabcpp','LYSabcpp','HISabcpp','ARGabcpp',], 'protein-comments' : ["""NIL""","""(Functions with HisMQP.)""","""(HisPMQJ is an ATP-dependent histidine transport system that is a member of the ATP-Binding
Cassette (ABC) Superfamily of transporters |CITS: [96381453]|. Based on sequence similarity, HisJ is the
periplasmic histidine-binding protein, HisQ and HisM are the integral membrane components, and HisP is
the ATP-binding component of the ABC transport complex |CITS: [98188231]|. Although the transport
properties of the His complex in E. coli have not yet been characterized, extensive investigations on
the orthologous proteins in Salmonella typhimurium have been reported. The His complex of
Salmonella typhimurium was purified and reconstituted into ATP-encapsulated proteoliposomes,
and histidine transport activity was observed |CITS: [97150838]|. His-mediated transport activity is
completely dependent on the presence of all four protein components and on the internal ATP concentration,
with apparent Km of 8 mM for ATP |CITS: [97150838] [89386658]|. The transport activity is
also affected by pH, temperature, and salt concentration |CITS: [97150838]|. Transport is irreversible and
accumulation reaches a plateau at which point transport ceases |CITS: [97150838]|. The transport complex is
inhibited by ADP and by high concentrations of internal histidine |CITS: [97150838]|.)""",]},
'B2802' : {'ecocyc-rxns': {"""DARABISOM-RXN""": """D-arabinose = D-ribulose""","""FUCISOM-RXN""": """L-fucose = L-fuculose""",},'ucsd-rxns' : ['FCI',], 'protein-comments' : ["""(An amber mutation has been generated |CITS: [12853150]|.)""",]},
'B2478' : {'ecocyc-rxns': {"""DIHYDRODIPICSYN-RXN""": """pyruvate + L-aspartate-semialdehyde = 2 H2O + L-2,3-dihydrodipicolinate""",},'ucsd-rxns' : ['DHDPS',], 'protein-comments' : ["""(Lys-161 is the active-site lysine residue of DHDPS. A reaction mechanism has been proposed |CITS: [8993314]|,
and studies of crystal structures of enzymes with mutations in various active site residues have provided further
evidence for a catalytic triad |CITS: [15066435]|.
Transcription of dapA increases in response to diaminopimelic acid limitation |CITS: [15158272]|.)""","""NIL""",]},
'B2574' : {'ecocyc-rxns': {"""QUINOLINATE-SYNTHE-MULTI-RXN""": """L-aspartate + O2 + dihydroxy-acetone-phosphate -> quinolinate + phosphate + H2O2 + 2 H2O""","""L-ASPARTATE-OXID-RXN""": """O2 + L-aspartate -> H2O2 + iminoaspartate""",},'ucsd-rxns' : ['ASPO4','ASPO3','ASPO5','ASPO6',], 'protein-comments' : ["""(L-aspartate oxidase is the first enzyme in the de novo NAD biosynthesis pathway. Quinolinate is the common
precursor of NAD+ and is synthesized from L-aspartate and DHAP in E. coli. This synthesis requires two
enzymes that may work as a multi-enzyme complex. L-aspartate oxidase, coded for by the nadB gene, is an
FAD-dependent enzyme catalyzing the oxidation of L-aspartate to iminoaspartate. Iminoaspartate is then
condensed with DHAP to form quinolinate under the action of quinolinate synthetase A, the gene product of
nadA |CITS: [361684][82098106][88296484]|. In the absence of quinolinate synthetase A, the
iminoaspartate formed by L-aspartate oxidase can spontaneously decay to oxaloacetate. |CITS: [82098106]|
The nadB gene was cloned |CITS: [2841129]| and the NadB enzyme has been overexpressed and purified to
homogeneity |CITS: [2187483]|.
Crystal structures of the apo- and holoenzymes have been determined, suggesting that an unusual
tertiary structure is shared by L-aspartate oxidase, the SdhA subunit of succinate dehydrogenase, and the FrdA
subunit of fumarate reductase |CITS: [10425677][11863440]|.)""","""(A complex of two enzymes that carry out adjacent reactions. The intermediate iminoaspartate is captive in the multi-complex.)""",]},
'B4231' : {'ecocyc-rxns': {},'ucsd-rxns' : ['RIBabcpp',], 'protein-comments' : ["""(membrane component of ABC transporter)""","""(YtfR, YtfS, YjfF, YtfT, and YtfQ are uncharacterized members
of the ABC superfamily of transporters |CITS: [99091701]|.
YtfR and YtfS are the putative ATP-binding components.
YjfF and YtfT are the putative membrane components.
YtfQ is the putative binding protein. Based on sequence
similarity they probably function together as an ATP-dependant
sugar transporter. The genes ytfR, ytfS, yjfF,
ytfT, and ytfQ probably constitute a single operon.)""",]},
'B2579' : {'ecocyc-rxns': {},'ucsd-rxns' : ['PFL','OBTFL',], 'protein-comments' : ["""(The yfiD gene encodes a glycyl radical protein that can replace an oxidatively damaged pyruvate formate-lyase subunit |CITS: [11444864]|. YfiD is expected to be involved in stress resistance |CITS: [10726772]|.
Residue Gly102 is predicted to be the glycyl radical site |CITS: [11444864]|. Pyruvate formate-lyase-activase catalyzes YfiD glycyl radical formation |CITS: [11932447]|. Formation of the YfiD glycyl radical is induced by acidic pH (as is yfiD expression) |CITS: [11932447]|. Pyruvate formate-lyase-deactivase does not appear to catalyze YfiD glycyl radical inactivation |CITS: [11932447]|. YfiD is phosphorylated in L-form (wall-less) E. coli |CITS: [9884220]|.
A yfiD mutant shows a defect in acid homeostasis under low-oxygen conditions |CITS: [11932447]|.
YfiD has similarity to pyruvate formate lyase |CITS: [10094700]|.
Regulation has been described |CITS: [9179852], [9767578], [10094700], [10726772], [11114930], [11169114], [11591692], [12107143], [12949096]|.)""",]},
'B2578' : {'ecocyc-rxns': {"""RXN0-1924""": """L-cysteine[cytosol] =L-cysteine[periplasmic space] ""","""RXN0-1923""": """O-acetyl-L-serine[cytosol] =O-acetyl-L-serine[periplasmic space] """,},'ucsd-rxns' : ['ACSERtpp','CYStpp',], 'protein-comments' : ["""(The yfiK gene product is, as inferred from sequence analysis, an integral membrane protein posessing six
predicted transmembrane helices and belonging to the RhtB family of export proteins. Overproduction of YfiK from a
plasmid results in the secretion of O acetylserine and cysteine into the medium but only when the organism
possesses a serine transacetylase that is feedback insensitive to cysteine |CITS:[12562784]|.)""",]},
'B2472' : {'ecocyc-rxns': {"""SUCCDIAMINOPIMDESUCC-RXN""": """H2O + N-succinyl-L,L-2,6-diaminopimelate = L,L-diaminopimelate + succinate""",},'ucsd-rxns' : ['SDPDS',], 'protein-comments' : ["""NIL""","""(The E. coli N-succinyl-L-diaminopimelate desuccinylase exists as a mixture of homodimers and
homotetramers. It is a metalloenzyme, and requires either Co(II) or Zn(II) for activity.
The enzyme is highly specific for its natural substrate |CITS: [3276674]|.
The dapE gene sequence bears similarity to argE, acetylornithine deacetylase |CITS: [92355499]|.)""",]},
'B2599' : {'ecocyc-rxns': {"""CHORISMATEMUT-RXN""": """chorismate = prephenate""","""PREPHENATEDEHYDRAT-RXN""": """prephenate -> phenylpyruvate + H2O + CO2""",},'ucsd-rxns' : ['CHORM','PPNDH',], 'protein-comments' : ["""NIL""","""(The N-terminal end of this bifunctional protein specifies
the chorismate mutase activity while the remainder of the
sequence specifies the second enzymatic activity, prephenate dehydratase.
The native enzyme is a dimer of identical subunits each containing a
dehydratase active site, a mutase active site and a phenylalanine
binding site.|CITS:[78023876]| The chorismate mutase and prephenate dehydratase
reactions occur at separate active sites. In contrast, the two active
sites of the closely related enzyme chorismate mutase/prephenate
dehydrogenase are interacting sites. |CITS: [85122698]| Studies of the overall
reaction using radioactive chorismate showed that prephenate, which is
formed from chorismate, dissociates from the mutase site and
equilibrates with the bulk medium before combining at the dehydratase
site. Also,the two activities are subject to differential
inhibition. |CITS:[78166022]| Further, the mutase site contains a lysine residue
which is not essential for dehydratase activity and the dehydratase site contains a
cysteine and a threonine residue neither of which is required for
mutase activity. |CITS:[83127414]| Differential inactivation of the
dehydratase and mutase activities by modification
of the most reactive sulfhydryl group provides evidence that the two
activities are catalyzed at separate sites on the enzyme, or at
sites that only overlap slightly. |CITS:[78023874]|)""",]},
'B2476' : {'ecocyc-rxns': {"""SAICARSYN-RXN""": """ATP + 4-carboxyaminoimidazole ribonucleotide + L-aspartate = ADP + phosphate + 5'-phosphoribosyl-4-(N-succinocarboxamide)-5-aminoimidazole""",},'ucsd-rxns' : ['PRASCS',], 'protein-comments' : ["""(Overproduction and purification of PurC |CITS: [1534690]|.)""","""NIL""",]},
'B0008' : {'ecocyc-rxns': {"""TRANSALDOL-RXN""": """D-glyceraldehyde-3-phosphate + D-sedoheptulose-7-phosphate = D-fructose-6-phosphate + D-erythrose-4-phosphate""",},'ucsd-rxns' : ['TALA',], 'protein-comments' : ["""(There are two closely related transaldolases in E. coli.)""","""NIL""",]},
'B1524' : {'ecocyc-rxns': {"""GLUTAMIN-RXN""": """L-glutamine + H2O = L-glutamate + ammonia""",},'ucsd-rxns' : ['GLUN',], 'protein-comments' : ["""(Based on sequence similarity, YneH is predicted to be a glutaminase |CITS: [12952533]|.)""",]},
'B0722' : {'ecocyc-rxns': {"""SUCCINATE-DEHYDROGENASE-(UBIQUINONE)-RXN""": """a ubiquinone + succinate = a ubiquinol + fumarate""",},'ucsd-rxns' : ['SUCDi',], 'protein-comments' : ["""(One of two membrane proteins in the four subunit enzyme. SdhC and SdhD are the large and small subunits of cytochrome
b556, respectively |CITS: [8550613]|.
The b556 type heme bridges both membrane
subunits |CITS: [99417502],[8550613]|. Published reports disagree
about whether mutation of SdhC-[His84] or SdhD-[His71] residues
eliminate coordination of the heme b |CITS: [11259408],[9521736]|. SdhC-[His84]
is involved in interaction with the quinone electron acceptor |CITS: [11259408]|. SdhC-[His84]
and SdhD-[His71] (with the associated heme b) are reported to be dispensable for assembly, while SdhC-[His30] is
required for proper assembly of the membrane-bound enzyme |CITS: [9521736]|.
Mutants lacking SdhC and SdhD show cytoplasmic succinate dehydrogenase activity using artificial electron acceptors,
in contrast to wild-type membrane-associated succinate-ubiquinone oxidoreductase activity |CITS: [8550613], [COLISALII]|.
Despite similar function, hydrophobicity, and protein size, the SdhC and SdhD subunits of succinate dehydrogenase do not share significant sequence identity with the corresponding membrane-binding subunits of fumarate reductase, FrdC and FrdD |CITS: [6383359]|.
Regulation has been described |CITS: [11917098], [10423529], [9720032], [9383149], [9209026], [7860604], [7783618], [8132465], [1885542], [2644240], [3309132], [6388571], [9383149]|.)""","""(SdhA and SdhB alone, devoid of the membrane-bound subunits SdhC and SdhD, exhibit cytoplasmic
succinate dehydrogenase activity that does not use ubiquinone as the electron acceptor |CITS: [COLISALII]|.)""","""(The enzyme has two catalytic subunits (SdhA, SdhB) plus two membrane subunits (SdhC, SdhD).
The succinate oxidation reaction, which is part of the aerobic respiratory chain and part of the Krebs cycle, oxidizes
succinate to fummarate while reducing ubiquinone to ubiquinol. It is closely related to fumarate reductase, which
carries out the reverse reaction. The succinate dehydrogenase and fumarate reductase can replace each other |CITS: [GUEST81]|.
The quinone-binding domains of the two enzymes differ significantly |CITS: [12788489]|.
The enzyme exists as a trimer with a total molecular weight of 360 K Daltons.
The structure of Sdh has been determined at 2.6 Angstroms resolution |CITS: [12560550]|.
The enzyme is specific for the optical isomer fumarate. Electron transfer occurs among
neighboring membrane-bound components of the electron transport chain.
Succinate dehydrogenase is made under aerobic conditions with succinate or acetate
as a carbon source. Enzyme synthesis is regulated by catabolite repression
|CITS: [3309132]|. Activation of the enzyme by covalent attachment of FAD to the SdhA enzyme subunit is promoted
by intermediates of the TCA cycle |CITS: [2659351]|. Expression of the enzyme is negatively controlled, under
conditons of anaaerobic growth, by ArcA and Fnr. These two regulatory proteins act independently |CITS: [9383149]|.
The cytochrome b556 (SdhC and SdhD subunits and heme b) is reported to be required for membrane association and stable activity of the enzyme |CITS: [8550613]|. Proper assembly of the enzyme complex shows a specific requirement for heme iron that is not rescued by other metalloporphyrins |CITS: [11405622]|. One report suggests that mutations that disrupt heme coordination do not disrupt enzyme function |CITS: [9521736]|, whereas another report suggests that the mutant proteins in question do retain heme binding activity |CITS: [11259408]|.
The membrane-associated four-subunit enzyme uses the electron acceptor ubiquinone-8 in vitro |CITS:[2644269]|. SdhC is the ubiquinone binding subunit |CITS: [9822661]|.
A single-step purification of overproduced succinate dehydrogenase is
described |CITS: [2644269]|. The enzyme is purified and separated into a distinct catalytic subcomplex (SdhA and SdhB) and membrane-anchoring activity (SdhC and SdhD) |CITS: [9092498]|. The four-subunit enzyme has been crystallized for structural studies |CITS: [11803025]|.
Succinate dehydrogenase may may play a role in infection, as the enzyme is necessary for succinate-mediated protection of stationary-phase cells from killing by a derivative of a human antimicrobial peptide (BPI) |CITS: [10760151]|.
Fumarate reductase is a similar enzyme, but is made under different
physiological conditions. Fumarate reductase is made under anaerobic
conditions with glucose as a carbon source. Succinate dehydrogenase and
fumarate reductase functions are partially interchangeable if
their regulation is manipulated such that succinate dehydrogenase is produced under
anaerobic conditions or fumarate reductase is produced aerobically |CITS: [6274999] [9811659]|.
)""",]},
'B1208' : {'ecocyc-rxns': {"""2.7.1.148-RXN""": """4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol + ATP = 2-phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol + ADP""",},'ucsd-rxns' : ['CDPMEK',], 'protein-comments' : ["""(IspE is an essential protein that acts in the mevalonate-independent pathway of isopentenyl diphosphate
biosynthesis |CITS: [11115399][Kuzuyama00a]|. IspE catalyzes ATP-dependent phosphorylation of
4-diphosphocytidyl-2-C-methyl-D-erythritol, producing
4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate |CITS: [10655484]|.
A mutant does not grow in complex media |CITS: [11361082]|. EMS-induced point mutants identifying residues
essential for catalytic activity have been isolated |CITS: [12859972]|.
A crystal structure of IspE has been solved at 2 A resolution, revealing the structural basis for substrate specificity
and catalysis. The enzyme crystallizes as a homodimer with a solvent-filled channel |CITS: [12878729]|.
IspE is a member of the GHMP kinase (galactokinase, homoserine kinase, mevalonate kinase, and
phosphomevalonate kinase) family |CITS: [10570138]|. Related proteins are widespread among bacterial pathogens,
indicating potential utility as an antibiotic drug target |CITS: [11361082]|.
)""","""NIL""",]},
'B4053' : {'ecocyc-rxns': {"""ALARACECAT-RXN""": """L-alanine = D-alanine""",},'ucsd-rxns' : ['ALAR',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B4054' : {'ecocyc-rxns': {"""BRANCHED-CHAINAMINOTRANSFERLEU-RXN""": """L-leucine + α-ketoglutarate = 2-ketoisocaproate + L-glutamate""","""TYRAMINOTRANS-RXN""": """p-hydroxyphenylpyruvate + L-glutamate = L-tyrosine + α-ketoglutarate""","""PHEAMINOTRANS-RXN""": """phenylpyruvate + L-glutamate = L-phenylalanine + α-ketoglutarate""",},'ucsd-rxns' : ['LEUTAi','PHETA1','TYRTA',], 'protein-comments' : ["""NIL""","""(This enzyme catalyzes the final reaction in the
biosynthesis of both phenylalanine and
tyrosine. Under normal physiological conditions phenylalanine and
tyrosine synthesis are primarily carried out by the aromatic
aminotransferase, the product of the tyrB gene. Only when the pool
sizes of phenylpyruvate and 4-hydroxyphenylpyruvate become very high
will the aspartate aminotransferase start to contribute to the
synthesis of these two amino acids. |CITS: [77165127]|)""",]},
'B4055' : {'ecocyc-rxns': {"""ACID-PHOSPHATASE-RXN""": """H2O + a phosphate monoester = an alcohol + phosphate""",},'ucsd-rxns' : ['NTD3pp','NTD2pp','R5PPpp','TYRPpp','NTD5pp','NTD4pp','NTD7pp','G2PPpp','NTD6pp','PTHRpp','NTD12pp','NTD1pp','PSP_Lpp','NTD10pp','NTD9pp','NTD11pp','NTD8pp',], 'protein-comments' : ["""(AphA is found at high abundance in vivo |CITS: [9298646]|.)""","""NIL""",]},
'B2678' : {'ecocyc-rxns': {"""ABC-26-RXN""": """ATP + L-proline[periplasmic space] + H2O =ADP + phosphate + L-proline[cytosol] """,},'ucsd-rxns' : ['CRNDabcpp','CRNabcpp','PROabcpp','CTBTabcpp',], 'protein-comments' : ["""NIL""","""(ProVWX, the high-affinity transport system for the osmoprotectant glycine betaine, is a member of the
ATP-Binding Cassette (ABC) Superfamily of transporters |CITS: [96381453]|. Based on sequence similarity,
ProV is the ATP-binding component of the transporter, ProW is the integral membrane component, and
ProX is the periplasmic binding component of the ABC transporter. The periplasmic protein, ProX, was
purified to homogeneity, and transport assays with the purified protein shows that it binds glycine betaine with
a high affinity (Kd of 1μM) |CITS: [87308168]|. This indicates that the ProVWX system is
well suited to scavenge glycine betaine from the environment efficiently and to achieve high intracellular
concentrations of this osmoprotectant. Many other osmoprotectants (e.g. proline, taurine, and ectoine) can
also be transported via the ProVWX transporter at lower affinities |CITS: [94280886]|. The genetic regulation
of proVWX statement has been studied using lacZ and phoA gene fusions, and it was
revealed that statement of the operon is low under regular osmotic conditions, but increases substantially at
high osmolarity |CITS: [94280886]|. The intracellular accumulation of glycine betaine by E. coli
permits growth in a high-osmolarity environment, which would otherwise strongly inhibit the proliferation of
the bacterial cells |CITS: [96381453]|. Glycine betaine is transported through both the ProVWX system and
the ProP transporter in E. coli.)""",]},
'B2679' : {'ecocyc-rxns': {"""ABC-26-RXN""": """ATP + L-proline[periplasmic space] + H2O =ADP + phosphate + L-proline[cytosol] """,},'ucsd-rxns' : ['CRNDabcpp','CRNabcpp','PROabcpp','CTBTabcpp',], 'protein-comments' : ["""NIL""","""(ProVWX, the high-affinity transport system for the osmoprotectant glycine betaine, is a member of the
ATP-Binding Cassette (ABC) Superfamily of transporters |CITS: [96381453]|. Based on sequence similarity,
ProV is the ATP-binding component of the transporter, ProW is the integral membrane component, and
ProX is the periplasmic binding component of the ABC transporter. The periplasmic protein, ProX, was
purified to homogeneity, and transport assays with the purified protein shows that it binds glycine betaine with
a high affinity (Kd of 1μM) |CITS: [87308168]|. This indicates that the ProVWX system is
well suited to scavenge glycine betaine from the environment efficiently and to achieve high intracellular
concentrations of this osmoprotectant. Many other osmoprotectants (e.g. proline, taurine, and ectoine) can
also be transported via the ProVWX transporter at lower affinities |CITS: [94280886]|. The genetic regulation
of proVWX statement has been studied using lacZ and phoA gene fusions, and it was
revealed that statement of the operon is low under regular osmotic conditions, but increases substantially at
high osmolarity |CITS: [94280886]|. The intracellular accumulation of glycine betaine by E. coli
permits growth in a high-osmolarity environment, which would otherwise strongly inhibit the proliferation of
the bacterial cells |CITS: [96381453]|. Glycine betaine is transported through both the ProVWX system and
the ProP transporter in E. coli.)""",]},
'B2676' : {'ecocyc-rxns': {"""RXN0-748""": """GDP + a reduced glutaredoxin 1 = dGDP + an oxidized glutaredoxin 1 + H2O""","""RXN0-747""": """ADP + a reduced glutaredoxin 1 = dADP + an oxidized glutaredoxin 1 + H2O""","""RXN0-722""": """UDP + a reduced glutaredoxin 1 = dUDP + an oxidized glutaredoxin 1 + H2O""","""RXN0-1""": """an acceptor + H2O + a 2'-deoxyribonucleoside diphosphate = a reduced acceptor + a ribonucleoside diphosphate""","""RIBONUCLEOSIDE-DIP-REDUCTII-RXN""": """CDP + a reduced glutaredoxin 1 = dCDP + an oxidized glutaredoxin 1 + H2O""",},'ucsd-rxns' : ['RNDR2b','RNDR2b','RNDR2b','RNDR2b','RNDR3b','RNDR3b','RNDR3b','RNDR3b','RNDR1b','RNDR1b','RNDR1b','RNDR1b','RNDR4b','RNDR4b','RNDR4b','RNDR4b',], 'protein-comments' : ["""(Expression of the nrdHIEF operon is increased by hydroxyurea |CITS: [8820648]| and oxidative stress
|CITS: [11278973]|. Expression is highest in minimal medium and in early log phase growth in complex medium;
deletion of Trx1 and Grx1 (trxA- grxA-) increases expression more than
100-fold |CITS: [11278973]|. nrdHIEF belongs to the Fur regulon |CITS: [11101675]|.
)""","""NIL""","""(The NrdE and NrdF proteins constitute a second ribonucleotide reductase (RDPR-II) in E. coli and
S. typhimurium. The enzyme has been studied in Salmonella. The Salmonella enzyme uses
dithiothreitol or reduced glutaredoxin as the electron donor instead of thioredoxin. The allosteric regulation of
RDPR-II also differs from the normally expressed RDPR-I enzyme |CITS: [95108064]|.
Review: |CITS: [15158709]|)""",]},
'B2677' : {'ecocyc-rxns': {"""ABC-26-RXN""": """ATP + L-proline[periplasmic space] + H2O =ADP + phosphate + L-proline[cytosol] """,},'ucsd-rxns' : ['CRNDabcpp','CRNabcpp','PROabcpp','CTBTabcpp',], 'protein-comments' : ["""NIL""","""(ProVWX, the high-affinity transport system for the osmoprotectant glycine betaine, is a member of the
ATP-Binding Cassette (ABC) Superfamily of transporters |CITS: [96381453]|. Based on sequence similarity,
ProV is the ATP-binding component of the transporter, ProW is the integral membrane component, and
ProX is the periplasmic binding component of the ABC transporter. The periplasmic protein, ProX, was
purified to homogeneity, and transport assays with the purified protein shows that it binds glycine betaine with
a high affinity (Kd of 1μM) |CITS: [87308168]|. This indicates that the ProVWX system is
well suited to scavenge glycine betaine from the environment efficiently and to achieve high intracellular
concentrations of this osmoprotectant. Many other osmoprotectants (e.g. proline, taurine, and ectoine) can
also be transported via the ProVWX transporter at lower affinities |CITS: [94280886]|. The genetic regulation
of proVWX statement has been studied using lacZ and phoA gene fusions, and it was
revealed that statement of the operon is low under regular osmotic conditions, but increases substantially at
high osmolarity |CITS: [94280886]|. The intracellular accumulation of glycine betaine by E. coli
permits growth in a high-osmolarity environment, which would otherwise strongly inhibit the proliferation of
the bacterial cells |CITS: [96381453]|. Glycine betaine is transported through both the ProVWX system and
the ProP transporter in E. coli.)""",]},
'B3093' : {'ecocyc-rxns': {"""TRANS-RXN-123""": """H+[periplasmic space] + galacturonate[periplasmic space] =galacturonate[cytosol] + H+[cytosol] ""","""TRANS-RXN-35""": """H+[periplasmic space] + glucuronate[periplasmic space] =H+[cytosol] + glucuronate[cytosol] """,},'ucsd-rxns' : ['GLCURt2rpp','GALURt2rpp',], 'protein-comments' : ["""(ExuT is a transporter for aldohexuronates such as D-galacturonate and
D-glucuronate. Mutations affecting the transport of hexuronates have
been shown to map to the exuT gene |CITS: [83218546]|.
ExuT is a member of the major facilitator superfamily (MFS) of
transporters |CITS: [98190790]| and probably functions as an
aldohexuronate/proton symporter. The exuT gene constitutes a
hexuronate-inducible single gene operon, whose expression is controlled
by the ExuR regulator |CITS: [81006687]|. Imported hexuronates are
initially metabolised to 2-keto-3-deoxy-D-gluconate.)""",]},
'B3092' : {'ecocyc-rxns': {"""GLUCUROISOM-RXN""": """glucuronate = fructuronate""","""GALACTUROISOM-RXN""": """galacturonate = D-tagaturonate""",},'ucsd-rxns' : ['GUI2','GUI1',], 'protein-comments' : ["""(Uronate isomerase catalyzes the initial step of isomerization of the alduronic to the keturonic acid in the glucuronate
and galacturonate degradation pathways.
Cofactor requirements of the enzyme are unclear; the initial report of purification of the enzyme states that
Zn2+ inhibits the enzyme |CITS: [AshwellJBC235,1559]|, while a later report states that uronate
isomerase is a metalloenzyme, with Zn2+ as the likely physiologically relevant cofactor
|CITS: [15358357]|.
)""",]},
'B2904' : {'ecocyc-rxns': {"""GCVMULTI-RXN""": """NAD+ + glycine + tetrahydrofolate = 5,10-methylene-THF + ammonia + CO2 + NADH""",},'ucsd-rxns' : ['GLYCL',], 'protein-comments' : ["""(The H-protein, coded for by the gcvH gene, is a
lipoylprotein that is reduced as it shuttles the
methylamine group of glycine from the P-protein to the T-protein and
is reoxidized by the dihydrolipoamide dehydrogenase. GcvH functions
as a substrate for the three enzymes of the gcv complex.
Residues 61-65 are predicted to contain the lipoyl modification (on lysine), based on conservation of these residues and their correspondence to the lipoate attachment site of the Pisum sativum protein |CITS: [1802033]|.
The interaction between GcvH and GcvT has been examined |CITS: [10491090], [12531904]|. Interaction between the two proteins may be necessary to form the folate binding site, in which the folate polyglutamyl region binds, exposing the pteridine ring |CITS: [12531904]|. The GcvT N terminus is important for interaction with GcvH, probably by mediating a conformational change, and residue D43 of GcvH is proximal to GcvT in the GcvH-GcvT complex |CITS: [10491090]|.
Glycine cleavage system (gcv) mutations cause a defect in utilization of glycine to form serine |CITS: [6358793]|.
GcvH has similarity to the glycine cleavage H-proteins of Pisum sativum (pea) and chicken liver |CITS: [1802033]|. Bovine |CITS: [1400316]| or Pisum sativum (pea) |CITS: [8617275]| glycine cleavage H-protein can be lipoylated upon production in E. coli.
Purification and overproduction of the enzymes of the glycine cleavage system have been described |CITS: [8375392]|.
Regulation has been described |CITS: [8375392], [8219277], [8181752], [3023185], [8423160], [8349552], [8188587], [7928983], [7894704], [7665470], [7665475], [11495998], [12101307]|.
Review: |CITS: [2643922]|.
)""","""NIL""","""NIL""","""NIL""","""(The glycine cleavage system is a multi-enzyme complex that
catalyzes the reversible oxidation of glycine and generates a C1 moiety. It is the second
major source of C1 units in the cell after serine hydroxymethyl
transferase.
One of the four
subunits, lipoamide dehydrogenase (E3), is shared with pyruvate
dehydrogenase and 2-oxoglutarate dehydrogenase.)""",]},
'B1207' : {'ecocyc-rxns': {"""PRPPSYN-RXN""": """ATP + D-ribose-5-phosphate = 5-phosphoribosyl 1-pyrophosphate + AMP""",},'ucsd-rxns' : ['PRPPS',], 'protein-comments' : ["""NIL""",]},
'B2907' : {'ecocyc-rxns': {"""2-OCTAPRENYL-6-METHOXYPHENOL-HYDROX-RXN""": """2-octaprenyl-6-methoxyphenol + O2 = H2O + 2-octaprenyl-6-methoxy-1,4-benzoquinone""",},'ucsd-rxns' : ['OMPHHX',], 'protein-comments' : ["""NIL""",]},
'B4119' : {'ecocyc-rxns': {"""ALPHAGALACTOSID-RXN""": """H2O + melibiose = β-D-glucose + β-D-galactose""",},'ucsd-rxns' : ['GALS3',], 'protein-comments' : ["""(Alpha-galactosidase was previously thought to be a tetramer, but is now believed to be a
dimer. |CITS: [88162811]|
An amber mutation has been generated |CITS: [12853150]|.)""","""NIL""",]},
'B1478' : {'ecocyc-rxns': {"""ALCOHOL-DEHYDROG-RXN""": """acetaldehyde + NADH = ethanol + NAD+""","""ALCOHOL-DEHYDROG-GENERIC-RXN""": """an alcohol + NAD+ = NADH + an aldehyde or ketone""",},'ucsd-rxns' : ['ALCD2x',], 'protein-comments' : ["""(AdhP is an ethanol-active medium-chain alcohol dehydrogenase/reductase. The enzyme is even more efficient in
the reverse direction of acetaldehyde reduction |CITS: [99337666]|.
AdhP did not show dehydrogenase activity in a high-throughput screen of purified proteins |CITS: [15808744]|.
Expression of AdhP is inducible by ethanol |CITS: [10406936]|.)""",]},
'B4132' : {'ecocyc-rxns': {"""TRANS-RXN-68""": """L-lysine[periplasmic space] + cadaverine[cytosol] + H+[periplasmic space] =L-lysine[cytosol] + cadaverine[periplasmic space] + H+[cytosol] """,},'ucsd-rxns' : ['CADVtpp',], 'protein-comments' : ["""(CadB is a probable lysine/cadaverine antiporter that is a member of the Amino Acid Polyamine
Organocation (APC) superfamily. The cadB gene is located on the same operon with cadA,
which encodes the lysine decarboxylase. Primer extension assays suggest that expression of the
cadBA operon is controlled by extracellular pH and lysine |CITS:[96404804]|. CadB is believed to
export cadaverine and import lysine and a proton via an antiport mechanism |CITS: [92210511]|. A
colorimetric assay measuring cadaverine excretion showed that cadaverine accumulated in the external
medium at pH 5.5, but not at pH 8, and not in the absence of CadA |CITS: [92210511]|. A CadB-minus
strain showed significant decrease in cadaverine excretion even in the presence of CadA
|CITS: [92210511]|. CadB, therefore, appears to function as a lysine/cadaverine antiporter, bringing in
lysine and excreting cadaverine, the end product of the CadA (lysine decarboxylase)-catalyzed
enzymatic reaction |CITS: [92210511]|. In order to balance the electrochemical charge inside the cell,
CadB may take in protons from the medium at the same time that it imports lysine into the cell
|CITS: [92210511]|. CadB has similarity to the Pseudomonas aeruginosa ArcD arginine/ornithine
antiporter |CITS: [92210511]|.)""",]},
'B1773' : {'ecocyc-rxns': {},'ucsd-rxns' : ['FBA',], 'protein-comments' : ["""(No information about this protein was found by a literature search conducted on December 28, 2005.
)""",]},
'B3577' : {'ecocyc-rxns': {},'ucsd-rxns' : ['XYLUt2pp',], 'protein-comments' : ["""(Based on sequence similarity, YiaM is a membrane-spanning component of the YiaMNO Binding Protein-dependent Secondary (TRAP) Transporter |CITS:[11524131]|)""","""(Based on sequence similarity, the yiaMNO genes encode the only tri-partite
ATP-independent periplasmic (TRAP) transporter in Escherichia coli. The TRAP
transporters share characteristics of both the ATP-binding cassette (ABC) and secondary
families of transporters |CITS:[11524131]|. Like the ABC transporters TRAP
transporters use an extracytoplasmic solute-binding protein but rather than ATP hydrolysis
the driving force is provided by either proton-(pmf) and/or sodium ion motive
force (smf) |CITS:[11524131]|. Based on sequence similarity, YiaO is the periplasmic
solute-binding protein and YiaM and YiaN are membrane-spanning proteins.
Deletion mutation experiments |CITS:[14668138]| showed that deletion of the yiaMNO
genes affected the ability of E.coli to utilize L-xylulose when
growth was measured using various carbon substrates. Solute transport studies
|CITS:[14668138]| determined that the yiaMNO deletion strain was capable
of utilizing L-xylulose but at a lower rate, indicating that the YiaMNO transporter is
involved in, but not essential for L-xylulose utilization. Purification and binding
studies |CITS:[14668138]| using YiaO showed that YiaO was able to bind L-xylulose.
Furthermore, spheroblasts expressing the YiaMN membrane domains were
stimulated to increase uptake of L-xylulose when incubated with the periplasmic
substrate-binding YiaO while those spheroblasts not expressing YiaMN showed no
such stimulation. Deletion of yiaMNO resulted in a delay of entry into stationary phase of cells
grown in LB with glucose, or minimal medium with glucose or other compounds. These cultures obtained a
higher stationary phase OD660 and higher c.f.u. numbers. Deletion of yiaMNO also
resulted in an increased lag time in cultures with high NaCl concentrations, and a reduction in biofilm
formation in minimal medium with glucose |CITS:[15870475]|.)""",]},
'B4111' : {'ecocyc-rxns': {"""TRANS-RXN-29A""": """H+[periplasmic space] + glycine betaine[periplasmic space] =H+[cytosol] + glycine betaine[cytosol] ""","""TRANS-RXN-29""": """H+[periplasmic space] + L-proline[periplasmic space] =H+[cytosol] + L-proline[cytosol] """,},'ucsd-rxns' : ['CTBTt2rpp','CRNDt2rpp','CRNt2rpp','PROt2rpp',], 'protein-comments' : ["""(ProP is a osmoprotectant/proton symporter capable of transporting
proline and glycine betaine. Studies in whole cells and membrane
vesicles have shown that ProP-mediated proline transport is inhibited
by protonophores |CITS: [89008366]| and ProP binds proline with a low
affinity (Km = 0.3 μM) |CITS: [80159844]|. ProP has also been
suggested to transport the osmoprotectants taurine |CITS: [91357464]|,
ectoine |CITS: [92332438]| and carnitine |CITS: [99088491]|.
ProP has been overproduced, purified and reconstituted in liposomes
as an active transporter. ProP-mediated transport in liposomes
required both the membrane potential and an osmotic upshift, suggesting
it functions as both a transporter and an osmosensor |CITS: [99152354]|.
ProP is a member of the major facilitator superfamily (MFS) of
transporters |CITS: [93040298]|.
Expression of proP is increased by osmotic upshock, amino acid
limitation and stationary phase |CITS: [95095960]|. ProP mediates the
uptake of osmoprotectants to adapt to increases in osmotic pressure.)""",]},
'B0680' : {'ecocyc-rxns': {"""GLUTAMINE--TRNA-LIGASE-RXN""": """tRNAgln + L-glutamine + ATP = L-glutaminyl-tRNAgln + diphosphate + AMP""",},'ucsd-rxns' : ['GLNTRS',], 'protein-comments' : ["""(Glutaminyl-tRNA synthetase (GlnRS) is a member of the family of aminoacyl tRNA synthetases, which interpret the
genetic code by covalently linking amino acids to their specific tRNA molecules. The reaction is driven by ATP
hydrolysis. GlnRS belongs to the Class I aminoacyl tRNA synthetases; apart from sequence motifs within the active
site, the different enzymes show little similarity in their primary amino acid sequences.
Sites required for the accurate recognition of the cognate tRNA have been identified |CITS: [7506418][8027995]|.
Various crystal structures of GlnRS have been solved |CITS: [1857417][2479982][8942633][12691748][12737824]|.
GlnRS enzyme levels increase with increasing growth rate |CITS: [2578447]|. GlnRS expression is regulated at the
transcriptional as well as posttranscriptional levels |CITS: [2578447][2186926][1681509]|. Overexpression of
wild-type GlnRS leads to mischarging of su+3 tRNATyr |CITS: [6389180]|.
Review: |CITS: [1725262]|)""",]},
'B1475' : {'ecocyc-rxns': {"""FORMATEDEHYDROG-RXN""": """formate + menaquinone-8 = CO2 + menaquinol""",},'ucsd-rxns' : ['FDH4pp','FDH5pp',], 'protein-comments' : ["""(FdnH contains four [4Fe-4S] clusters and one C-terminal transmembrane helix |CITS: [1834669][11884747]|. FdnH
serves as a conduit for electrons that are transferred from the formate oxidation site in FdnG to the menaquinone
associated with the FdnI subunit of formate dehydrogenase-N |CITS: [11884747]|.)""","""NIL""","""(The proton motive force (PMF), composed of an electrochemical gradient and a concentration difference of protons
across the inner membrane, allows generation of the ubiquitous energy carrier ATP by ATP synthase. The PMF itself
can be generated by oxidative phosphorylation, using molecular oxygen as the terminal electron acceptor.
In addition to molecular oxygen, E. coli can use alternative terminal electron acceptors to generate the PMF.
Formate dehydrogenase-N is part of one such system. Expression of formate dehydrogenase-N is induced by
nitrate and anaerobiosis, mediated by NarL and Fnr, respectively |CITS: [2168848][12923080]|. Formate
dehydrogenase-N oxidizes formate in the periplasm, transferring electrons via the quinone pool in the cytoplasmic
membrane to nitrate reductase, which transfers electrons to nitrate in the cytoplasm
|CITS: [4905536][4616697][Jones80]|.
Formate dehydrogenase-N is one of three formate dehydrogenases in E. coli |CITS: [7747941]|.
A crystal structure of formate dehydrogenase-N has been determined at 1.6 A resolution |CITS: [11884747]|.
Review: |CITS: [12788488]|)""",]},
'B1474' : {'ecocyc-rxns': {"""FORMATEDEHYDROG-RXN""": """formate + menaquinone-8 = CO2 + menaquinol""",},'ucsd-rxns' : ['FDH4pp','FDH5pp',], 'protein-comments' : ["""(FdnG is the catalytic subunit of formate dehydrogenase-N. It contains the bis-molybdopterin guanine
dinucleotide (MGD) cofactor and selenocysteine |CITS: [1834669]|.
FdnG is translocated to the periplasm via the Tat system; interaction with the FdnI subunit localizes the protein to the
periplasmic face of the cytoplasmic membrane |CITS: [9649434][11929547]|.
Production of FdnG is regulated at the translational level. A segment of the mRNA encoding the N terminus of FdnG
is able to form a stable stem-loop structure; disruption of the structure by site-directed mutagenesis leads to
overproduction of FdnG-β-galactosidase and FdnG-CAT translational fusion proteins; if such mutations are
introduced at the chromosomal fdnG locus, formate dehydrogenase-N activity increases |CITS: [15342602]|.)""","""NIL""","""(The proton motive force (PMF), composed of an electrochemical gradient and a concentration difference of protons
across the inner membrane, allows generation of the ubiquitous energy carrier ATP by ATP synthase. The PMF itself
can be generated by oxidative phosphorylation, using molecular oxygen as the terminal electron acceptor.
In addition to molecular oxygen, E. coli can use alternative terminal electron acceptors to generate the PMF.
Formate dehydrogenase-N is part of one such system. Expression of formate dehydrogenase-N is induced by
nitrate and anaerobiosis, mediated by NarL and Fnr, respectively |CITS: [2168848][12923080]|. Formate
dehydrogenase-N oxidizes formate in the periplasm, transferring electrons via the quinone pool in the cytoplasmic
membrane to nitrate reductase, which transfers electrons to nitrate in the cytoplasm
|CITS: [4905536][4616697][Jones80]|.
Formate dehydrogenase-N is one of three formate dehydrogenases in E. coli |CITS: [7747941]|.
A crystal structure of formate dehydrogenase-N has been determined at 1.6 A resolution |CITS: [11884747]|.
Review: |CITS: [12788488]|)""",]},
'B4117' : {'ecocyc-rxns': {"""ARGDECARBOX-RXN""": """L-arginine = CO2 + agmatine""",},'ucsd-rxns' : ['ARGDC',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B1476' : {'ecocyc-rxns': {"""FORMATEDEHYDROG-RXN""": """formate + menaquinone-8 = CO2 + menaquinol""",},'ucsd-rxns' : ['FDH4pp','FDH5pp',], 'protein-comments' : ["""(FdnI, the membrane subunit of formate dehydrogenase-N, contains two heme b556 groups and a site
for menaquinone reduction. It contains four transmembrane helices, which, together with the single transmembrane
helix of FdnH and a cardiolipin molecule, form a tightly packed trimer in the inner membrane
|CITS: [1834669][11884747]|.)""","""NIL""","""(The proton motive force (PMF), composed of an electrochemical gradient and a concentration difference of protons
across the inner membrane, allows generation of the ubiquitous energy carrier ATP by ATP synthase. The PMF itself
can be generated by oxidative phosphorylation, using molecular oxygen as the terminal electron acceptor.
In addition to molecular oxygen, E. coli can use alternative terminal electron acceptors to generate the PMF.
Formate dehydrogenase-N is part of one such system. Expression of formate dehydrogenase-N is induced by
nitrate and anaerobiosis, mediated by NarL and Fnr, respectively |CITS: [2168848][12923080]|. Formate
dehydrogenase-N oxidizes formate in the periplasm, transferring electrons via the quinone pool in the cytoplasmic
membrane to nitrate reductase, which transfers electrons to nitrate in the cytoplasm
|CITS: [4905536][4616697][Jones80]|.
Formate dehydrogenase-N is one of three formate dehydrogenases in E. coli |CITS: [7747941]|.
A crystal structure of formate dehydrogenase-N has been determined at 1.6 A resolution |CITS: [11884747]|.
Review: |CITS: [12788488]|)""",]},
'B2889' : {'ecocyc-rxns': {"""IPPISOM-RXN""": """Δ3-isopentenyl-PP = dimethylallyl-pyrophosphate""",},'ucsd-rxns' : ['IPDDI',], 'protein-comments' : ["""NIL""",]},
'B2156' : {'ecocyc-rxns': {"""TRANS-RXN-58""": """L-lysine[periplasmic space] + H+[periplasmic space] =L-lysine[cytosol] + H+[cytosol] """,},'ucsd-rxns' : ['LYSt2pp',], 'protein-comments' : ["""(LysP is one of two principal systems responsible for the uptake of
lysine, the other is the ArgT ABC transporter. LysP is specific for
lysine while ArgT also transports arginine and ornithine. Inactivation of the
lysP gene decreased lysine accumulation and could be complemented by
the cloned lysP gene |CITS: [92250419]|. LysP-mediated lysine
transport is increased by growth in acidic media, anaerobiosis or high
concentrations of lysine |CITS: [92250419]|.
Topological analysis using B-lactamase fusions has shown that LysE
consists of 12 transmembrane segments |CITS: [96032017]|. LysE is a member
of the APC superfamily of amino acid transporters and probably functions
as a lysine/proton symporter.
In the absence of exogenous lysine, LysP has been shown to affect the
expression of the cadB, encoding a cadaverine/lysine antiporter
|CITS: [94252996]|.)""",]},
'B2703' : {'ecocyc-rxns': {"""TRANS-RXN-169""": """phosphoenolpyruvate + D-sorbitol[periplasmic space] =D-sorbitol-6-phosphate[cytosol] + pyruvate """,},'ucsd-rxns' : ['SBTptspp',], 'protein-comments' : ["""(contains PTS Enzyme IIB and IIC2 domains)""","""(GutABE, the glucitol PTS permease, belongs to the functional superfamily
of the phosphoenolpyruvate (PEP)-dependent, sugar transporting
phosphotransferase system (PTS). The PTS transports and simultaneously
phosphorylates its sugar substrates in a process called group
translocation. GutAB takes up exogenous glucitol, releasing the
phosphate ester into the cell cytoplasm in preparation for oxidation
to fructose-6-P and subsequent metabolism, primarily via glycolysis
|CITS: [94066914]|.
GutABE comprises the Enzyme IIGut complex. The
enzyme possesses a split IIC domain unlike all other characterized Enzyme
II complexes of the PTS |CITS: [94066914]|. GutA is a (putative) 4 TMS integral
membrane protein of 187 amino acyl residues. GutE is a larger protein of
319 residues that includes the hydrophilic IIB domain fused to a
hydrophobic (putative) 4 TMS domain |CITS: [97035393]|. GutB is the hydrophilic IIA
domain. Thus, the integral membrane IIC constituent of the glucitol
permease is split in half and encoded by two distinct genes, gutA and gutE.
gutB and gutE, respectively, encode the IIA and IIB constituents.
The IIB domain of GutE and the IIA (GutB) protein are localized to the
cytoplasmic side of the membrane. The overall PTS-mediated phosphoryl
transfer reaction, requiring the two general energy coupling proteins of
the PTS, Enzyme I and HPr, as well as the three domains of the Enzyme II
complex is:
PEP --> Enzyme I(his~~P)
--> HPr(his~~P)
--> IIA(his~~P) -->
IIB(cys~~P) -(IIC)-> glucitol-6-P.
GutABE transports glucitol with low micromolar affinities.
The gut operon is inducible in wild type E. coli K12
by the presence of exogenous glucitol. The gut operon
(gutABDMRQ) contains the gutA, gutB and gutE genes,
encoding the Enzyme IIGut complex, and the
gutD gene encoding glucitol-6-P dehydrogenase that oxidizes
glucitol-6-P to fructose-6-P. GutM and GutR are positive and
negative transcriptional regulators of gut operon expression,
respectively |CITS: [89094828]|. The function of GutQ is not known |CITS: [89094828]|. gut
operon expression is under the control of the cyclic AMP-cyclic
AMP receptor protein (CRP) complex.
)""",]},
'B0583' : {'ecocyc-rxns': {"""ENTMULTI-RXN""": """6 ATP + 3 L-serine + 3 2,3-dihydroxybenzoate = 6 diphosphate + 6 AMP + enterobactin""","""ENTDB-RXN""": """coenzyme A + apo-EntB = aryl carrier protein / isochorismatase + 3',5'-ADP""","""ENTD-RXN""": """coenzyme A + apo-serine activating enzyme = 3',5'-ADP + serine activating enzyme""",},'ucsd-rxns' : ['ENTCS',], 'protein-comments' : ["""(AcpS is the founding member of a 4'-phosphopantetheinyl (P-pant) transferase protein family that includes E. coli EntD, E. coli o195 protein, and Bacillus subtilis Sfp; family members share two conserved motifs but relatively low sequence identity overall |CITS: [8939709]|.)""","""NIL""",]},
'B3612' : {'ecocyc-rxns': {"""3PGAREARR-RXN""": """3-phosphoglycerate = 2-phosphoglycerate""",},'ucsd-rxns' : ['PGM',], 'protein-comments' : ["""NIL""",]},
'B2883' : {'ecocyc-rxns': {"""GUANINE-DEAMINASE-RXN""": """H2O + guanine = ammonia + xanthine""",},'ucsd-rxns' : ['GUAD',], 'protein-comments' : ["""(YgfP has 36% identity to human guanine deaminase |CITS: [10913105]| and similarity to allantoate amidohydrolase |CITS: [10986234]|.)""",]},
'B1302' : {'ecocyc-rxns': {"""GABATRANSAM-RXN""": """α-ketoglutarate + 4-aminobutyrate = L-glutamate + succinate semialdehyde""",},'ucsd-rxns' : ['ABTA',], 'protein-comments' : ["""(PuuE was identified as a putrescine-inducible GABA aminotransferase, which allows cells to grow on putrescine as
the sole source of nitrogen even in the absence of GabT |CITS: [15590624]|.
The function of genes in the puu gene cluster was initially inferred by similarity with the ipuABCDEGFH
operon in Pseudomonas sp. |CITS: [15590624]|)""",]},
'B0521' : {'ecocyc-rxns': {},'ucsd-rxns' : ['CBMKr',], 'protein-comments' : ["""(The Pseudomonas aeruginosa ArcC carbamate kinase has been characterized |CITS: [3040889], [2537202]|.)""",]},
'B0522' : {'ecocyc-rxns': {"""RXN0-742""": """5-aminoimidazole ribonucleotide + ATP + H2O + CO2 = N5-carboxyaminoimidazole ribonucleotide + ADP + phosphate""",},'ucsd-rxns' : ['AIRC2',], 'protein-comments' : ["""(PurK and PurE were previously thought to be two subunits of AIR carboxylase |CITS: [89123019]|,
though more recent
studies have shown the enzymes to be subunits of a distinct carboxylase and mutase,
respectively |CITS: [8117684]|.
Crystal structures determined of PurK in complex with sulfate and Mg-ADP |CITS: [10569930]|.
While this protein is a member of the ATP grasp superfamily, it lacks conservation within
the substrate specificity (Omega) loop |CITS: [10569930]| .
PurK exhibits AIR-dependent
ATPase activity that does not show
bicarbonate dependence and AIR is
not carboxylated during ATP hydrolysis |CITS:[1534690]|. High
concentration of HCO3- partially rescues the defect of a purK mutant
in growth in the absence of purines, probably by perturbing the balance of AIR toward N5-CAIR, and overproduction of PurE further increases rescue
in the presence of HC03- |CITS: [7918411]|. Nonenzymatic carboxylation
of AIR occurs, though, under physiological
conditions, ATP must be added as a second substrate for AIR
carboxylation reaction to occur in E. coli. PurK is required for AIR conversion to CAIR under low HCO3- concentrations |CITS: [89123019]|.
Overproduction and purification of PurK |CITS: [1534690]|.
The analysis of the purE locus at the nucleotide
sequence level disclosed that purE1 and purE2 cistrons correspond to
two distinct, overlapping genes, purE and purK |CITS: [2644189]|.)""","""NIL""",]},
'B0523' : {'ecocyc-rxns': {"""RXN0-743""": """N5-carboxyaminoimidazole ribonucleotide = 4-carboxyaminoimidazole ribonucleotide""",},'ucsd-rxns' : ['AIRC3',], 'protein-comments' : ["""(PurK and PurE were previously thought to be two subunits of AIR carboxylase |CITS: [89123019]|,
though more recent
studies have shown the enzymes to be subunits of a distinct carboxylase and mutase,
respectively |CITS: [8117684]|.
Crystal structure of octameric enzyme determined with and without CAIR substrate |CITS: [10574791]|.
Reaction is reversible |CITS: [10074353]|. Reaction mechanism (direct carboxylate transfer) discussed |CITS: [10074353]|.
High
concentration of HCO3- partially rescues the defect of a purK mutant
in growth in the absence of purines, probably by perturbing the balance of AIR toward N5-CAIR, and overproduction of PurE further increases rescue
in the presence of HC03- |CITS: [7918411]|.
Overproduction and purification |CITS: [1534690]|.
The analysis of the purE locus at the nucleotide
sequence level disclosed that purE1 and purE2 cistrons correspond to
two distinct, overlapping genes, purE and purK |CITS: [2644189]|.)""","""NIL""",]},
'B0524' : {'ecocyc-rxns': {"""LIPIDXSYNTHESIS-RXN""": """H2O + UDP-2,3-bis(3-hydroxymyristoyl)glucosamine = 2,3-bis(3-hydroxymyristoyl)-β-D-glucosaminyl 1-phosphate + UMP""",},'ucsd-rxns' : ['USHD',], 'protein-comments' : ["""(LpxH is essential for growth |CITS: [12000771]|.
LpxH and CDP-diglyceride hydrolase (Cdh) show redundant activity in vitro, but Cdh does not substitute for LpxH in vivo |CITS:[12000771]|.
Similar proteins are found in Gram-negative bacteria, but not in Gram-positive bacteria |CITS: [12000770]|. LpxH has 51% identity to a putative protein from Haemophilus influenzae |CITS: [12000770]|. A Pseudomonas aeruginosa homolog functionally complements the inviability of an mutant |CITS:[12000771]|.
Purification of LpxH is described |CITS: [12000770]|.
LpxH: Lipid X (2,3-diacylglucosamine-1-phosphate) |CITS: [12000770]|.
)""",]},
'B0526' : {'ecocyc-rxns': {"""CYSTEINE--TRNA-LIGASE-RXN""": """tRNAcys + L-cysteine + ATP -> L-cysteinyl-tRNAcys + diphosphate + AMP""",},'ucsd-rxns' : ['CYSTRS',], 'protein-comments' : ["""(Cysteinyl-tRNA synthetase (CysRS) is a member of the family of aminoacyl-tRNA synthetases, which interpret the
genetic code by covalently linking amino acids to their specific tRNA molecules. The reaction is driven by ATP
hydrolysis. CysRS belongs to the Class I aminoacyl tRNA synthetases |CITS: [2203971][7647112]|.
CysRS is a monomer in solution |CITS: [2014166]|. The N-terminal domain of CysRS is active in adenylate synthesis,
while the C-terminal domain is able to bind and discriminate tRNA. The two domains can not complement each other
in trans, showing that full enzymatic activity requires covalent continuity |CITS: [15882062]|.
Specificity determinants within tRNACys that are important for recognition by CysRS have been
identified |CITS: [1373131][8341698][8338841][8643362][7585255][11054287][11160931]|. Specificity determinants
and residues within CysRS that are important for catalytic activity have been investigated |CITS: [8916927]|.
A crystal structure of CysRS bound to tRNACys was determined at 2.3 Å resolution, showing
extensive base-selective and shape-specific RNA-protein interactions |CITS: [15489861]|. The efficiency of CysRS
aminoacylation is modulated by the G15-G48 Levitt pair together with tertiary nucleotides surrounding it in
tRNACys |CITS: [10860750]|.
Unlike other aminoacyl-tRNA synthetases, CysRS does not possess an editing mechanism to discriminate against
non-cognate amino acids |CITS: [371674]|. Crystal structures of CysRS in the apo- and cysteine-bound state have
been determined at 2.3 and 2.6 Å resolution, revealing a zinc ion at the base of the active site cleft
|CITS: [12032090]|. The zinc ion is responsible for the ability of CysRS to bind cysteine specifically, although CysRS
does not possess amino acid editing activity |CITS: [12662918][12974627]|.
Unlike other class I aminoacyl-tRNA synthetases, CysRS is able to attach cysteine to both the 2' and 3' hydroxyl
groups of A76 in tRNACys. However, aminoacylation of the 3' hydroxyl group has a 20-fold lower
kcat/Km than that of the 2' hydroxyl group. The conserved nucleotide U73 in
tRNACys appears to confer this flexibility |CITS: [15826650]|.
Review: |CITS: [10966471]|
)""",]},
'B2239' : {'ecocyc-rxns': {"""GLYCPDIESTER-RXN""": """H2O + a glycerophosphodiester -> an alcohol + sn-glycerol-3-phosphate""",},'ucsd-rxns' : ['GPDDA3pp','GPDDA2pp','GPDDA5pp','GPDDA4pp','GPDDA1pp',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B0529' : {'ecocyc-rxns': {"""METHENYLTHFCYCLOHYDRO-RXN""": """H2O + 5,10-methenyl-THF = N10-formyl-THF""","""METHYLENETHFDEHYDROG-NADP-RXN""": """NADP+ + 5,10-methylene-THF = NADPH + 5,10-methenyl-THF""",},'ucsd-rxns' : ['MTHFC','MTHFD',], 'protein-comments' : ["""(Early purification studies indicated that the bifunctional
protein had a structure of five dissimilar subunits. However, subsequent
work has shown that the protein is indeed a homodimer |CITS:
[92084696]|.)""","""NIL""",]},
'B2234' : {'ecocyc-rxns': {"""RXN0-1""": """an acceptor + H2O + a 2'-deoxyribonucleoside diphosphate = a reduced acceptor + a ribonucleoside diphosphate""","""RIBONUCLEOSIDE-DIP-REDUCTI-RXN""": """a thioredoxin disulfide + H2O + a 2'-deoxyribonucleoside diphosphate = a reduced thioredoxin + a ribonucleoside diphosphate""","""CDPREDUCT-RXN""": """dCDP + a thioredoxin disulfide + H2O = CDP + a reduced thioredoxin""","""UDPREDUCT-RXN""": """dUDP + a thioredoxin disulfide + H2O = UDP + a reduced thioredoxin""","""ADPREDUCT-RXN""": """dADP + a thioredoxin disulfide + H2O = ADP + a reduced thioredoxin""","""GDPREDUCT-RXN""": """dGDP + a thioredoxin disulfide + H2O = GDP + a reduced thioredoxin""",},'ucsd-rxns' : ['RNDR4','RNDR4','RNDR3','RNDR3','RNDR2','RNDR2','RNDR1','RNDR1',], 'protein-comments' : ["""(The B1 protein of ribonucleoside-diphosphate reductase consists of two polypeptide chains of similar
or identical size. Both polypeptides have isoleucine as the
COOH-terminal residue, however the NH2-terminals are different, one
has glutamic acid, the other aspartic acid |CITS: [73218477]|. The
B1 protein contains the binding sites for the allosteric effectors as
well as the binding sites for the ribonucleoside diphosphate
substrates. There are two substrate binding sites per B1 molecule and
they are distinct from the effector binding sites. |CITS: [79009978]|
NrdA and/or NrdB are required for growth of a nrdD or nrdG null mutant under microaerophilic conditions
|CITS: [8954104]|.
Review: |CITS: [15158709]|)""","""NIL""","""NIL""",]},
'B0480' : {'ecocyc-rxns': {"""5'-NUCLEOTID-RXN""": """a ribonucleoside monophosphate + H2O = a ribonucleoside + phosphate""","""UDPSUGARHYDRO-RXN""": """a UDP-sugar + H2O = UMP + an α-D-aldose-1-phosphate""",},'ucsd-rxns' : ['NTD3pp','NTD2pp','UDPGPpp','NTD5pp','UGLCURPpp','NTD4pp','NTD7pp','NTD6pp','NTD12pp','UACGALPpp','NTD1pp','UACGAMPpp','NTD10pp','NTD9pp','NTD11pp','NTD8pp','UDPGALPpp',], 'protein-comments' : ["""(Salmonella has a different gene and enzyme, ushB. In E. coli
ushB is cryptic and in Salmonella ushA is cryptic. |CITS:
[94116835]|)""",]},
'B3386' : {'ecocyc-rxns': {"""RIBULP3EPIM-RXN""": """D-ribulose-5-phosphate = D-xylulose-5-phosphate""",},'ucsd-rxns' : ['RPE',], 'protein-comments' : ["""(Ribulose phosphate 3-epimerase is an enzyme of the non-oxidative branch of the pentose phosphate pathway.
An rpe mutant strain does not grow on minimal medium containing either ribose or xylose, but grows when both
sugars are present |CITS: [9729441]|. rpe mutant strains have a growth defect in complex medium and a more
severe growth defect in minimal medium containing glycolytic carbon sources or gluconate
|CITS: [7603433][9194706][9729441]|. A mutation in rpe, drsE30, supresses the temperature-sensitive
growth defect of the dnaR130 mutant allele |CITS: [9194706]|.
Review: |CITS: [8572885]|)""",]},
'B0954' : {'ecocyc-rxns': {"""RXN0-2144""": """β-hydroxy-cis-Δ5-dodecenoyl-ACP = H2O + trans-Δ3-cis-Δ5-dodecenoyl-ACP""","""FABAUNSATDEHYDR-RXN""": """β-hydroxydecanoyl-ACP = trans-Δ2-decenoyl-ACP + H2O""","""3-HYDROXYDECANOYL-ACP-DEHYDR-RXN""": """a D-3-hydroxy-acyl-ACP = a trans-Δ2-enoyl-acyl-ACP + H2O""","""TRANS-2-DECENOYL-ACP-ISOM-RXN""": """trans-Δ2-decenoyl-ACP = cis-Δ3-decenoyl-ACP""",},'ucsd-rxns' : ['3HAD160','3HAD161','3HAD100','3HAD80','3HAD120','3HAD121','3HAD60','3HAD180','3HAD181','T2DECAI','3HAD40','3HAD141','3HAD140',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B3480' : {'ecocyc-rxns': {"""ABC-20-RXN""": """Ni2+[periplasmic space] + ATP + H2O =Ni2+[cytosol] + ADP + phosphate """,},'ucsd-rxns' : ['NI2uabcpp',], 'protein-comments' : ["""NIL""","""(The NikABCDE ATP-dependent nickel (II) uptake system is a member of the ATP-Binding Cassette (ABC)
Superfamily of transporters |CITS: [96381453]|. The Nik system exhibits significant sequence similarity to
the components of other ABC transporters for dipeptides or oligopeptides |CITS: [95020649]|. Based on
sequence similarity, NikA is the periplasmic binding protein, NikB and NikC are the membrane components,
and NikD and NikE are the ATP-binding components of the ABC transporter. The nickel-binding
properties of the protein have been studied by monitoring the quenching of intrinsic protein fluorescence
|CITS: [95172074]|. NikA binds one atom of nickel per molecule of protein with a Kd of less
than 0.1 μM. The transporter's high specificity for nickel ion has also been demonstrated by
high-performance immobilized-metal-ion affinity chromatography |CITS:[95172074]|. The structure of NikA
has been determined to a resolution of 1.8 angstroms showing that it binds FeEDTA(H2O)
with very high affinity. It also binds the nickel ion associated with a metallophore which is at least similar
to EDTA |CITS:[16011372]|. Insertional mutation in the nik operon severely reduces nickel transport
ability |CITS:[95020649]|. Nickel is an important cofactor in a variety of enzymatic reactions in prokaryotes
|CITS:[20112624]|. However, nickel at high intracellular concentrations is toxic because it can catalyze the
formation of reactive forms of oxygen that can damage cellular constituents |CITS: [20112624]|. Because of
the toxicity of nickel, the synthesis of the Nik system is tightly controlled by nickel concentration. At high
nickel concentrations (0.3 mM) synthesis of Nik is completely repressed by the protein NikR
|CITS:[20112624]|. Expression of NikABCDE corresponds to expression of NiFe hydrogenases for which
nickel is a cofactor. Mutation and LacZ fusion experiments show that nitrate, via the activity of the NarLX
two-component system, represses expression of nikABCDE considerably. NikABCDE is
upregulated by FNR under anaerobic conditions |CITS:[16159764]|.
)""",]},
'B0484' : {'ecocyc-rxns': {},'ucsd-rxns' : ['CU1abcpp',], 'protein-comments' : ["""(YbaR is an uncharacterized member of the P-type ATPase cation transporter family |CITS:[94202222]|.
Based on sequence similarity, it may function as a copper transporting ATPase.)""",]},
'B2874' : {'ecocyc-rxns': {},'ucsd-rxns' : ['CBMKr',], 'protein-comments' : ["""(No information about this protein was found by a literature search conducted on January 10, 2006.)""",]},
'B0356' : {'ecocyc-rxns': {"""RXN-2962""": """S-hydroxymethylglutathione + NAD(P)+ = S-formylglutathione + NAD(P)H + H+""",},'ucsd-rxns' : ['FALDH2','ALCD2x','ALCD19',], 'protein-comments' : ["""(Glutathione-dependent formaldehyde dehydrogenase (GS-FDH) belongs to the family of class III alcohol
dehydrogenases. Glutathione and formaldehyde combine non-enzymatically to form hydroxymethylglutathione, the
true substrate of the GS-FDH catalyzed reaction. The product, S-formylglutathione, is further metabolized to formic
acid. The functional role of GS-FDH may be in the metabolism of endogenously formed formaldehyde and detoxifying
exogenous formaldehyde. |CITS: [92118844] [97472270]|
Transcription of the frmRAB operon is induced by formaldehyde, but not S-nitrosoglutathione
|CITS: [9333139][15466022]|.)""","""(
)""",]},
'B0355' : {'ecocyc-rxns': {"""S-FORMYLGLUTATHIONE-HYDROLASE-RXN""": """S-formylglutathione + H2O = formate + glutathione""",},'ucsd-rxns' : ['SFGTHi',], 'protein-comments' : ["""(FrmB is a promiscuous serine hydrolase; its highest specific activity is with the substrate S-formylglutathione.
Sulfhydryl inhibitors affect enzymatic activity |CITS: [16567800]|.
FrmB is encoded in an operon with FrmR and FrmA, which are proteins involved in the oxidation of formaldehyde.
FrmB has similarity to the S-formylglutathione hydrolase of Paracoccus denitrificans |CITS: [15466022]| and
a paralog, YeiG |CITS: [16567800]|.
Formaldehyde stimulates expression of frmB 45-fold in wild type and 70-fold in a yeiG deletion
background. Under normal growth conditions, neither a frmB deletion mutant nor a frmB yeiG double
mutant have a detectable growth defect. Addition of 0.4 mM formaldehyde to the growth medium caused only a small
growth defect in the frmB single mutant, while the growth rate of the double mutant drops to 43% of wild type
|CITS: [16567800]|.)""",]},
'B0353' : {'ecocyc-rxns': {"""TRANS-RXN-61""": """H+[periplasmic space] + 3-(3-hydroxyphenyl)propionate[periplasmic space] =H+[cytosol] + 3-(3-hydroxyphenyl)propionate[cytosol] """,},'ucsd-rxns' : ['HCINNMt2rpp','HPPPNt2rpp',], 'protein-comments' : ["""(MhpT is a putative 3-hydroxyphenylpropionic acid transporter. The mhpT
gene is located immediately downstream of the mhpA-E operon, responsible for
catabolism of 3-hydroxyphenylpropionate |CITS: [97252486]|. MhpT is a
member of the major facilitator superfamily of transporters and shares a high degree of
sequence similarity with PcaK, a 4-hydroxybenzoate transporter from Pseudomonas
putida |CITS: [97252486]|. MhpT may function as a 3-hydroxyphenylpropionate/proton
symporter. Imported 3-hydroxyphenylpropionate is converted to
2,3-dihydroxyphenylpropionate and ultimately degraded to Krebs cycle intermediates.)""",]},
'B2871' : {'ecocyc-rxns': {"""4.3.1.15-RXN""": """2,3-diaminopropionate + H2O -> 2 ammonia + pyruvate""",},'ucsd-rxns' : ['DAPAL',], 'protein-comments' : ["""(The ygeX gene encodes 2,3-diaminopropionate ammonia-lyase. The enzyme is not stereospecific and
catalyzes the α,β-elimination of both the D and L stereoisomer of 2,3-diaminopropionate
|CITS: [12596860][12821154]|. 2,3-diaminopropionate ammonia-lyase also exhibits weak activity toward D-serine,
and does not exhibit activity toward L-serine, D-β-Cl-alanine, or L-β-Cl-alanine |CITS: [12596860]|.
The amino-terminal methionine residue is removed from the mature protein |CITS: [12821154]|. The enzyme is
homodimeric and contains a pyridoxal 5'-phosphate prosthetic group |CITS: [12596860][12821154]|.
The enzyme belongs to the fold-type II family of PLP-containing enzymes |CITS: [12596860]|. Preliminary X-ray
crystallization studies have been performed |CITS: [12925808]|.
)""","""NIL""",]},
'B0351' : {'ecocyc-rxns': {"""ACETALD-DEHYDROG-RXN""": """NAD+ + coenzyme A + acetaldehyde = NADH + acetyl-CoA""",},'ucsd-rxns' : ['ACALD',], 'protein-comments' : ["""NIL""",]},
'B0350' : {'ecocyc-rxns': {"""2-OXOPENT-4-ENOATE-HYDRATASE-RXN""": """2-oxopent-4-enoate + H2O = 4-hydroxy-2-ketovalerate""",},'ucsd-rxns' : ['OP4ENH',], 'protein-comments' : ["""NIL""",]},
'B2407' : {'ecocyc-rxns': {"""XANTHOSINEPHOSPHORY-RXN""": """xanthosine + phosphate = ribose-1-phosphate + xanthine""",},'ucsd-rxns' : ['PUNP5','PUNP4','PUNP6','PUNP7','PUNP3',], 'protein-comments' : ["""NIL""","""(The trimeric form is also active with less substrate
specificity. |CITS: [88107903]|)""",]},
'B2406' : {'ecocyc-rxns': {"""TRANS-RXN-31""": """H+[periplasmic space] + xanthosine[periplasmic space] =H+[cytosol] + xanthosine[cytosol] """,},'ucsd-rxns' : ['THMDt2rpp','CYTDt2rpp','XTSNt2rpp','ADNt2rpp','INSt2rpp','URIt2rpp',], 'protein-comments' : ["""(XapB is a probable xanthosine transporter. The xapB gene is located in
a xanthosine-inducible operon with xapA, encoding xanthosine phosphorylase
|CITS: [96032385]|. Growth on xanthosine is greatly reduced in xapB mutants, and XapB
was demonstrated to fractionate with the cell membrane. XapB is a member of the
major facilitator superfamily of transporters |CITS: [98190790]| and shares a high
degree of similarity with the nucleoside transporter NupG. XapB therefore is
probably a xanthosine/proton symporter. Imported xanthosine is cleaved by XapA
to yield xanthine which can be used in nucleotide synthesis or as a nitrogen
source, and ribose-1-phosphate which can be used as a carbon source.)""",]},
'B4226' : {'ecocyc-rxns': {"""INORGPYROPHOSPHAT-RXN""": """H2O + diphosphate -> 2 phosphate""",},'ucsd-rxns' : ['PPA',], 'protein-comments' : ["""NIL""","""(The enzyme is a hexamer, arranged as a dimer of trimers in the crystal structure |CITS: [9201917]|.)""",]},
'B2400' : {'ecocyc-rxns': {"""GLURS-RXN""": """tRNAGlu + L-glutamate + ATP = L-glutamyl-tRNAGlu + diphosphate + AMP""",},'ucsd-rxns' : ['GLUTRS',], 'protein-comments' : ["""NIL""",]},
'B1092' : {'ecocyc-rxns': {"""MALONYL-COA-ACP-TRANSACYL-RXN""": """acyl carrier protein + malonyl-CoA = malonyl-ACP + coenzyme A""",},'ucsd-rxns' : ['MCOATA',], 'protein-comments' : ["""(The fabD gene is part of a fatty acid biosynthesis operon
and the malonyl-CoA transacylase is part of a multienzyme fatty acid
synthase II complex. |CITS: [92234941]|)""",]},
'B4025' : {'ecocyc-rxns': {"""PGLUCISOM-RXN""": """β-D-glucose-6-phosphate = D-fructose-6-phosphate""",},'ucsd-rxns' : ['PGI',], 'protein-comments' : ["""(phosphoglucose isomerase is found primarily in the cytoplasm)""",]},
'B4024' : {'ecocyc-rxns': {"""ASPARTATEKIN-RXN""": """L-aspartate + ATP = L-aspartyl-4-phosphate + ADP""",},'ucsd-rxns' : ['ASPK',], 'protein-comments' : ["""NIL""","""(This reaction, the phosphorylation of aspartate, is the first step in the biosynthesis of 4 different amino acids,
namely lysine, methionine and threonine (through homoserine), and isoleucine (which is synthesized from threonine).
In E. coli there are three isozymes that catalyze this step, namely aspartate
kinase I, II and III. Each of the kinases is controlled by one of the end products of the different pathways
(threonine, methionine and lysine, respectively). Two of the three enzymes (aspartate kinase I and II) are
multifunctional proteins, also catalyzing the reaction of homoserine dehydrogenase |CITS: [4148765]|.
Aspartate kinase III does not have an associated homoserine dehydrogenase activity (it is not part of the lysine
biosynthesis pathway).)""",]},
'B0197' : {'ecocyc-rxns': {"""RXN0-4522""": """H2O + ATP + L-methionine[periplasmic space] =phosphate + ADP + L-methionine[cytosol] ""","""TRANS-RXN0-202""": """H2O + ATP + D-methionine[periplasmic space] =phosphate + ADP + D-methionine[cytosol] """,},'ucsd-rxns' : ['METabcpp','METDabcpp',], 'protein-comments' : ["""(periplasmic binding protein component of ABC transporter)""","""(The formerly designated abc-yaeE-yaeC putative ABC transporter gene cluster (now renamed metNIQ genes) have
been shown to be involved in the uptake of D-methionine in E. coli Deletion of the cluster resulted in a strain which was
completely unable to grow in minimal media with D-methionine present. Complementation studies showed that nothing less than
the full complement of the three genes was able to utilize D-methionine indicating that all three are necessary for proper transport
system function |CITS: [22206499]|. Based on sequence similarity, MetN is the putative ATPase, MetI is the membrane spanning region
and MetQ is the substrate-binding domain |CITS: [22206499]|.
MetQ is the major binding protein for both L- and D-methionine as well as their analogues such as N-formyl methionine.
L-methionine effectively competes for D-methionine transport while D-methionine does not strongly compete with L-methionine transport.
The difference in inhibition between the two isomers is due to the low Km for L-methionine which is 15-fold lower than tha for D-methionine.
The MetNIQ transport system represents a novel family in the ABC type permease superfamily. All membrane proteins within this
family exhibit five putative alpha helical membrane spanners. |CITS: [12819857]|)""",]},
'B3870' : {'ecocyc-rxns': {"""GLUTAMINESYN-RXN""": """ammonia + L-glutamate + ATP -> L-glutamine + ADP + phosphate""",},'ucsd-rxns' : ['GLNS',], 'protein-comments' : ["""NIL""","""NIL""","""NIL""",]},
'B2979' : {'ecocyc-rxns': {},'ucsd-rxns' : ['GLYCTO4','GLYCTO3','GLYCTO2',], 'protein-comments' : ["""(E. coli cells harboring a plasmid containing glcDEF have glycolate oxidase activity in crude cell extracts;
an insertion mutant in either glcD, glcE or glcF abolishes this activity |CITS: [8606183]|.)""",]},
'B3875' : {'ecocyc-rxns': {},'ucsd-rxns' : ['H2Otex',], 'protein-comments' : ["""(OmpL is a member of the OmpG porin Family. It has been shown to localize to the outer membrane and exhibits
porin type properties allowing a non-specific group of solutes smaller than 600 Daltons to pass into and out of
the periplasm. |CITS: [11080145]| Sequence analysis suggests that it has a β-barrel structure consisting
of 12 β-strands. |CITS: [11080145]| It has also been claimed to have an effect on redox potential in the
periplasm |CITS: [11080145]|, however this point is currently contested. |CITS: [12660153]| OmpL also
shows a low, but possibly significant similarity to members of the Cyclodextrin Porin (CDP) family. |CITS: [12192075]|)""",]},
'B2975' : {'ecocyc-rxns': {"""TRANS-RXN-104""": """H+[periplasmic space] + lactate[periplasmic space] =H+[cytosol] + lactate[cytosol] ""","""TRANS-RXN-105""": """H+[periplasmic space] + glycolate[periplasmic space] =H+[cytosol] + glycolate[cytosol] """,},'ucsd-rxns' : ['D-LACt2pp','L-LACt2rpp','GLYCLTt2rpp',], 'protein-comments' : ["""(YghK, also named GlcA, is a glycolate transporter that belongs to the Lactate Permease Family (LctP) |CITS:
[20156664]|, due to its strong sequence similarity with the L-lactate permease, LldP. The yghK gene is
located in the glc operon. Expression studies using Northern blot analysis and lacZ fusion
experiments have shown that the yghK gene is transcribed from the same promoter as the other
glc structural genes |CITS: [21178909]|. Expression of this operon is induced by growth on glycolate and
is under the control of an activator protein, GlcC |CITS: [21178909]|. Growth of a yghK::cat mutant
on glycolate was not totally abolished, but its rate was much lower than that of the parental strain, indicating
that YghK probably functions as a glycolate transporter, although glycolate can also enter the cell through
another transport system |CITS: [21178909]|. The lactate permease LldP was also found to be capable of
glycolate transport. Growth on glycolate was abolished in a double mutant of the paralogous genes
yghK and lldP, and restored with plasmids expressing either YghK or LldP |CITS:
[21178909]|. Characterization of the putative substrates for these two related permeases showed, in both cases,
specificity for the 2-hydroxy-monocarboxylates glycolate, L-lactate, and D-lactate |CITS: [21178909]|.
)""",]},
'B0066' : {'ecocyc-rxns': {"""ABC-32-RXN""": """ATP + thiamine[periplasmic space] + H2O =ADP + phosphate + thiamine[cytosol] """,},'ucsd-rxns' : ['THMabcpp',], 'protein-comments' : ["""NIL""","""(The ABC transporter ThiBPQ was functionally characterized in Salmonella typhimurium where it is
required for the uptake of thiamine and thiamine pyrophosphate |CITS:[9535878]|. Its ortholog in
E. coli, SfuABC, has not been functionally characterized yet but presumably also function in
thiamine uptake. thiB (sfuA) encodes periplasmic thiamine binding protein. thiP
(sfuB) encodes inner membrane permease, and thiQ(sfuC) encodes
energy-transducing ATPase.
)""",]},
'B0199' : {'ecocyc-rxns': {"""RXN0-4522""": """H2O + ATP + L-methionine[periplasmic space] =phosphate + ADP + L-methionine[cytosol] ""","""TRANS-RXN0-202""": """H2O + ATP + D-methionine[periplasmic space] =phosphate + ADP + D-methionine[cytosol] """,},'ucsd-rxns' : ['METabcpp','METDabcpp',], 'protein-comments' : ["""(ATP binding component of ABC transporter)""","""(The formerly designated abc-yaeE-yaeC putative ABC transporter gene cluster (now renamed metNIQ genes) have
been shown to be involved in the uptake of D-methionine in E. coli Deletion of the cluster resulted in a strain which was
completely unable to grow in minimal media with D-methionine present. Complementation studies showed that nothing less than
the full complement of the three genes was able to utilize D-methionine indicating that all three are necessary for proper transport
system function |CITS: [22206499]|. Based on sequence similarity, MetN is the putative ATPase, MetI is the membrane spanning region
and MetQ is the substrate-binding domain |CITS: [22206499]|.
MetQ is the major binding protein for both L- and D-methionine as well as their analogues such as N-formyl methionine.
L-methionine effectively competes for D-methionine transport while D-methionine does not strongly compete with L-methionine transport.
The difference in inhibition between the two isomers is due to the low Km for L-methionine which is 15-fold lower than tha for D-methionine.
The MetNIQ transport system represents a novel family in the ABC type permease superfamily. All membrane proteins within this
family exhibit five putative alpha helical membrane spanners. |CITS: [12819857]|)""",]},
'B0198' : {'ecocyc-rxns': {"""RXN0-4522""": """H2O + ATP + L-methionine[periplasmic space] =phosphate + ADP + L-methionine[cytosol] ""","""TRANS-RXN0-202""": """H2O + ATP + D-methionine[periplasmic space] =phosphate + ADP + D-methionine[cytosol] """,},'ucsd-rxns' : ['METabcpp','METDabcpp',], 'protein-comments' : ["""(membrane component of ABC transporter)""","""(The formerly designated abc-yaeE-yaeC putative ABC transporter gene cluster (now renamed metNIQ genes) have
been shown to be involved in the uptake of D-methionine in E. coli Deletion of the cluster resulted in a strain which was
completely unable to grow in minimal media with D-methionine present. Complementation studies showed that nothing less than
the full complement of the three genes was able to utilize D-methionine indicating that all three are necessary for proper transport
system function |CITS: [22206499]|. Based on sequence similarity, MetN is the putative ATPase, MetI is the membrane spanning region
and MetQ is the substrate-binding domain |CITS: [22206499]|.
MetQ is the major binding protein for both L- and D-methionine as well as their analogues such as N-formyl methionine.
L-methionine effectively competes for D-methionine transport while D-methionine does not strongly compete with L-methionine transport.
The difference in inhibition between the two isomers is due to the low Km for L-methionine which is 15-fold lower than tha for D-methionine.
The MetNIQ transport system represents a novel family in the ABC type permease superfamily. All membrane proteins within this
family exhibit five putative alpha helical membrane spanners. |CITS: [12819857]|)""",]},
'B0052' : {'ecocyc-rxns': {"""PDXA-RXN""": """phospho-hydroxy-threonine + NAD+ = 1-amino-propan-2-one-3-phosphate + NADH + CO2""",},'ucsd-rxns' : ['PDX5PS',], 'protein-comments' : ["""(The crystal structure of PdxA has been solved at 1.96 A resolution. The protein forms a dimer, with the active site
located at the interface between the two subunits |CITS: [12896974]|.)""",]},
'B0864' : {'ecocyc-rxns': {"""ABC-4-RXN""": """ATP + L-arginine[periplasmic space] + H2O =ADP + phosphate + L-arginine[cytosol] """,},'ucsd-rxns' : ['ARGabcpp',], 'protein-comments' : ["""NIL""","""(The ArtPMQJI arginine transporter is a member of the ATP Binding Cassette (ABC) transporter superfamily
|CITS: [98254124]|. ArtJ shows similarity to arginine-binding periplasmic protein components of other ABC
transporters. Expression studies show that ArtJ is localized to the periplasmic fractions of E. coli
and hybridization studies using radiolabeled arginine showed that part of the radioactivity co-eluted with
ArtJ, indicating that L-arginine is the natural substrate for ArtJ |CITS: [96111488]|. Furthermore, overexpression
of ArtJ resulted in stimulation of arginine uptake. In minimal medium, ArtJ was found in the periplasmic
extracts of E. coli but its presence was greatly diminished in high-arginine content medium
|CITS: [96111488]|. Sequence similarity, including a highly conserved ATP-binding consensus site, and
hydropathy analyses indicate that ArtP is highly homologous to the HisP ATP-binding protein of the
Histidine-LAO transporters (HisJQMP complexes) of S. typhimurium and E. coli . ArtQ
and ArtM are hydrophobic proteins and exhibit some homology to HisQ and HisM, membraneous
components of the Histidine-LAO ABC transport system, and to other ABC transporter integral membrane
proteins |CITS:[96111488]|. ArtQ and ArtM presumably function as integral membrane components and
couple the ATPase activity of ArtP to the transport of L-arginine across the inner membrane. ArtI exhibits
homology with a number of ABC transporter periplasmic binding proteins, but its substrate is not known
|CITS:[98254124]|.)""",]},
'B0007' : {'ecocyc-rxns': {"""TRANS-RXN-125""": """Na+[periplasmic space] + L-alanine[periplasmic space] =Na+[cytosol] + L-alanine[cytosol] """,},'ucsd-rxns' : ['ALAt4pp','GLYt4pp',], 'protein-comments' : ["""(The YaaJ protein is an uncharacterised member of the
AGSS family of transporters. Based on sequence similarity
YaaJ may function as a sodium/alanine symporter. The yaaJ
gene may be co-transcribed with the yaaA gene.)""",]},
'B2253' : {'ecocyc-rxns': {"""RXN0-1863""": """UDP-L-Ara4O + L-glutamate = α-ketoglutarate + UDP-L-Ara4N""",},'ucsd-rxns' : ['UDPKAAT',], 'protein-comments' : ["""(ArnB is a UDP-L-Ara4O C-4" transaminase |CITS: [12704196]| that acts in a pathway (along with Ugd, ArnA, ArnC, and ArnT) that is active in certain arnA mutants and which modifies lipid A phosphates with 4-amino-4-deoxy-L-arabinose (L-Ara4N), causing increased resistance to polymyxin |CITS: [11706007]|.
ArnB is a pyridoxal phosphate-containing enzyme |CITS: [12704196]|. The reaction catalyzed by ArnB is reversible, but it has a Keq of about 0.1 in the direction from UDP-L-Ara4O toward UDP-L-Ara4N |CITS: [12704196]|.
ArnB localizes to the cytoplasm |CITS: [12704196]| .
Structural and biochemical characterization of Salmonella typhimurium ArnB has been performed; crystal structures of the enzyme are presented and discussed with respect to catalysis |CITS: [12429098]|.
Arn: "L-Ara4N (4-amino-4-deoxy-L-arabinose) biosynthesis" |CITS: [11706007]|.
Pmr: "polymyxin resistance")""",]},
'B3052' : {'ecocyc-rxns': {"""RXN0-4342""": """D-β-D-heptose-1-phosphate + ATP = ADP-D-glycero-D-manno-heptose + diphosphate""","""RXN0-4341""": """D-α,β-D-heptose-7-phosphate + ATP = D-β-D-heptose-1,7-bisphosphate + ADP""",},'ucsd-rxns' : ['GMHEPK','GMHEPAT',], 'protein-comments' : ["""(HldE is a bifunctional protein with an N-terminal ribokinase superfamily domain and a C-terminal cytidylyltransferase
superfamily domain; the two domains are genetically separable |CITS: [10629197]|. Structural modelling of the
ribokinase domain using E. coli |FRAME: RIBOKIN-MONOMER| led to the identification of amino acid residues
potentially essential for catalysis, and site-directed mutagenesis of potential ATP binding site residues resulted in
a dominant negative mutant phenotype |CITS: [16030223]|. HldE appears to function as a dimer in vivo
|CITS: [16030223]|.
HldE is involved in ADP-heptose formation |CITS: [1527014]|, catalyzing two steps in the pathway |CITS: [11751812]|.
A heptoseless mutant contains a transposon insertion in the hldE gene |CITS: [10629197]|. hldE
mutations were reported to result in increased expression of gabT and induction of mucoidy |CITS: [15576807]|.
)""","""NIL""",]},
'B1300' : {'ecocyc-rxns': {"""RXN0-3922""": """γ-glutamyl-γ-aminobutyraldehyde + NAD(P)+ + H2O = γ-glutamyl-γ-aminobutyrate + NAD(P)H + H+""",},'ucsd-rxns' : ['GGGABADr','ALDD2x',], 'protein-comments' : ["""(PuuC is inferred to be the γ-glutamyl-γ-aminobutyraldehyde dehydrogenase in a putrescine
utilization pathway; together with PuuB, γ-glutamyl-γ-aminobutyrate is produced from
γ-glutamylputrescine |CITS: [15590624]|.
The function of genes in the puu gene cluster was initially inferred by similarity with the ipuABCDEGFH
operon in Pseudomonas sp. |CITS: [15590624]|
The puuC, puuB, and puuE genes may form an operon |CITS: [9150200][1840553]|.)""",]},
'B3972' : {'ecocyc-rxns': {"""UDPNACETYLMURAMATEDEHYDROG-RXN""": """NADP+ + UDP-N-acetylmuramate = NADPH + UDP-GlcNAc-enolpyruvate""",},'ucsd-rxns' : ['UAPGR',], 'protein-comments' : ["""NIL""",]},
'B2947' : {'ecocyc-rxns': {"""GLUTATHIONE-SYN-RXN""": """glycine + L-γ-glutamylcysteine + ATP = glutathione + phosphate + ADP""",},'ucsd-rxns' : ['GTHS',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B0003' : {'ecocyc-rxns': {"""HOMOSERKIN-RXN""": """homoserine + ATP = O-phospho-L-homoserine + ADP""",},'ucsd-rxns' : ['HSK',], 'protein-comments' : ["""NIL""","""(Homoserine kinase (ThrB) catalyzes the conversion of homoserine to
O-phospho-L-homoserine en route to generating threonine.
ThrB phosphorylates homoserine to generate O-phospho-L-homoserine |CITS: [6097184]|.
In addition to the kM values reported below, the kMs for both ATP and homoserine
have been reported to be 0.3mM |CITS: [4364023]|. Though it is a substrate, homoserine
can actually cause partial inhibition of the reaction at higher concentrations, with
a kI of ~2mM |CITS: [6097184]|. ThrB has been subject to kinetic and mechanistic
analysis |CITS: [6097184][8660667]|.
ThrB is required for growth of pdxB mutants on glucose and
3-hydroxyhomoserine or D-glycoaldehyde |CITS: [8595869]|.
Translation of ThrA and ThrB is coupled |CITS: [2542227]|.)""",]},
'B2257' : {'ecocyc-rxns': {"""RXN0-2001""": """KDO2-lipid A + 2 4-amino-4-deoxy-L-arabinose -> L-Ara4N-modified KDO2-Lipid A + 2 H2O""",},'ucsd-rxns' : ['LA4NTpp',], 'protein-comments' : ["""(ArnT is the 4-amino-4-deoxy-L-arabinose (L-Ara4N) transferase that catalyzes addition of L-Ara4N to lipid A under some conditions (polymyxin resistant mutants) |CITS: [11535604]|. The Salmonella typhimurium enzyme has been characterized |CITS: [11535604]|.)""",]},
'B2128' : {'ecocyc-rxns': {},'ucsd-rxns' : ['GLYBabcpp','CHLabcpp',], 'protein-comments' : ["""(membrane component of ABC transporter)""","""(YehX, YehW, YehY, YehZ are uncharacterized members
of the ABC superfamily of transporters |CITS: [99091701]|.
YehX is the putative ATP binding component, YehW and YehY
are the membrane components, and YehZ is the putative
periplasmic binding protein. Based on sequence similarity
they probably function together as an ATP-dependant
osmoprotection transporter. The yehX, yehW,
yehY, and yehZ genes are located
within a single operon.
Osmotic shock and entry into stationary phase induced transcription of the yehZYXW operon,
which was dependent upon σs |CITS:[15251200]|.)""",]},
'B0002' : {'ecocyc-rxns': {"""ASPARTATEKIN-RXN""": """L-aspartate + ATP = L-aspartyl-4-phosphate + ADP""","""HOMOSERDEHYDROG-RXN""": """homoserine + NAD(P)+ = L-aspartate-semialdehyde + NAD(P)H + H+""",},'ucsd-rxns' : ['HSDy','ASPK',], 'protein-comments' : ["""NIL""","""(This reaction, the phosphorylation of aspartate, is the first step in the biosynthesis of 4 different amino acids,
namely lysine, methionine and threonine (through homoserine), and isoleucine (which is synthesized from threonine).
In E. coli there are three isozymes that catalyze this step, namely aspartate
kinase I, II and III. Each of the kinases is controlled by one of the end products of the different pathways
(threonine, methionine and lysine, respectively). Two of the three enzymes (aspartate kinase I and II) are
multifunctional proteins, also catalyzing the reaction of homoserine dehydrogenase |CITS: [4148765]|.
Aspartate kinase III does not have an associated homoserine dehydrogenase activity (it is not part of the lysine
biosynthesis pathway).
The two activities of aspartate kinase I are located in two separate domains. The aspartate kinase domain is
associated with the amino-terminal part of the protein, while the homoserine dehydrogenase domain is on the
carboxy-terminal part |CITS: [73028842]|.)""",]},
'B2283' : {'ecocyc-rxns': {"""NADH-DEHYDROG-A-RXN""": """ubiquinone-8 + NADH = ubiquinol-8 + NAD+""",},'ucsd-rxns' : ['NADH17pp','NADH18pp','NADH16pp',], 'protein-comments' : ["""(This subunit contains two 4Fe-4S clusters, N4 and N7. |CITS: [93389724] [98256007][15520003][15683249]|
NuoG is part of the soluble NADH dehydrogenase fragment, which represents the electron input part of NADH
dehydrogenase I |CITS: [7607227][9485311]|.)""","""(The soluble NADH dehydrogenase fragment represents the electron input part of NADH
dehydrogenase I |CITS: [7607227][9485311]|.)""","""(There is a cluster of 13 genes that code for NADH dehydrogenase I. Six of the subunits are peripheral proteins and
the other seven are very hydrophobic |CITS: [94178656] [98256007]|. Three-dimensional reconstruction of the
complex based on cryo-electron microscopy showed an L-shaped form with an integral membrane and a peripheral
arm |CITS: [9514725]|. A model of the spatial arrangement of the subunits and the possible functional mechanism of
proton pumping has been proposed |CITS: [12923180]|.)""",]},
'B2282' : {'ecocyc-rxns': {"""NADH-DEHYDROG-A-RXN""": """ubiquinone-8 + NADH = ubiquinol-8 + NAD+""",},'ucsd-rxns' : ['NADH17pp','NADH18pp','NADH16pp',], 'protein-comments' : ["""(This subunit was thought to contain the ubiquinone binding site |CITS: [93389724] [98256007]|, which has since been
shown to be located in the NuoM subunit |CITS: [12730198]|.
NuoH is part of the inner membrane component of NADH dehydrogenase I |CITS: [7607227]|.)""","""(There is a cluster of 13 genes that code for NADH dehydrogenase I. Six of the subunits are peripheral proteins and
the other seven are very hydrophobic |CITS: [94178656] [98256007]|. Three-dimensional reconstruction of the
complex based on cryo-electron microscopy showed an L-shaped form with an integral membrane and a peripheral
arm |CITS: [9514725]|. A model of the spatial arrangement of the subunits and the possible functional mechanism of
proton pumping has been proposed |CITS: [12923180]|.)""",]},
'B1059' : {'ecocyc-rxns': {"""RXN0-301""": """O2 + H2O + N-methyltryptophan = L-tryptophan + H2O2 + formaldehyde""","""N-METHYL-L-AMINO-ACID-OXIDASE-RXN""": """O2 + H2O + a N-methyl-L-amino acid = H2O2 + formaldehyde + an amino acid""",},'ucsd-rxns' : ['MTRPOX','SARCOX',], 'protein-comments' : ["""NIL""",]},
'B2280' : {'ecocyc-rxns': {"""NADH-DEHYDROG-A-RXN""": """ubiquinone-8 + NADH = ubiquinol-8 + NAD+""",},'ucsd-rxns' : ['NADH17pp','NADH18pp','NADH16pp',], 'protein-comments' : ["""(Point mutations at conserved residues have been analyzed; mutation of Val65, which is located in the most
conserved transmembrane segment, causes significant reduction of coupled electron transfer activity
|CITS: [15736965]|.
NuoJ is part of the inner membrane component of NADH dehydrogenase I |CITS: [7607227]|.
)""","""(There is a cluster of 13 genes that code for NADH dehydrogenase I. Six of the subunits are peripheral proteins and
the other seven are very hydrophobic |CITS: [94178656] [98256007]|. Three-dimensional reconstruction of the
complex based on cryo-electron microscopy showed an L-shaped form with an integral membrane and a peripheral
arm |CITS: [9514725]|. A model of the spatial arrangement of the subunits and the possible functional mechanism of
proton pumping has been proposed |CITS: [12923180]|.)""",]},
'B0418' : {'ecocyc-rxns': {"""PGPPHOSPHA-RXN""": """an L-1-phosphatidylglycerol-phosphate + H2O = an L-1-phosphatidyl-glycerol + phosphate""",},'ucsd-rxns' : ['PGPP180pp','PGPP161pp','PGPP181','PGPP180','PGPP120pp','PGPP141','PGPP140','PGPP160pp','PGPP120','PGPP161','PGPP160','PGPP141pp','PGPP140pp','PGPP181pp',], 'protein-comments' : ["""NIL""",]},
'B2286' : {'ecocyc-rxns': {"""NADH-DEHYDROG-A-RXN""": """ubiquinone-8 + NADH = ubiquinol-8 + NAD+""",},'ucsd-rxns' : ['NADH17pp','NADH18pp','NADH16pp',], 'protein-comments' : ["""(It was originally thought that there were 2 separate genes,
nuoC and nuoD, as in other bacteria, but this is not the case. E. coli has
one protein coded for by the nuoC or nuoCD gene. This subunit
may function as the proton channel. |CITS: [98256007]|
NuoC is part of the connecting fragment of NADH dehydrogenase I |CITS: [7607227]|.)""","""(This complex is thought to connect the soluble fragment of NADH dehydrogenase I to the inner membrane
components |CITS: [7607227]|.)""","""(There is a cluster of 13 genes that code for NADH dehydrogenase I. Six of the subunits are peripheral proteins and
the other seven are very hydrophobic |CITS: [94178656] [98256007]|. Three-dimensional reconstruction of the
complex based on cryo-electron microscopy showed an L-shaped form with an integral membrane and a peripheral
arm |CITS: [9514725]|. A model of the spatial arrangement of the subunits and the possible functional mechanism of
proton pumping has been proposed |CITS: [12923180]|.)""",]},
'B2285' : {'ecocyc-rxns': {"""NADH-DEHYDROG-A-RXN""": """ubiquinone-8 + NADH = ubiquinol-8 + NAD+""",},'ucsd-rxns' : ['NADH17pp','NADH18pp','NADH16pp',], 'protein-comments' : ["""(This subunit contains the N1a 2Fe-2S cluster |CITS: [93389724][98256007][15683249][15922336]|.
NuoE is part of the soluble NADH dehydrogenase fragment, which represents the electron input part of NADH
dehydrogenase I |CITS: [7607227][9485311]|.)""","""(The soluble NADH dehydrogenase fragment represents the electron input part of NADH
dehydrogenase I |CITS: [7607227][9485311]|.)""","""(There is a cluster of 13 genes that code for NADH dehydrogenase I. Six of the subunits are peripheral proteins and
the other seven are very hydrophobic |CITS: [94178656] [98256007]|. Three-dimensional reconstruction of the
complex based on cryo-electron microscopy showed an L-shaped form with an integral membrane and a peripheral
arm |CITS: [9514725]|. A model of the spatial arrangement of the subunits and the possible functional mechanism of
proton pumping has been proposed |CITS: [12923180]|.)""",]},
'B2284' : {'ecocyc-rxns': {"""NADH-DEHYDROG-A-RXN""": """ubiquinone-8 + NADH = ubiquinol-8 + NAD+""",},'ucsd-rxns' : ['NADH17pp','NADH18pp','NADH16pp',], 'protein-comments' : ["""(This subunit contains the FMN and NADH binding sites, and the N3 4Fe-4S cluster |CITS: [93389724] [98256007]|.
The cysteine residues responsible for ligation of the 4Fe-4S cluster were identified by site-directed mutagenesis
|CITS: [15922336]|.
NuoF is part of the soluble NADH dehydrogenase fragment, which represents the electron input part of NADH
dehydrogenase I |CITS: [7607227][9485311]|.)""","""(The soluble NADH dehydrogenase fragment represents the electron input part of NADH
dehydrogenase I |CITS: [7607227][9485311]|.)""","""(There is a cluster of 13 genes that code for NADH dehydrogenase I. Six of the subunits are peripheral proteins and
the other seven are very hydrophobic |CITS: [94178656] [98256007]|. Three-dimensional reconstruction of the
complex based on cryo-electron microscopy showed an L-shaped form with an integral membrane and a peripheral
arm |CITS: [9514725]|. A model of the spatial arrangement of the subunits and the possible functional mechanism of
proton pumping has been proposed |CITS: [12923180]|.)""",]},
'B0414' : {'ecocyc-rxns': {"""RIBOFLAVINSYNREDUC-RXN""": """5-amino-6-(5'-phosphoribitylamino)uracil + NADP+ = 5-amino-6-(5'-phosphoribosylamino)uracil + NADPH + H+""","""RIBOFLAVINSYNDEAM-RXN""": """H2O + 2,5-diamino-6-(ribosylamino)-4-(3H)-pyrimidinone 5'-phosphate = 5-amino-6-(5'-phosphoribosylamino)uracil + ammonia""",},'ucsd-rxns' : ['DHPPDA2','APRAUR',], 'protein-comments' : ["""(The subunit structure is unknown.)""",]},
'B0415' : {'ecocyc-rxns': {"""LUMAZINESYN-RXN""": """5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione + 3,4-dihydroxy-2-butanone-4-P = 6,7-dimethyl-8-(1-D-ribityl)lumazine + phosphate + 2 H2O""",},'ucsd-rxns' : ['RBFSb',], 'protein-comments' : ["""(The ribE gene encodes lumazine synthase, an enzyme that catalyzes the penultimate step in the riboflavin
biosynthesis pathway. The protein forms a hollow icosahedral capsid composed of 60 subunits. Unlike lumazine
synthase from Bacillus subtilis, the E. coli enzyme is not physically associated with any other enzyme of
the riboflavin biosynthetic pathway, including riboflavin synthase |CITS: [8969176]|.
)""","""NIL""",]},
'B2288' : {'ecocyc-rxns': {"""NADH-DEHYDROG-A-RXN""": """ubiquinone-8 + NADH = ubiquinol-8 + NAD+""",},'ucsd-rxns' : ['NADH17pp','NADH18pp','NADH16pp',], 'protein-comments' : ["""(Site-specific mutagenesis of conserved charged amino acid residues has elucidated possible functional roles for
Asp79 and Glu81 |CITS: [15175326]|.
NuoA is part of the inner membrane component of NADH dehydrogenase I |CITS: [7607227]|.
)""","""(There is a cluster of 13 genes that code for NADH dehydrogenase I. Six of the subunits are peripheral proteins and
the other seven are very hydrophobic |CITS: [94178656] [98256007]|. Three-dimensional reconstruction of the
complex based on cryo-electron microscopy showed an L-shaped form with an integral membrane and a peripheral
arm |CITS: [9514725]|. A model of the spatial arrangement of the subunits and the possible functional mechanism of
proton pumping has been proposed |CITS: [12923180]|.)""",]},
'B0411' : {'ecocyc-rxns': {},'ucsd-rxns' : ['GUAtex','DCYTtex','INStex','DADNtex','URItex','ADNtex','DURItex',], 'protein-comments' : ["""(Tsx is a protein involved with the permeation of ribo- and deoxy-nucleosides, across the outer membrane of E. coli.
It also allows the entry of the antibiotic albicidin, and serves as a receptor for bacteriophage and colicins |CITS: [3276691]|
It is believed to form a 14 strand β-barrel porin.
The crystal structure of Tsx has been determined up to 3.1 A co-crystallized with a range of nucleosides |CITS:[15272310]|. Tsx has been shown to localize to the cellular poles |CITS:[15130122]|.)""",]},
'B1054' : {'ecocyc-rxns': {"""LAUROYLACYLTRAN-RXN""": """KDO2-lipid IVA + lauroyl-ACP = KDO2-(lauroyl)-lipid IVA + acyl carrier protein""",},'ucsd-rxns' : ['EDTXS1',], 'protein-comments' : ["""NIL""",]},
'B3750' : {'ecocyc-rxns': {"""ABC-28-RXN""": """ATP + D-ribose[periplasmic space] + H2O =ADP + phosphate + D-ribose[cytosol] """,},'ucsd-rxns' : ['RIBabcpp',], 'protein-comments' : ["""NIL""","""(RbsABC is an ATP-dependent ribose transporter that is a member of the ATP-Binding Cassette (ABC)
Superfamily of transporters |CITS: [99121048]|. Based on sequence similarity, RbsA is the ATP-binding
constituent, RbsB is the periplasmic substrate-binding protein, and RbsC form the transmembrane
constituent of the transporter |CITS: [99121048]|. Mutations in each of the components eliminated transport
of ribose at external concentration of 1 μM, indicating that the components make up a transport system
that is responsible for high-affinity ribose transport. However, these mutants are able to grow normally on
high concentrations of the sugar, suggesting that there is at least a second, low-affinity transport system for
ribose in E. coli |CITS: [84212237]|. Hydrophobicity analysis has shown that RbsC contains six
transmembrane helices, while alkaline phosphatase fusions and the use of inside-out vesicles with proteolysis
have shown that the C and N termini are both on the cytoplasmic side of the membrane.)""",]},
'B0222' : {'ecocyc-rxns': {"""RXN0-4301""": """D-sedoheptulose-7-phosphate = D-α,β-D-heptose-7-phosphate""",},'ucsd-rxns' : ['S7PI',], 'protein-comments' : ["""(The lpcA gene encodes sedoheptulose 7-phosphate isomerase, catalyzing the first step in the biosynthesis
of a core component of lipopolysaccharide. Mutants in lpcA were found to confer novobiocin hypersensitivity
and conjugation deficiency when mutated; lpcA mutants were shown to contain lipopolysaccharides lacking
heptose |CITS: [4926688][785207][8631969]|.
lpcA = "LPS-core synthesis" |CITS: [4926688]|
gmhA = "glycero-mannose-heptose synthesis" |CITS: [11751812]|)""",]},
'B0221' : {'ecocyc-rxns': {"""ACYLCOADEHYDROG-RXN""": """an acyl-CoA + FAD -> FADH2 + a Δ2-enoyl-CoA""",},'ucsd-rxns' : ['ACOAD1f','ACOAD2f','ACOAD3f','ACOAD4f','ACOAD6f','ACOAD7f','ACOAD8f','ACOAD5f',], 'protein-comments' : ["""(The previously uncharacterized yafH open reading frame has been shown to encode the FadE acyl-CoA
dehydrogenase enzyme |CITS: [11771124][12057976]|. The fadE62 mutation is a single base deletion within
yafH, resulting in a frame shift mutation, and yafH can complement the phenotype of the fadE62 mutant
strain |CITS: [12057976]|.)""",]},
'B2507' : {'ecocyc-rxns': {"""GMP-SYN-GLUT-RXN""": """H2O + L-glutamine + xanthosine-5-phosphate + ATP = L-glutamate + GMP + diphosphate + AMP""","""GMP-SYN-NH3-RXN""": """ATP + xanthosine-5-phosphate + ammonia = AMP + diphosphate + GMP""",},'ucsd-rxns' : ['GMPS2',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B2492' : {'ecocyc-rxns': {},'ucsd-rxns' : ['FORt2pp','FORtppi',], 'protein-comments' : ["""(FocB is a putative formate transporter, belonging to the FNT
family of formate and nitrite transporters |CITS: [99184734]|.
The focB gene is located in the putative twelve gene hyf
operon, which includes nine genes encoding a putative formate
hydrogenlyase complex |CITS: [98048487]|. FocB is highly similar
to the formate transporter FocA, and presumably functions as a
formate transporter reponsible for uptake of formate to provide
a substrate for the formate hydrogenlyase.)""",]},
'B3974' : {'ecocyc-rxns': {"""PANTOTHENATE-KIN-RXN""": """pantothenate + ATP = D-4'-phosphopantothenate + ADP""",},'ucsd-rxns' : ['PNTK',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B2490' : {'ecocyc-rxns': {},'ucsd-rxns' : ['FHL',], 'protein-comments' : ["""(The hyfJ gene is part of the hyf operon, and expression of adjacent genes may be translationally coupled
|CITS: [12426353]|. The HyfJ protein is similar to HycH, the formate hydrogenlyase maturation protein responsible
for processing of the large subunit (HycE) of hydrogenase 3.)""",]},
'B4013' : {'ecocyc-rxns': {"""HOMSUCTRAN-RXN""": """homoserine + succinyl-CoA = O-succinyl-L-homoserine + coenzyme A""",},'ucsd-rxns' : ['HSST',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B3990' : {'ecocyc-rxns': {"""THIAZOLSYN2-RXN""": """L-tyrosine + 1-deoxy-D-xylulose 5-phosphate + This-COSH protein = 4-methyl-5-(β-hydroxyethyl)thiazole phosphate + 4-hydroxybenzyl alcohol + C1 of tyrosine + ThiS protein""",},'ucsd-rxns' : ['THZPSN',], 'protein-comments' : ["""NIL""","""(The ThiGH complex catalyzes the conversion of 1-deoxy-D-xylulose 5-phosphate to a thiazole
as part of thiamine synthesis.
ThiG and ThiH combine to form a complex containing an iron-sulfuer cluster |CITS: [12650933]|.
Together, they are required for the synthesis of
4-methyl-5-(β-hydroxyethyl)thiazole phosphate, which is the rate-limiting
step in thiamine synthesis |CITS: [8432721][14757766]|.)""",]},
'B0861' : {'ecocyc-rxns': {"""ABC-4-RXN""": """ATP + L-arginine[periplasmic space] + H2O =ADP + phosphate + L-arginine[cytosol] """,},'ucsd-rxns' : ['ARGabcpp',], 'protein-comments' : ["""(ArtM)""","""(The ArtPMQJI arginine transporter is a member of the ATP Binding Cassette (ABC) transporter superfamily
|CITS: [98254124]|. ArtJ shows similarity to arginine-binding periplasmic protein components of other ABC
transporters. Expression studies show that ArtJ is localized to the periplasmic fractions of E. coli
and hybridization studies using radiolabeled arginine showed that part of the radioactivity co-eluted with
ArtJ, indicating that L-arginine is the natural substrate for ArtJ |CITS: [96111488]|. Furthermore, overexpression
of ArtJ resulted in stimulation of arginine uptake. In minimal medium, ArtJ was found in the periplasmic
extracts of E. coli but its presence was greatly diminished in high-arginine content medium
|CITS: [96111488]|. Sequence similarity, including a highly conserved ATP-binding consensus site, and
hydropathy analyses indicate that ArtP is highly homologous to the HisP ATP-binding protein of the
Histidine-LAO transporters (HisJQMP complexes) of S. typhimurium and E. coli . ArtQ
and ArtM are hydrophobic proteins and exhibit some homology to HisQ and HisM, membraneous
components of the Histidine-LAO ABC transport system, and to other ABC transporter integral membrane
proteins |CITS:[96111488]|. ArtQ and ArtM presumably function as integral membrane components and
couple the ATPase activity of ArtP to the transport of L-arginine across the inner membrane. ArtI exhibits
homology with a number of ABC transporter periplasmic binding proteins, but its substrate is not known
|CITS:[98254124]|.)""",]},
'B1186' : {'ecocyc-rxns': {"""TRANS-RXN-130""": """3 H+[periplasmic space] + 2 Na+[cytosol] =2 Na+[periplasmic space] + 3 H+[cytosol] """,},'ucsd-rxns' : ['NAt3_1p5pp',], 'protein-comments' : ["""(NhaB is one of the two known sodium ion/proton antiporters in E. coli, along with NhaA.
NhaA and NhaB do not share detectable sequence similarity, but they have similar putative
secondary structures, composed of 12 transmembrane segments connected with hydrophilic
loops |CITS: [99224327]|. NhaB has been shown to be involved in the intracellular pH
regulation under alkaline conditions. A nhaB knockout mutant was unable to grow in a
high pH medium (above 8.0), and the intracellular pH was not maintained at the regular level
|CITS: [95122454], [93131914]|. Complementation of the nhaB mutant with the
cloned nhaA gene increased sodium ion/proton antiporter activity, but did not restore
the defects in growth and intracellular pH. Thus, NhaB is essential for the regulation of intracellular
pH under alkaline conditions. Using thermodynamic and kinetic methods, the sodium ion/proton
exchange reaction of the protein was shown to have a stoichiometry of 2:3 |CITS: [95014461]|.
In contrast to NhaA, whose activity is extremely pH-dependent, NhaB shows only slight
pH-dependence. The Vmax of NhaB for sodium ion stays relatively constant
in response to a pH increase, while the Km value decreases with an increase in pH
(7.2 to 8.5) |CITS: [95014461]|.)""",]},
'B3196' : {'ecocyc-rxns': {"""TRANS-RXN-128""": """Na+[periplasmic space] + Ca2+[cytosol] =Na+[cytosol] + Ca2+[periplasmic space] """,},'ucsd-rxns' : ['CAt6pp',], 'protein-comments' : ["""(YrbG is an uncharacterized member of the
CaCA family of metal cation exchangers
|CITS: [99184734]|. Based on sequence similarity,
it probably functions as a sodium ion/calcium
ion exchanger.)""",]},
'B2498' : {'ecocyc-rxns': {"""URACIL-PRIBOSYLTRANS-RXN""": """diphosphate + UMP = 5-phosphoribosyl 1-pyrophosphate + uracil""",},'ucsd-rxns' : ['UPPRT',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B3991' : {'ecocyc-rxns': {"""THIAZOLSYN2-RXN""": """L-tyrosine + 1-deoxy-D-xylulose 5-phosphate + This-COSH protein = 4-methyl-5-(β-hydroxyethyl)thiazole phosphate + 4-hydroxybenzyl alcohol + C1 of tyrosine + ThiS protein""",},'ucsd-rxns' : ['THZPSN',], 'protein-comments' : ["""NIL""","""(The ThiGH complex catalyzes the conversion of 1-deoxy-D-xylulose 5-phosphate to a thiazole
as part of thiamine synthesis.
ThiG and ThiH combine to form a complex containing an iron-sulfuer cluster |CITS: [12650933]|.
Together, they are required for the synthesis of
4-methyl-5-(β-hydroxyethyl)thiazole phosphate, which is the rate-limiting
step in thiamine synthesis |CITS: [8432721][14757766]|.)""",]},
'B1800' : {'ecocyc-rxns': {},'ucsd-rxns' : ['MALDDH',], 'protein-comments' : ["""(No information about this protein was found by a literature search conducted on December 28, 2005.
)""",]},
'B1801' : {'ecocyc-rxns': {},'ucsd-rxns' : ['GLYBt2pp','CHLt2pp','GLYt2pp',], 'protein-comments' : ["""(YeaV is an uncharacterized member of the Betaine, Carnitine, Choline Transporter (BCCT)
family |CITS:[95115548]|. Based on bioinformatic analysis, YeaV shows highest amino acid sequence
similarity with carnitine transporters.)""",]},
'B3197' : {'ecocyc-rxns': {"""DARAB5PISOM-RXN""": """D-arabinose 5-phosphate = D-ribulose-5-phosphate""",},'ucsd-rxns' : ['A5PISO',], 'protein-comments' : ["""(D-arabinose-5-phosphate is a precursor for KDO (2-keto-3-deoxy-octonate), a constituent in the cell wall
lipopolysaccharide. Arabinose-5-phosphate isomerase is responsible for the interconversion of
D-ribulose-5-phosphate and D-arabinose-5-phosphate. The enzyme was originally isolated and partially
characterized from E. coli strain B. As E. coli K-12 has limited D-arabinose metabolism, there was
some uncertainty whether or not this enzyme is present in K-12 |CITS: [67041910]|.
Purification of overproduced protein is described; YrbH is a tetramer in solution. The reaction kinetics, specificity,
and optimal conditions have been characterized, and the physical characteristics of the active site are discussed
|CITS: [12805358]|.
Isozymes may be present in E. coli |CITS: [12805358]|.)""","""NIL""",]},
'B1805' : {'ecocyc-rxns': {"""ACYLCOASYN-RXN""": """coenzyme A + a fatty acid + ATP = an acyl-CoA + diphosphate + AMP""",},'ucsd-rxns' : ['FACOAL160t2pp','FACOAL140t2pp','FACOAL60t2pp','FACOAL161t2pp','FACOAL180t2pp','FACOAL100t2pp','FACOAL141t2pp','FACOAL80t2pp','FACOAL120t2pp','FACOAL181t2pp',], 'protein-comments' : ["""(The FadD protein, encoding fatty acyl-CoA synthetase, can transport long chain fatty acids across the inner
membrane in an in vitro system |CITS: [15067008]|.)""","""NIL""",]},
'B2033' : {'ecocyc-rxns': {},'ucsd-rxns' : ['O16AT',], 'protein-comments' : ["""(No information about this protein was found by a literature search
conducted on February 26, 2004.)""",]},
'B2746' : {'ecocyc-rxns': {"""RXN0-302""": """2-phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol = CMP + 2-C-methyl-D-erythritol-2,4-cyclodiphosphate""",},'ucsd-rxns' : ['MECDPS',], 'protein-comments' : ["""(IspF acts in the mevalonate-independent pathway of isopentenyl diphosphate biosynthesis
|CITS: [11115399][10694574][Takagi00]|. The protein is essential for cell survival, and reduced abundance causes
a severe growth defect with filamentous cell morphology and sensitivity to antibiotics that target the cell wall
|CITS: [12270818][11361082]|. A mutant does not grow in complex media |CITS: [11361082]|. EMS-induced point
mutants identifying residues essential for catalytic activity have been isolated |CITS: [12859972]|.
The enzyme is a homotrimer with three active sites located at the clefts between monomers |CITS: [11786530]
[11829504]|. Crystal structures of the enzyme are reported |CITS: [11786530][11829504][11997478][15608374]|.
IspF is observed in a complex with cytidine 5'-diphosphate and Mn2+ at 1.8 angstroms resolution
|CITS: [11997478]|, in a complex with Mn2+ at 2.8 angstroms resolution |CITS: [11786530]|, and in a
complex with Mn2+, CMP, and MECDP at 2.8 angstroms resolution |CITS: [11786530]|. A
Zn2+ ion is found at the active site, where it plays a role in catalysis |CITS: [11829504][11997478]|.
Related proteins are widespread among bacterial pathogens, but not among eukaryotes, indicating potential utility as
an antibiotic drug target |CITS: [11361082]|. IspF has similarity to a protein from Plasmodium falciparum that is
a candidate antimalarial drug target |CITS: [11389720]|.
Some organisms produce bifunctional proteins with domains with similarity to the IspD and IspF proteins, which are
separate polypeptides in E. coli |CITS: [10518523]|.)""","""NIL""",]},
'B1907' : {'ecocyc-rxns': {"""TRANS-RXN-77""": """H+[periplasmic space] + L-tyrosine[periplasmic space] =H+[cytosol] + L-tyrosine[cytosol] """,},'ucsd-rxns' : ['TYRt2rpp',], 'protein-comments' : ["""(TyrP is a tyrosine-specific permease. It is a member of the Hydroxy/Aromatic Amino Acid Permease
(HAAP) family. Studies, |CITS:[91317725]| found a single promoter whose expression was repressed by
TyrR protein in the presence of tyrosine and activated by TyrR protein in the presence of phenylalanine.)""",]},
'B2868' : {'ecocyc-rxns': {"""RXN0-901""": """xanthine + NAD+ + H2O = urate + NADH + H+""","""RXN0-902""": """hypoxanthine + H2O = 2 H+ + xanthine""",},'ucsd-rxns' : ['HXAND','XAND',], 'protein-comments' : ["""(XdhC has similarity to the iron-binding regions of Drosophila melanogaster xanthine dehydrogenase and Desulfovibrio gigas aldehyde oxidoreductase |CITS: [10986234]|.
)""","""(XdhA-XdhB-XdhC is a putative heterotrimeric xanthine dehydrogenase |CITS: [10986234]|.
Degradation of hypoxanthine, xanthosine, inosine, or allantoin does not provide adequate nitrogen to support cell growth under aerobic conditions, in contrast to degradation of adenine or adenosine, which does support cell growth |CITS: [10986234]|. Hypoxanthine, guanosine, inosine, or xanthosine (but not allantoin) speeds the growth of cells utilizing aspartate as the nitrogen source |CITS: [10986234]|.
Xanthine degradation to allantoin has been observed |CITS: [10986234]|.
It is suggested that xanthine dehydrogenase plays a role in purine salvage, perhaps by favoring production of GMP rather than AMP |CITS: [10986234]|.)""",]},
'B2530' : {'ecocyc-rxns': {"""RXN0-308""": """L-cysteine + a protein cysteine -> L-alanine + protein-S-sulfanylcysteine""",},'ucsd-rxns' : ['THZPSN',], 'protein-comments' : ["""(The E. coli iscS gene encodes cysteine desulfurase, which converts L-cysteine to L-alanine and sulfur. The
enzyme is also active with L-selenocysteine. The sulfur initially forms a cysteine persulfide within the enzyme and is
then transferred elsewhere. The enzyme is necessary for synthesis of 2-thiouridine modified tRNA(Glu) in an in
vitro system |CITS: [12549933]|.
The sulfur generated in the reaction can be utilized in several ways: donated to ThiI which in turns transfers the
sulfur to U8-tRNA synthesizing s4U8-tRNA; Fe-S cluster synthesis; supplied to the Fe-S cluster of
biotin synthase during the synthase reaction; donated to ThiS during thiamin biosynthesis and possibly used in NAD
synthesis. |CITS: [96279148] [20245547] [20068850] [20219102]
[10739946] [20347927] [20379012] [20381327]|
In-frame deletion mutants lacking IscS are auxotrophic for thiamin and nicotinic acid and exhibit a slow growth rate
|CITS: [10781607]|. IscS is required for the biosynthesis of all thionucleotides |CITS: [12446632]| and for efficient
repair of damaged iron-sulfur clusters |CITS: [15308657]|. Mutants in active site residues have been studied
|CITS: [14978044]|.
)""","""NIL""",]},
'B0731' : {'ecocyc-rxns': {"""RXN0-2522""": """phosphoenolpyruvate + 2-O-α-mannosyl-D-glycerate[periplasmic space] =2-(α-D-mannosyl)-3-phosphoglycerate[cytosol] + pyruvate """,},'ucsd-rxns' : ['MANGLYCptspp',], 'protein-comments' : ["""(MngA is a phosphotransferase type permease. It is involved in the uptake of 2-O-alpha-Mannosyl-D-glycerate followed by its phosphorylation.
The gene encodes PTS Enzyme IIA, IIB and IIC domains necessary for phosphotransferase mediated transport. This
transport system exhibits sequence similarity with fructose PTS systems. |CITS: [14645248]|)""","""(Frx (HrsA), a putative PTS permease, belongs to the functional
superfamily of the phosphoenolpyruvate (PEP)-dependent, sugar
transporting phosphotransferase system (PTS). The PTS transports
and simultaneously phosphorylates its sugar substrates in a process
called group translocation. Frx presumably takes up an exogenous
sugar, releasing the phosphate ester into the cell cytoplasm in
preparation for metabolism (1).
Frx is a fructose-like PTS permease with the domain order IIA-IIB-IIC
(2, 3). Nothing is known about its sugar specificity, its function
or regulation of its synthesis. The overall PTS-mediated phosphoryl
transfer reaction, requiring the two general energy coupling proteins
of the PTS, Enzyme I and HPr, as well as the three domains of
the Enzyme II complex is:
PEP --> Enzyme I(his~~P)
--> HPr(his~~P)
--> IIA(his~~P) -->
IIB(cys~~P) -(IIC)-> β-glucoside-6-P.)""",]},
'B0639' : {'ecocyc-rxns': {"""NICONUCADENYLYLTRAN-RXN""": """ATP + nicotinate nucleotide = diphosphate + deamido-NAD""",},'ucsd-rxns' : ['NNATr','NMNAT',], 'protein-comments' : ["""(Nicotinate-mononucleotide adenylyltransferase is an essential enzyme involved in de novo biosynthesis and
salvage of NAD+ and NADP+. Both nicotinate mononucleotide (NMN) and nicotinamide mononucleotide (NAMN) are
substrates, but the rate of adenylation of NMN is at least 20 times faster than that of NAMN |CITS: [10894752]|.
The NadD protein has been overexpressed and purified |CITS: [10894752]|. Crystal structures of the enzyme alone
and in a complex with deamido-NAD have been determined and show that ligand binding causes conformational
changes in regions surrounding the active site. Several protein main chain amides and a positive helix dipole
specifically interact with the deamidated pyridine nucleotide. Crystal structures of archeal nicotinate-mononucleotide
adenylyltransferases show differences in the architecture of the active site, enzyme-ligand interactions and the
conformation of the bound dinucleotide |CITS: [11796112]|.
The nadD72 mutant allele was first isolated as a spontaneous temperature-sensitive mutation named 72c in
the fusB gene |CITS: [353503]|. The mutant phenotype is pleiotropic; at the permissive temperature, the strain
is more tolerant to fusidic acid and supersensitive to trimethoprim. The ts phenotype can be rescued by sublethal
amounts of chloramphenicol |CITS: [353503]|. Further characterization of the 72c mutation showed it to be an allele of
nadD (nadD72), where a frameshift mutation leads to a change in 10 amino acids and addition of 17
amino acids to the NadD protein. The mutant protein can synthesize very little NAD+ and NADPH at the permissive
temperature and essentially none at the non-permissive temperature |CITS: [12949168]|. The nadD74 allele
encodes an amino acid change in the ATP-binding site of NadD. On miminal medium, the mutant shows temperature
sensitivity due to a reduction in NAD+ synthesis; at the permissive temperature, NAD+ synthesis is reduced, but
sufficient to support normal growth |CITS: [12949168]|. Additional mutants in nadD have been isolated and
characterized |CITS: [16153292]|.
)""",]},
'B0733' : {'ecocyc-rxns': {"""CYT-UBIQUINOL-OXID-RXN""": """ubiquinol-8 + O2 = ubiquinone-8 + 2 H2O""",},'ucsd-rxns' : ['CYTBDpp',], 'protein-comments' : ["""(CydA contains the heme b558 component of cytochrome bd-I |CITS: [6376497]|. The CydA protein has nine
transmembrane helices, placing the oxygen reactive site near the periplasmic surface |CITS: [15013751]|.
Expression of cydAB is negatively regulated by Fnr, induced by anaerobiosis via the ArcA/ArcB
two-component regulatory system |CITS: [2172211][9302022]|, and repressed by H-NS under aerobic conditions,
resulting in maximal expression under microaerobic conditions |CITS: [11123679]|. Expression is induced by iron
limitation |CITS: [1478458]| and H2O2 exposure |CITS: [11016692]|, and is sensitive to the
level of DNA supercoiling |CITS: [11238966]|.)""","""NIL""",]},
'B0732' : {'ecocyc-rxns': {},'ucsd-rxns' : ['MANPGH',], 'protein-comments' : ["""(The mngB gene encodes an alpha-mannosidase |CITS: [14645248]|.)""",]},
'B3551' : {'ecocyc-rxns': {"""RXN0-3621""": """L-methionine sulfoxide + e- + H+ -> L-methionine + H2O""","""R401-RXN""": """d-biotin d-sulfoxide + 2 e- + 2 H+ = biotin + H2O""",},'ucsd-rxns' : ['BSORy','BSORx',], 'protein-comments' : ["""(BisC was first identified as a biotin sulfoxide reductase that reduces a spontaneous oxidation product of biotin, biotin
d-sulfoxide (BDS), back to biotin. The function of the reductase is unknown, but it may
allow scavenging of BDS as a biotin source. It may also protect the cell from oxidation damage. |CITS: [90202748]
[82119950] [MethEnz62-379] [97166177]|
BisC also exhibits methionine-S-sulfoxide reductase activity, acting specifically on the S enantiomer in
the free, but not the protein-bound form |CITS: [15601707]|.)""",]},
'B3553' : {'ecocyc-rxns': {"""RXN0-300""": """glycerate + NADP+ = hydroxypyruvate + NADPH""","""GLYOXYLATE-REDUCTASE-(NADP+)-RXN""": """glycolate + NADP+ = NADPH + glyoxylate""","""1.1.1.215-RXN""": """NADP+ + gluconate = 2-dehydro-D-gluconate + NADPH""","""YIAE1-RXN""": """2,5-didehydro-D-gluconate + NADPH = 5-ketogluconate + NADP+""","""YIAE2-RXN""": """2-dehydro-D-gluconate + NADPH = L-idonate + NADP+""",},'ucsd-rxns' : ['2DGULRy','2DGULRx','2DGLCNRx','DKGLCNR2x','DKGLCNR2y','GLYCLTDy','GLYCLTDx','2DGLCNRy','HPYRRy','HPYRRx',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B0632' : {'ecocyc-rxns': {"""3.4.16.4-RXN""": """D-alanyl-D-alanine + H2O = 2 D-alanine""",},'ucsd-rxns' : ['MDDCP2pp','MDDCP1pp','MDDCP5pp','MDDCP4pp','MDDCP3pp',], 'protein-comments' : ["""(D-alanyl-D-alanine carboxypeptidase (DacA) is a penicillin-sensitive, membrane-bound enzyme required
for trimming the carboxy-terminal D-alanyl residues from cell wall precursors. It catalyzes D-alanine
carboxypeptidase activity, including the cleavage of D-alanine from the model substrate
bisacetyl-L-lysyl-D-alanyl-D-alanine |CITS: [351612][6995448][1740130][6363404][345275]|.
DacA also binds penicillin stoichiometrically |CITS: [1740130]|.
A number of residues in DacA are necessary for its penicillin-binding and D-alanyl-D-alanine
carboxypeptidase activities. Serine-44 is the active site that binds the β-lactam ring of
penicillin |CITS: [3888981]|. Mutations at this site and at lysine-213 lose both the penicillin-binding
and carboxypeptidase activities. A mutant at lysine-47 has no carboxypeptidase function but continues to
bind and hydrolyse penicillin, though the latter activity is greatly slowed. Mutations in the
SXN active-site motif at serine-110-glycine-111-asparagine-112 and at aspartate-175, histidine-216 and threonine-217 also
lose carboxypeptidase function |CITS: [7980393]|. Cysteine-115 is not required for the
carboxypeptidase function of DacA |CITS: [3276680]|.
The carboxy-terminal 100 residues are not required for penicillin binding, but
contribute to carboxypeptidase function, as the truncated mutant is only 40% active |CITS: [842480]|.
Carboxy-terminally truncated DacA can be made fully functional by the addition of the carboxy-terminal anchor
from DacC or DacD, but not from DacB or an unrelated membrane protein. Fusion of the amino-terminal enzymatic
domain of DacA to the carboxy-terminal beta sheet of DacC makes a functional protein, though the opposite
fusion does not complement a dacA null |CITS: [12057958]|.
Both the DacA active site and membrane domain are required for maintenance of proper cell morphology |CITS: [11325933]|.
Note that all the residues in this paragraph are referred to by their
position in the amino-terminally processed, mature form of DacA that lacks 29 residues from its
amino-terminus.
The amino-terminus of DacA is sufficient to allow transport of a an outer
membrane fusion protein to the outer membrane, though this is not where DacA itself is localized. Processing
of DacA is SecA dependent |CITS: [3908094]|.
At least the final ten residues in the carboxy-terminus of DacA are needed to anchor it to the periplasmic
face of the inner membrane, though eighteen are required for full binding |CITS: [3536487][3330754]|.
Truncated, unbound DacA is water soluble, functional in vitro and
can be crystallized |CITS: [3276513]|. The carboxy-terminal eighteen residues of DacA are sufficient
to anchor a heterofusion protein to the inner membrane, whereas the signal sequence is
dispensable for DacA localization |CITS: [3054422]|. DacA anchors to the inner membrane even in the
absence of anionic phospholipids |CITS: [7607402]|. Surface pressure tests reveal that the DacA-membrane
interaction is mostly hydrophobic in character |CITS: [9858668]|. Membrane anchoring depends on the alpha-helical
conformation of the eighteen residues at the carboxy-terminus |CITS: [9371419][9858668]|.
This section of the protein appears to be deeply imbedded in various test membranes, which may suggest
oblique orientation within the inner membrane in vivo |CITS: [12444970]|. Though DacA becomes
urea-extractable in the presence of benzyl penicillin, indicating a role for the non-membrane domain of
the protein in membrane anchoring, the ability to anchor probably does not involve a conformational change
in the carboxy-terminal alpha helix itself |CITS: [8486152][11779187]|.
Mutations in dacA can lead to defective peptidoglycan morphology, resulting in branching when cell division
is blocked and failure to divide properly when the regulatory gene bolA is overexpressed |CITS: [15576782][12562782][12354237][11325933]|. Deletion of dacA suppresses mutations in the cell division gene ftsK |CITS: [7592387]|.
dacA mutants are viable, as are dacA dacC double mutants and even strains with deletions of up to eight of the known penicillin-binding
proteins at once, dacA included |CITS: [7002911][3903044][10383966]|.
BolA controls transcription of dacA, and through it controls the peptidoglycan layer |CITS: [12354237]|.
Overexpression of DacA has deleterious effects including lysis during early exponential phase growth, but overexpression of soluble DacA is possible, and leads
to formation of ordered DacA crystals within cells |CITS: [6348028][11325933][1490594]|.
The crystal structure of DacA has been
determined to a 1.9 Angstrom resolution |CITS:[14555648]|.)""",]},
'B3654' : {'ecocyc-rxns': {"""RXN-5076""": """xanthine[periplasmic space] + H+[periplasmic space] =xanthine[cytosol] + H+[cytosol] """,},'ucsd-rxns' : ['ADEt2rpp','XANt2pp','GUAt2pp',], 'protein-comments' : ["""(The YicE protein is a member of the NCS2 family of nucleobase transporters. YicE is a specific,
high-affinity, proton motive force-dependent xanthine transporter with a Km of 2.9 to 3.8 μM
|CITS:[16096267]|. YicE is unable to transport guanine, hypoxanthine, uric acid, and uracil, or to
efficiently recognize certain xanthine or uric acid analogues |CITS:[16096267]|.
)""",]},
'B3653' : {'ecocyc-rxns': {"""TRANS-RXN-122""": """Na+[periplasmic space] + L-glutamate[periplasmic space] =Na+[cytosol] + L-glutamate[cytosol] """,},'ucsd-rxns' : ['GLUt4pp',], 'protein-comments' : ["""(GltS is a sodium dependent glutamate transporter which is specific for
D- and L-glutamate. E. coli K12 cannot grow on glutamate as a
sole carbon and nitrogen source, selection of mutants which can grow
on glutamate (Glt+) are typically due to mutations which overexpress either
the GltS or GltP glutamate transporters |CITS: [90218004]|. Transduction
of a gltS knockout mutation into a gltS overexpressing
strain renders the cell Glts-, and this phenotype could be complemented
by the cloned gltS gene |CITS: [91203811]|. Whole cell transport
experiments have shown that GltS is sodium dependent with a Km of approx
1.5 μM |CITS: [78046051]|. This has been confirmed in E. coli membrane
vesicles, where GltS was shown to function via an electrogenic symport
mechanism with L-glutamate co-transported with at least two sodium ions
|CITS: [96154946]|. GltS is the only characterised member of the GltS
family of transporters.)""",]},
'B0635' : {'ecocyc-rxns': {},'ucsd-rxns' : ['MCTP2App','MCTP1App',], 'protein-comments' : ["""(The mrdA (or pbpA) gene encodes the PBP2 protein responsible for maintaining the rod cell shape and mecillinam sensitivity in E. coli along with rodA |CITS:[6243629]|, |CITS:[1091862]|. The pbpA and rodA genes are members of a single transcriptional unit called the rodA operon, and rodA also has its own promoter within the pbpA gene |CITS:[2644207]|, |CITS:[6300030]|. Biochemical assays have shown that PBP2 is probably a bifunctional enzyme involved in the formation and cross-linking of peptidoglycan by transglycosylation and transpeptidation |CITS:[3009484]|. The active site was identified by the SXXK box at serine 330 |CITS:[3533535]|. The transpeptidase activity and penicillin-binding property of PBP2 are separable |CITS:[2656638]|. PBP2 exists at an estimated 10 to 20 copies per cell |CITS:[319999]|. The pbpA gene has been found to be deleterious for growth at high copy number |CITS:[6348028]|. PBP2 has no signal peptide, and a stretch of 25 non-ionic amino acids in the N-terminal region anchors the protein in the inner membrane |CITS:[3533535]|. GFP-PBP2 fusions have been shown to localize in the cylindrical portion of the cell membrane as well as at the site of constriction prior to division, but not in the old pole. The signal at the site of constriction disappears just before separation of daughter cells. This localization at mid-cell was dependent upon active PBP3, though PBP2 was found to not be a stable component of the divisome. PBP2 is active at the division site and required to maintain the diameter of the newly formed pole there |CITS:[12519203]|.
Mutation or inhibition of PBP2 alone or coupled with mutation or inhibition of other proteins involved in murein synthesis or cell division have been isolated and characterized. |CITS:[345275]|, |CITS:[201607]|, |CITS:[363690]|, |CITS:[6243629]|, |CITS:[6451612]|, |CITS:[7007327]|, |CITS:[7027927]|, |CITS:[3894330]|, |CITS:[2066344]|, |CITS:[8407846]|, |CITS:[2656638]|, |CITS:[1038366]|, |CITS:[1103132]|, |CITS:[11418550]|.
Buoyant density studies of pbpA mutants have been performed |CITS:[1885519]|.
)""",]},
'B3650' : {'ecocyc-rxns': {"""GDPPYPHOSKIN-RXN""": """ATP + GDP = AMP + guanosine 5'-diphosphate,3'-diphosphate""","""PPGPPSYN-RXN""": """guanosine 5'-diphosphate,3'-diphosphate + H2O = diphosphate + GDP""",},'ucsd-rxns' : ['PPGPPDP','GDPDPK',], 'protein-comments' : ["""NIL""",]},
'B4238' : {'ecocyc-rxns': {"""NRDACTMULTI-RXN""": """reduced flavodoxin + inactive ribonucleoside triphosphate reductase + S-adenosyl-L-methionine = 5'-deoxyadenosine + oxidized flavodoxin + active ribonucleoside triphosphate reductase + L-methionine""","""RXN0-745""": """ATP + reduced flavodoxin = dATP + oxidized flavodoxin + H2O""","""RXN0-746""": """GTP + reduced flavodoxin = dGTP + oxidized flavodoxin + H2O""","""RXN0-724""": """UTP + reduced flavodoxin = dUTP + oxidized flavodoxin + H2O""","""RXN0-723""": """CTP + reduced flavodoxin = dCTP + oxidized flavodoxin + H2O""","""RIBONUCLEOSIDE-TRIP-REDUCT-RXN""": """reduced flavodoxin + a ribonucleoside triphosphate = H2O + oxidized flavodoxin + a 2'-deoxyribonucleoside triphosphate""",},'ucsd-rxns' : ['RNTR3c','RNTR3c','RNTR3c','RNTR3c','RNTR4c','RNTR4c','RNTR4c','RNTR4c','RNTR1c','RNTR1c','RNTR1c','RNTR1c','RNTR2c','RNTR2c','RNTR2c','RNTR2c',], 'protein-comments' : ["""(The NrdD reductase is activated by the NrdG activase under anaerobic conditions and is inactivated by oxygen.
The protein is highly sensitive to O2.
An nrdD null mutant does not grow under entirely anaerobic conditions, but grows under aerobic or
microaerophilic conditions due to the activity of NrdA and/or NrdB |CITS: [8954104]|.)""","""NIL""","""(The anaerobic nucleoside-triphosphate reductase activating
system is composed of three enzymes and several compounds. Anaerobic
nucleoside-triphosphate reductase is activated through the action of a
specific activating enzyme, nucleoside-triphosphate reductase
activase, flavodoxin NADP+ reductase, S-adenosylmethionine, flavodoxin
and NADPH. All of these components form a multi-enzyme complex with
the ribonucleoside reductase itself. |CITS: [93194782] [95155298]|)""",]},
'B4239' : {'ecocyc-rxns': {"""TRE6PHYDRO-RXN""": """trehalose 6-phosphate + H2O = β-D-glucose-6-phosphate + β-D-glucose""",},'ucsd-rxns' : ['TRE6PH',], 'protein-comments' : ["""NIL""",]},
'B2464' : {'ecocyc-rxns': {"""TRANSALDOL-RXN""": """D-glyceraldehyde-3-phosphate + D-sedoheptulose-7-phosphate = D-fructose-6-phosphate + D-erythrose-4-phosphate""",},'ucsd-rxns' : ['TALA',], 'protein-comments' : ["""(There are two closely related transaldolases in E. coli.
Regulation has been described |CITS: [11350954]|. Transcription is induced by the CreBC two-component system by minimal media growth conditions |CITS: [11350954]|.)""",]},
'B2052' : {'ecocyc-rxns': {"""1.1.1.271-RXN""": """NADP+ + GDP-L-fucose = NADPH + GDP-4-dehydro-6-deoxy-D-mannose""",},'ucsd-rxns' : ['GDMANE','GOFUCR',], 'protein-comments' : ["""(GDP-fucose synthase is a bifunctional enzyme that catalyzes the two-step synthesis of GDP-fucose from
GDP-4-dehydro-6-deoxy-D-mannose via a GDP-4-dehydro-6-L-deoxygalactose intermediate |CITS: [9473059]|.
The presence of the GDP-4-dehydro-6-L-deoxygalactose intermediate was initially postulated, but not shown
|CITS: [13705522]|. The epimerase reaction can occur in the absence of the NADPH cofactor |CITS: [10480878]|.
The enzyme belongs to the reductase-epimerase-dehydrogenase (RED) superfamily. Its N-terminal domain
contains a six-stranded NADP+ binding Rossmann fold domain |CITS: [9817848]|. Crystal structure data suggests
that there is a single active site |CITS: [9862812]|. The reaction follows a random bi-bi mechanism |CITS: [10480878]|.
Mutants in proposed active site residues have been isolated and characterized |CITS: [11021971]|.
The enzyme is a homodimer |CITS: [9761875][9817848]|.)""","""NIL""",]},
'B2053' : {'ecocyc-rxns': {"""GDPMANDEHYDRA-RXN""": """GDP-D-mannose -> H2O + GDP-4-dehydro-6-deoxy-D-mannose""",},'ucsd-rxns' : ['GMAND',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B2051' : {'ecocyc-rxns': {"""GDP-GLUCOSIDASE-RXN""": """GDP-D-glucose + H2O = β-D-glucose + GDP""","""GDPMANMANHYDRO-RXN""": """GDP-D-mannose + H2O = GDP + mannose""",},'ucsd-rxns' : ['GDPMNH',], 'protein-comments' : ["""(GDP-mannose mannosyl hydrolase is able to hydrolyze both GDP-mannose and GDP-glucose.
Its biological role is as yet unknown, though it may participate in the regulation of cell wall biosynthesis by influencing
the cell concentration of GDP-mannose or GDP-glucose. Another possible
role is providing GDP for the synthesis of GDP-fucose. |CITS: [96025790]|)""",]},
'B1606' : {'ecocyc-rxns': {"""DIHYDROFOLATEREDUCT-RXN""": """NADP+ + tetrahydrofolate = NADPH + 7,8-dihydrofolate""",},'ucsd-rxns' : ['DHFR',], 'protein-comments' : ["""(The folM gene encodes a dihydrofolate reductase |CITS: [14617668]|.)""",]},
'B2750' : {'ecocyc-rxns': {"""ADENYLYLSULFKIN-RXN""": """APS + ATP = 3'-phosphoadenylyl-sulfate + ADP""",},'ucsd-rxns' : ['ADSK',], 'protein-comments' : ["""NIL""","""(The enzyme exists predominantly as a homodimer, but a
tetrameric form exists when the enzyme is dephosphorylated. |CITS:
[SatischandranJBC264,15012]|)""",]},
'B4232' : {'ecocyc-rxns': {"""F16BDEPHOS-RXN""": """fructose-1,6-bisphosphate + H2O = D-fructose-6-phosphate + phosphate""",},'ucsd-rxns' : ['FBP',], 'protein-comments' : ["""NIL""","""(fructose 1,6 bisphosphatase is necessary for growth on
substances such as glycerol, succinate and acetate.|CITS:[88335617]|
In nondenaturing conditions the enzyme is present in several
aggregated forms in which the tetramer seems to predominate
at low enzyme concentrations. |CITS:[84022600]|)""",]},
'B4233' : {'ecocyc-rxns': {"""RXN0-2361""": """UDP-N-acetylmuramate + L-Ala-D-Glu-meso-A2pm + ATP -> UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminoheptanedioate + ADP + phosphate""",},'ucsd-rxns' : ['UM4PL','UM3PL',], 'protein-comments' : ["""(The mpl gene encodes UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-meso-diaminopimelate ligase, which acts in murein recycling |CITS: [8808921]|.
An mpl mutation is not lethal |CITS: [8808921]|.
Mpl, "murein peptide ligase" |CITS: [8808921]|.
Review: |CITS: [9158731]|.)""",]},
'B1602' : {'ecocyc-rxns': {"""1.6.1.2-RXN""": """NAD+ + NADPH = NADH + NADP+""",},'ucsd-rxns' : ['THD2pp','NADTRHD',], 'protein-comments' : ["""NIL""","""(Pyridine nucleotide transhydrogenase catalyzes the reversible transfer of a hydride ion equivalent between NAD and
NADP. The enzyme functions as a proton pump, translocating protons from the cytosolic side of the membrane to
the outside. The functional enzyme assembles as a tetramer composed of two alpha and two beta subunits. PntAB
is a major source of NADPH in the cell |CITS: [14660605]|.
E. coli contains both a soluble and a membrane-bound proton-translocating pyridine nucleotide
transhydrogenase. The soluble pyridine nucleotide transhydrogenase is the sthA gene product; its primary
physiological role appears to be the reoxidation of NADPH |CITS: [11731130][14660605]|. The two
transhydrogenases are also distinguished by the stereospecificity of the reducing equivalents transfer. SthA is a
BB-specific transhydrogenase, while PntAB is AB-specific.
Transcription of pntA is downregulated by growth on acetate |CITS: [14660605]|.
)""",]},
'B1603' : {'ecocyc-rxns': {"""1.6.1.2-RXN""": """NAD+ + NADPH = NADH + NADP+""",},'ucsd-rxns' : ['THD2pp','NADTRHD',], 'protein-comments' : ["""NIL""","""(Pyridine nucleotide transhydrogenase catalyzes the reversible transfer of a hydride ion equivalent between NAD and
NADP. The enzyme functions as a proton pump, translocating protons from the cytosolic side of the membrane to
the outside. The functional enzyme assembles as a tetramer composed of two alpha and two beta subunits. PntAB
is a major source of NADPH in the cell |CITS: [14660605]|.
E. coli contains both a soluble and a membrane-bound proton-translocating pyridine nucleotide
transhydrogenase. The soluble pyridine nucleotide transhydrogenase is the sthA gene product; its primary
physiological role appears to be the reoxidation of NADPH |CITS: [11731130][14660605]|. The two
transhydrogenases are also distinguished by the stereospecificity of the reducing equivalents transfer. SthA is a
BB-specific transhydrogenase, while PntAB is AB-specific.
Transcription of pntA is downregulated by growth on acetate |CITS: [14660605]|.
)""",]},
'B4237' : {'ecocyc-rxns': {"""NRDACTMULTI-RXN""": """reduced flavodoxin + inactive ribonucleoside triphosphate reductase + S-adenosyl-L-methionine = 5'-deoxyadenosine + oxidized flavodoxin + active ribonucleoside triphosphate reductase + L-methionine""","""RNTRACTIV-RXN""": """S-adenosyl-L-methionine + inactive ribonucleoside triphosphate reductase = 5'-deoxyadenosine + active ribonucleoside triphosphate reductase + L-methionine""",},'ucsd-rxns' : ['RNTR3c','RNTR3c','RNTR4c','RNTR4c','RNTR1c','RNTR1c','RNTR2c','RNTR2c',], 'protein-comments' : ["""(An nrdG null mutant does not grow under entirely anaerobic conditions, but grows under
aerobic or microaerophilic conditions due to the activity of NrdA and/or NrdB |CITS: [8954104]|.
The NrdG activase activates the NrdD reductase under anaerobic conditions.)""","""NIL""","""(The anaerobic nucleoside-triphosphate reductase activating
system is composed of three enzymes and several compounds. Anaerobic
nucleoside-triphosphate reductase is activated through the action of a
specific activating enzyme, nucleoside-triphosphate reductase
activase, flavodoxin NADP+ reductase, S-adenosylmethionine, flavodoxin
and NADPH. All of these components form a multi-enzyme complex with
the ribonucleoside reductase itself. |CITS: [93194782] [95155298]|)""",]},
'B3809' : {'ecocyc-rxns': {"""DIAMINOPIMEPIM-RXN""": """L,L-diaminopimelate = meso-diaminopimelate""",},'ucsd-rxns' : ['DAPE',], 'protein-comments' : ["""NIL""",]},
'B1897' : {'ecocyc-rxns': {"""TREHALOSEPHOSPHA-RXN""": """trehalose 6-phosphate + H2O = trehalose + phosphate""",},'ucsd-rxns' : ['TRE6PP',], 'protein-comments' : ["""(E. coli contains two trehalose-6-phosphate phosphatases, a biosynthetic enzyme encoded by the otsB
gene, and a catabolic one encoded by the treE gene |CITS: [91334986][92121128]|. Phosphatase activity of
OtsB was found in a high-throughput screen of purified proteins |CITS: [15808744]|.
Expression of biosynthetic enzyme OtsB is increased under osmotic stress |CITS: [3131312]| and induced during the
transition to stationary phase and by low temperature in a sigmaS-dependent manner |CITS: [1744047][12105274]|.
Stability of otsBA mRNA is increased approximately 10-fold at 16 degrees C compared to 37 degrees C
|CITS: [12105274]|. Accumulation of trehalose at low temperatures enhances cell viability |CITS: [12105274]|. An
otsBA double mutant is more sensitive than wild type to heat shock during stationary phase, but not during
exponential growth |CITS: [1744047]|.
OtsB: "osmoregulatory trehalose synthesis" |CITS: [3131312]|
Reviews: |CITS: [8391102][12626396]|)""",]},
'B3860' : {'ecocyc-rxns': {"""DISULFOXRED-RXN""": """a protein with reduced sulfide groups = a protein with oxidized disulfide bonds""",},'ucsd-rxns' : ['DSBAO2','DSBAO1',], 'protein-comments' : ["""NIL""",]},
'B0096' : {'ecocyc-rxns': {"""UDPACYLGLCNACDEACETYL-RXN""": """UDP-3-O-(3-hydroxymyristoyl)-N-acetylglucosamine + H2O -> UDP-3-O-(3-hydroxymyristoyl)glucosamine + acetate""",},'ucsd-rxns' : ['UHGADA',], 'protein-comments' : ["""NIL""",]},
'B3517' : {'ecocyc-rxns': {"""GLUTDECARBOX-RXN""": """L-glutamate -> CO2 + 4-aminobutyrate""",},'ucsd-rxns' : ['GLUDC',], 'protein-comments' : ["""(There are two distinct E. coli GAD polypeptides which are
highly similar to one another. They map to different positions and
neither is where the gene gadS is said to be located. GadS is also
known as a synonym for the gene coding for glutamate decarboxylase
alpha, gadA. |CITS: [92394884]|
Regulation has been described |CITS: [12940989]|.)""","""NIL""",]},
'B1539' : {'ecocyc-rxns': {"""RXN0-2201""": """L-serine + NADP+ -> 2-aminomalonate-semialdehyde + NADPH + H+""",},'ucsd-rxns' : ['LSERDHr','DSERDHr','ATHRDHr',], 'protein-comments' : ["""(The ydfG gene encodes a homotetrameric NADP(+)-dependent 3-hydroxy acid dehydrogenase
|CITS: [12535615]|.)""","""NIL""",]},
'B3114' : {'ecocyc-rxns': {"""KETOBUTFORMLY-RXN""": """2-oxobutanoate + coenzyme A = propionyl-CoA + formate""","""PYRUVFORMLY-RXN""": """formate + acetyl-CoA = pyruvate + coenzyme A""",},'ucsd-rxns' : ['PFL','OBTFL',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B2153' : {'ecocyc-rxns': {"""GTP-CYCLOHYDRO-I-RXN""": """GTP + H2O = formate + 7,8-dihydroneopterin 3'-triphosphate""",},'ucsd-rxns' : ['GTPCI',], 'protein-comments' : ["""NIL""","""(GTP cyclohydrolase I is an allosteric enzyme that catalyzes the first step in the biosynthesis of tetrahydrofolate
|CITS: [68234722] [92172284] [93092993]|. The enzymatic reaction has a complex mechanism and appears to
encompass four steps, with the intermediates being enzyme-bound. Detailed studies of the kinetics and reaction
mechanism of the enzyme have been performed |CITS: [11056154][11866535][12559918]|.
Crystal structures and electron microscope observations of GTP cyclohydrolase I have shown a homodecamer that
forms a torus |CITS: [7663943][7473713][12559918]|. The active site appears to be located between dimers, and the
active enzyme is composed of a pentamer of five dimers |CITS: [8618856][12297008]|. Each polypeptide seems to
contain one GTP binding site |CITS: [76260232][92172284]|.
)""",]},
'B3116' : {'ecocyc-rxns': {"""TRANS-RXN-71""": """H+[periplasmic space] + L-serine[periplasmic space] =H+[cytosol] + L-serine[cytosol] ""","""TRANS-RXN-72""": """H+[periplasmic space] + L-threonine[periplasmic space] =H+[cytosol] + L-threonine[cytosol] """,},'ucsd-rxns' : ['THRt2rpp','SERt2rpp',], 'protein-comments' : ["""(TdcC is a threonine transport system, likely to function as a threonine/proton
symporter. Disruption of tdcC reduced threonine uptake under anaerobic
conditions, and this defect could be complemented by the cloned tdcC
gene |CITS: [90330531]|. The TdcC transport system displayed a Km of approx
6 μM and threonine transport was inhibited by uncouplers, suggesting it
is a high affinity threonine/proton symporter |CITS: [90330531]|. TdcC has
also been shown to be a proton-driven serine transporter |CITS: [98158336]|.
TdcC is a member of the STP family of amino acid transporters, and is
homologous to the serine transporter SdaC.
The tdcC gene is located in the tdcABC operon, which also codes
for threonine dehydratase |CITS: [89033926]|. Expression of tdc-lacZ fusions
has indicated that this operon is expressed under anaerobic conditions
|CITS: [90330531]|. Threonine and serine imported under anaerobic conditions
are degraded to ammonia and the corresponding α-keto acids.)""",]},
'B3117' : {'ecocyc-rxns': {"""THREDEHYD-RXN""": """L-threonine -> 2-oxobutanoate + ammonia""",},'ucsd-rxns' : ['THRD_L',], 'protein-comments' : ["""NIL""","""(The enzyme is induced in anaerobic conditions in rich medium.)""",]},
'B1901' : {'ecocyc-rxns': {"""ABC-2-RXN""": """H2O + α-L-arabinose[periplasmic space] + ATP =α-L-arabinose[cytosol] + phosphate + ADP """,},'ucsd-rxns' : ['ARBabcpp',], 'protein-comments' : ["""NIL""","""(The AraFGH arabinose transporter is a member of the ATP Binding Cassette (ABC) transporter superfamily.
Expression of all three components was necessary to complement high-affinity arabinose transport in an
araFGH knockout strain |CITS: [89255061]| Membrane vesicle studies have shown that there are
two main arabinose uptake systems in E. coli: the low affinity proton-driven AraE transporter and a
high affinity ATP-driven system utilizing AraF as a binding protein |CITS:[82205973]|. The AraF binding
protein has been purified, crystallized and its high resolution structure shown to bind arabinose
|CITS:[78070158]|. Based on sequence similarity, AraH is the membrane component and AraG is the
ATP-binding component of this ABC transporter |CITS: [88062740]|.)""",]},
'B3290' : {'ecocyc-rxns': {},'ucsd-rxns' : ['Kt2pp','Kt2pp',], 'protein-comments' : ["""(trkA mutants were identified in a kdp background as
requiring significantly elevated levels of K+ for growth
|CITS:[4942756]|. trkA encodes part of a K+
transport system |CITS:[4942756]|. The TrkA system is constitutive
with a Km of 1.5 mM |CITS:[4578]|. K+ uptake by TrkA
is both ATP-dependent and protonmotive force (pmf)-driven |CITS:[320207]|,
though K+ exchange is not dependent upon the pmf
|CITS:[359759]|. TrkA is inhibited by high intracellular K+
|CITS:[359759]| and by low pH |CITS:[6405784]|. Efflux of K+
by TrkA depends upon the intracellular concentration of K+
|CITS:[7042336]|. trkE, trkG, and trkH mutations reduced
or prevented binding of TrkA to the membrane |CITS:[2674131]|.
The TrkG and TrkH membrane proteins were identified as two different
but nearly equivalent systems of K+ uptake, each requiring
TrkA and TrkE |CITS:[1987159]|. UV crosslinking studies showed binding
of TrkA to NAD+ but not to ATP |CITS:[8412700]|. The TrkA pump may
be involved in regulation of pH in anaerobically growing cells at alkaline
pH |CITS:[9829260]|. The F0F1 ATPase is
dependent on TrkA when cells are grown anaerobically on glucose at
alkaline pH |CITS:[12804571]|.)""",]},
'B0124' : {'ecocyc-rxns': {"""GLUCDEHYDROG-RXN""": """β-D-glucose + a ubiquinone = glucono-δ-lactone + a ubiquinol""",},'ucsd-rxns' : ['GLCDpp',], 'protein-comments' : ["""NIL""",]},
'B0125' : {'ecocyc-rxns': {"""GUANPRIBOSYLTRAN-RXN""": """guanine + 5-phosphoribosyl 1-pyrophosphate -> diphosphate + GMP""","""HYPOXANPRIBOSYLTRAN-RXN""": """diphosphate + inosine-5'-phosphate = 5-phosphoribosyl 1-pyrophosphate + hypoxanthine""",},'ucsd-rxns' : ['GUAPRT','HXPRT',], 'protein-comments' : ["""NIL""",]},
'B0126' : {'ecocyc-rxns': {"""CARBODEHYDRAT-RXN""": """H2CO3 = H2O + CO2""",},'ucsd-rxns' : ['HCO3E',], 'protein-comments' : ["""(The can gene encodes a carbonic anhydrase |CITS: [14563877]|.
A can mutant shows a defect in growth under normal atmospheric conditions, but the mutant can grow under conditions with a high exogenous or endogenous supply of CO2 |CITS: [14563877]|.
Can has similarity to CynT, and induction of cynT expression suppresses phenotypes of a can mutant |CITS: [14563877]|. A can cynT double mutant is only viable under high CO2 conditions |CITS: [12784642]|. Expression of a carbonic anhydrase from Methanosarcina thermophila partially functionally complements phenotypes of a can mutant |CITS: [14563877]|.
Regulation has been described |CITS: [14563877]|.)""",]},
'B1876' : {'ecocyc-rxns': {"""ARGININE--TRNA-LIGASE-RXN""": """tRNAarg + L-arginine + ATP = L-arginyl-tRNAarg + diphosphate + AMP""",},'ucsd-rxns' : ['ARGTRS',], 'protein-comments' : ["""(ArgS is a member of the family of aminoacyl tRNA synthetases, which interpret the genetic code by covalently linking amino acids to their specific tRNA molecules. The reaction is driven by ATP hydrolysis.
ArgS belongs to the Class I aminoacyl tRNA synthetases; apart from sequence motifs within the active site, the different enzymes show little similarity in their primary amino acid sequences.
The argS gene has been cloned; the protein coding region uses the unusual initiation codon GUG and has a codon usage pattern which is typical for highly expressed genes |CITS: [2668891]|.
Several mutations in the argS gene have been described. The MA5002 mutant encodes a serine in place of arginine at position 134, close to the active site. The purified enzyme shows defects in enzymatic activity and Km value for ATP |CITS: [2183195]|.
The lov-1 mutation confers a slow growth phenotype as well as mecillinam resistance, which appears to be dependent on the RelA-mediated stringent response |CITS: [1563353]|. Similarly, an argS mutant conferring novobiocin resistance has been isolated |CITS: [10217798]|.
A mutant deleting the arginine residue at position 245 was constructed, and the resulting protein was purified by renaturation from inclusion bodies; the specific activity of the purified enzyme was 0.3 % of the native enzyme |CITS: [12167998]|.
The crystal structure of the ArgS enzyme has been determined at 2.8 Å and 3.1 Å resolutions |CITS: [9416614]|.
Conformational changes induced by interactions with tRNA substrates have been studied |CITS: [14672708][12860413][12232610]|, and specific interations with nucleotide residues in some tRNA species have been determined |CITS: [11733016]|.
)""",]},
'B4090' : {'ecocyc-rxns': {"""RXN0-303""": """D-allose-6-phosphate = D-allulose-6-phosphate""","""RIB5PISOM-RXN""": """D-ribose-5-phosphate = D-ribulose-5-phosphate""",},'ucsd-rxns' : ['ALLPI','RPI',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B3058' : {'ecocyc-rxns': {"""H2NEOPTERINALDOL-RXN""": """dihydro-neo-pterin -> glycolaldehyde + 6-hydroxymethyl-dihydropterin""",},'ucsd-rxns' : ['DHNPA2',], 'protein-comments' : ["""(Dihydroneopterin aldolase is an enzyme in the tetrahydrofolate biosynthesis pathway, an important antibacterial drug
target.
FolB can also catalyze the reversible epimerization of the 3' position of dihydroneopterin, yielding dihydromonapterin
|CITS: [9651328]|.)""","""NIL""",]},
'B1873' : {'ecocyc-rxns': {"""1.7.2.3-RXN""": """trimethylamine + 2 oxidized cytochrome c + H2O -> trimethylamine-N-oxide + 2 reduced cytochrome c + 2 H+""",},'ucsd-rxns' : ['DMSOR2pp','DMSOR1pp','TMAOR1pp','TMAOR2pp',], 'protein-comments' : ["""(TorY is a c-type cytochrome that is anchored to the inner membrane. |CITS: [20461225]|)""","""(The torYZ-encoded trimethylamine N-oxide (TMAO) reductase III
represents a third TMAO respiratory system in E. coli. TorZ
is the catalytic subunit and TorY the pentahemic
c-type cytochrome subunit. The enzyme has broad substrate
specificity; it is able to reduce N- and S-oxide compounds. TMAO is
the best substrate for the enzyme. |CITS: [20461225]|
Expression of torYZ is very low and not inducible by TMAO, DMSO or BSO |CITS: [20461225]|.)""",]},
'B1872' : {'ecocyc-rxns': {"""1.7.2.3-RXN""": """trimethylamine + 2 oxidized cytochrome c + H2O -> trimethylamine-N-oxide + 2 reduced cytochrome c + 2 H+""",},'ucsd-rxns' : ['DMSOR2pp','DMSOR1pp','TMAOR1pp','TMAOR2pp',], 'protein-comments' : ["""(TorZ is the catalytic subunit of TMAO reductase III.
The TorZ protein was first identified as a biotin sulfoxide (BSO)
reductase, and the gene was named bisZ |CITS: [8919859]|. Recent work
has shown that the reductase is more efficient with TMAO
as a substrate than BSO. TorZ is exported to the periplasm via the Tat pathway. |CITS: [20461225]|)""","""(The torYZ-encoded trimethylamine N-oxide (TMAO) reductase III
represents a third TMAO respiratory system in E. coli. TorZ
is the catalytic subunit and TorY the pentahemic
c-type cytochrome subunit. The enzyme has broad substrate
specificity; it is able to reduce N- and S-oxide compounds. TMAO is
the best substrate for the enzyme. |CITS: [20461225]|
Expression of torYZ is very low and not inducible by TMAO, DMSO or BSO |CITS: [20461225]|.)""",]},
'B0087' : {'ecocyc-rxns': {"""PHOSNACMURPENTATRANS-RXN""": """UDP-N-acetylmuramoyl-pentapeptide + undecaprenyl phosphate = N-acetylmuramoyl-pentapeptide-diphosphoundecaprenol + UMP""",},'ucsd-rxns' : ['PAPPT3',], 'protein-comments' : ["""NIL""",]},
'B0086' : {'ecocyc-rxns': {"""UDP-NACMURALGLDAPAALIG-RXN""": """D-alanyl-D-alanine + UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminoheptanedioate + ATP = UDP-N-acetylmuramoyl-pentapeptide + phosphate + ADP""",},'ucsd-rxns' : ['UGMDDS',], 'protein-comments' : ["""NIL""",]},
'B0085' : {'ecocyc-rxns': {"""UDP-NACMURALGLDAPLIG-RXN""": """meso-diaminopimelate + UDP-N-acetylmuramoyl-L-alanyl-D-glutamate + ATP = UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminoheptanedioate + phosphate + ADP""",},'ucsd-rxns' : ['UAAGDS',], 'protein-comments' : ["""NIL""",]},
'B0084' : {'ecocyc-rxns': {},'ucsd-rxns' : ['MCTP2App','MCTP1App',], 'protein-comments' : ["""(FtsI (penicillin-binding protein 3, PBP3) is an essential cell division protein |CITS: [1103132]| which is present at low
abundance of about 100 molecules per cell |CITS: [9379897]|. Binding of beta-lactam antibiotics to FtsI inhibits FtsI
activity and is lethal |CITS: [3902760]|. FtsI is localized to the division site; localization is dependent on FtsZ, FtsA,
FtsQ, FtsL, and FtsW, but not FtsN |CITS: [9379897][9603865][9882665][11703663][11807049]|. FtsA alone can
force FtsI to localize to the cell poles independently of the Z ring, suggesting that FtsA and FtsI interact in a separate
pathway |CITS: [15516588]|. This is supported by bacterial two-hybrid evidence |CITS: [14663069]|.
FtsI contains a small N-terminal cytoplasmic domain, a transmembrane helix and a C-terminal periplasmic region that
can be separated into a noncatalytic and a catalytic domain |CITS: [2677607][9614966]|. The cytoplasmic domain
and transmembrane helix are essential for its role in cell division |CITS: [9260951][8631709]|. The transmembrane
helix is necessary and sufficient for localization of FtsI to the Z ring |CITS: [9882665][14702319][15601716]|. The
noncatalytic periplasmic domain is required for recruitment of FtsN |CITS: [14702319]|. The catalytic C-terminal
domain contains the transpeptidase activity and is involved in peptidoglycan synthesis at the division septum
|CITS: [6450748][3531167][9260951]|. Constriction of the Z ring during cell division requires the transpeptidase
activity of FtsI |CITS: [9012823]|. The C-terminal 349 amino acids contain the penicillin-binding region
|CITS: [6092133]|. A fraction of FtsI molecules are modified with glycerol and fatty acids |CITS: [3053665]|.
Overproduction of FtsI suppresses the filamentous phenotype of strains with mutations in ftsI and ftsH
|CITS: [3316193]|.
Inactivation of FtsI by binding of beta-lactam antibiotics or mutagenesis induces the SOS response via the DpiBA
two-component signal transduction system. The resulting cell division arrest may enable survival of the cells despite
exposure to otherwise lethal antibiotics |CITS: [15308764]|.
Selected reviews: |CITS: [15491352][12626683][9614966]|)""",]},
'B2281' : {'ecocyc-rxns': {"""NADH-DEHYDROG-A-RXN""": """ubiquinone-8 + NADH = ubiquinol-8 + NAD+""",},'ucsd-rxns' : ['NADH17pp','NADH18pp','NADH16pp',], 'protein-comments' : ["""(This subunit contains the two 4Fe-4S clusters N6a and N6b. |CITS: [93389724][98256007][11352750]|
NuoI is part of the connecting fragment of NADH dehydrogenase I |CITS: [7607227]|.)""","""(This complex is thought to connect the soluble fragment of NADH dehydrogenase I to the inner membrane
components |CITS: [7607227]|.)""","""(There is a cluster of 13 genes that code for NADH dehydrogenase I. Six of the subunits are peripheral proteins and
the other seven are very hydrophobic |CITS: [94178656] [98256007]|. Three-dimensional reconstruction of the
complex based on cryo-electron microscopy showed an L-shaped form with an integral membrane and a peripheral
arm |CITS: [9514725]|. A model of the spatial arrangement of the subunits and the possible functional mechanism of
proton pumping has been proposed |CITS: [12923180]|.)""",]},
'B0870' : {'ecocyc-rxns': {"""LTAA-RXN""": """L-allo-threonine = glycine + acetaldehyde""",},'ucsd-rxns' : ['ALATA_D2','THRA2i','THRAi','ALATA_L2',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B0871' : {'ecocyc-rxns': {"""RXN0-2022""": """pyruvate + acetaldehyde -> acetoin + CO2""","""PYRUVOXID-RXN""": """pyruvate + ubiquinone-8 + H2O = acetate + CO2 + ubiquinol-8""",},'ucsd-rxns' : ['POX',], 'protein-comments' : ["""(Metabolism of pyruvate via pyruvate oxidase is less efficient than the route via the pyruvate dehydrogenase multienzyme complex; however, the pyruvate oxidase route is important for wild-type growth efficiency and responsible for a significant amount of pyruvate metabolism under aerobic conditions |CITS: [11390679]|.
The enzyme is a homotetramer |CITS: [791368], [321031], [6985891], [6752142]|. Multimerization does not appear to be necessary for enzyme activity |CITS: [2040613]|, however, the domain that interacts with lipid appears to be formed by contribution from two subunits |CITS: [2040613], [9305946], [7713884]|.
The active site residue V380 is an important determinant of substrate specificity |CITS: [11104678]|. The C terminus contains a region of amphipathic alpha helix secondary structure; this region mediates binding to lipids (or detergents) and the concomitant activation of the enzyme |CITS: [2663858], [3902830]|. Pyruvate causes a conformational change in the C terminus, which goes from a solvent-inaccessible state in which the C termini within the tetramer do not interact with each other to a solvent-accessible state in which C termini are proximal |CITS: [9305946], [7713884]|. Interaction with lipids or detergents renders the C termini solvent-inaccessible |CITS: [9305946]|.
Mutations of poxB that diminish pyruvate oxidase enzymatic activity (but not PoxB protein abundance) cause lack of growth in the absence of acetate in a aceEF mutant background |CITS: [6341362]|. Mutant proteins lacking three or nine C-terminal amino acids are defective in activity and in interaction with detergents |CITS: [2663858]|. A mutant protein lacking the C-terminal 24 amino acids exhibits activity in vitro but is defective in lipid activation and detergent binding, and this mutant protein does not support activity in vivo |CITS: [3527254]|. An A467T or P536S mutation causes a defect in activation of the enzyme by lipid |CITS: [3522547]|. An E564P mutation causes a defect in activity and in activation of the enzyme by phospholipid or detergent, whereas a D560P mutation, which lies outside of the predicted lipid-binding region, does not cause defects |CITS: [2663858]|. An R572G mutation shows a partial defect in membrane association and activity in vivo, but does not display apparent defects in vitro |CITS: [2663858]|. Some mutations affect the conformation of the C terminus in the presence of lipid |CITS: [9305946]|. C-terminal cysteine scanning mutations have been generated |CITS: [9305946]|. A V380A, L253F double point mutant exhibits a specific defect in activity toward pyruvate without any defect in activity toward the alternate substrate, 2-oxobutanoate |CITS: [11104678]|. An L253F mutation stimulates enzyme activity |CITS: [11104678]|. A null mutant exhibits wild-type rpoS expression |CITS: [8022274]|.
PoxB has similarity to E. coli IlvB |CITS: [3016647]|, IlvG |CITS: [3016647]|, IlvI |CITS: [3016647]|, and glyoxylate carboligase (Gcl) |CITS: [8440684]|. PoxB also has similarity to pyruvate decarboxylase of Saccharomyces cerevisiae and Zymomonas mobilis. PoxB has similarity to acetohydroxy acid synthases (AHAS) |CITS: [3045082]|.
Purification of the enzyme has been described |CITS: [791368], [3310893]|.
Regulation has been described |CITS: [8022274], [8596457], [9473030]|. Gene expression and protein abundance increases at stationary phase |CITS: [8022274]| Induction requires RpoS |CITS: [8022274], [9473030]|. Gene expression decreases under anaerobic conditions |CITS: [8022274]| and in response to the herbicide and acetolactate synthase inhibitor, sulfometuron methyl |CITS: [9473030]|.)""","""NIL""",]},
'B3794' : {'ecocyc-rxns': {"""UDPMANACATRANS-RXN""": """UDP-N-acetyl-β-D-mannosaminouronate + undecaprenyl-N-acetyl-α-D-glucosaminyl-pyrophosphate = undecaprenyl N-acetyl-glucosaminyl-N-acetyl-mannosaminuronate pyrophosphate + UDP""",},'ucsd-rxns' : ['ACMAMUT',], 'protein-comments' : ["""NIL""",]},
'B2538' : {'ecocyc-rxns': {"""HCAMULTI-RXN""": """3-phenylpropionate + NADH + O2 + H+ = cis-3-(carboxyethyl)-3,5-cyclohexadiene-1,2-diol + NAD+""",},'ucsd-rxns' : ['PPPNDO','CINNDO',], 'protein-comments' : ["""NIL""","""NIL""","""(The 3-phenylpropionate dioxygenase component is the product of the hcaA1 and
hcaA2 genes. HcaC codes for a ferredoxin and hcaD encodes a ferredoxin NAD+
reductase. |CITS: [98269008]|)""",]},
'B3729' : {'ecocyc-rxns': {"""L-GLN-FRUCT-6-P-AMINOTRANS-RXN""": """D-fructose-6-phosphate + L-glutamine -> D-glucosamine-6-phosphate + L-glutamate""",},'ucsd-rxns' : ['GF6PTA',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B3728' : {'ecocyc-rxns': {"""ABC-27-RXN""": """ATP + phosphate[periplasmic space] + H2O =ADP + phosphate[cytosol] + phosphate[cytosol] """,},'ucsd-rxns' : ['PIuabcpp',], 'protein-comments' : ["""NIL""","""(PstABCS is an ATP-dependent phosphate uptake system that is a member of the ATP-Binding Cassette
(ABC) Superfamily of transporters |CITS: [96381453]|. PstABCS is responsible for inorganic phosphate (Pi)
uptake under Pi starvation conditions. Inorganic phosphate is an essential component in cellular function
since phosphorylation of nucleic acids, lipids, sugars, and proteins are important for gene regulation and
signaling |CITS: [91054431]|. Based on sequence similarity, PstA and PstC are the membrane components
of the ABC transporter, while PstS is the periplasmic phosphate binding protein |CITS: [91054431]|, and
PstB is the ATP-binding component of the ABC transporter |CITS: [91054431]|. Whole cell transport
assay indicates that the Pst system has a Km of 0.20 μM |CITS: [82030542]|. Transcription
of the Pst system is induced by Pi starvation, as opposed to the Pit phosphate transport system that is
expressed regardless of Pi level |CITS: [91054431]|.)""",]},
'B0423' : {'ecocyc-rxns': {"""TRNA-S-TRANSFERASE-RXN""": """[IscS]-S-sulfanylcysteine + a tRNA = [IscS]-cysteine + tRNA containing a thionucleotide""","""THIFIS-RXN""": """ThiS-COAMP + L-cysteine = ThiS-COSH + L-alanine + AMP""",},'ucsd-rxns' : ['THZPSN',], 'protein-comments' : ["""(ThiI is required for the synthesis of the thiazole moiety of thiamine and plays a role in the conversion of uridine to
4-thiouridine at position 8 in tRNA |CITS: [6178725][9592144]|. The enzyme is specific for the U8 residue of tRNA;
the substrate specificity appears to be conferred by the secondary and tertiary structure of tRNA |CITS: [15037613]|.
The ThiI protein, but not the IscS protein, was shown to interact with tRNA. In vitro studies using
radiolabelled sulfur showed transfer of sulfur from IscS to ThiI; if tRNA is included, the sulfur appears
to be incorporated into the tRNA in a ThiI- and ATP-dependent manner. Based on these results, a model for
mobilization and transfer of sulfur from cysteine via IscS and ThiI to U8 of tRNA has been presented |CITS: [10753862]|.
The Cys-456 |CITS: [10722656]| and Cys-344 |CITS: [11443125]| residues are critical for the sulfur transfer function
of ThiI, and a mechanism for sulfur transfer including the formation of a disulfide bond between
Cys-456 and Cys-344 during turnover has been proposed |CITS: [11443125]|.
The assignment of thiI to either of the previously identified UV-resistant mutants nuvA or nuvC
remains unclear.)""",]},
'B0907' : {'ecocyc-rxns': {"""PSERTRANSAMPYR-RXN""": """3-hydroxy-4-phospho-hydroxy-α-ketobutyrate + L-glutamate = phospho-hydroxy-threonine + α-ketoglutarate""","""PSERTRANSAM-RXN""": """3-phospho-serine + α-ketoglutarate = 3-phospho-hydroxypyruvate + L-glutamate""",},'ucsd-rxns' : ['OHPBAT','PSERT',], 'protein-comments' : ["""(Epitope-tagged protein overproduced and purified |CITS: [7751290]|.)""","""NIL""",]},
'B4485' : {'ecocyc-rxns': {},'ucsd-rxns' : ['RIBabcpp',], 'protein-comments' : ["""(ATP-binding component of ABC transporter)""","""(YtfR, YtfS, YjfF, YtfT, and YtfQ are uncharacterized members
of the ABC superfamily of transporters |CITS: [99091701]|.
YtfR and YtfS are the putative ATP-binding components.
YjfF and YtfT are the putative membrane components.
YtfQ is the putative binding protein. Based on sequence
similarity they probably function together as an ATP-dependant
sugar transporter. The genes ytfR, ytfS, yjfF,
ytfT, and ytfQ probably constitute a single operon.)""",]},
'B3727' : {'ecocyc-rxns': {"""ABC-27-RXN""": """ATP + phosphate[periplasmic space] + H2O =ADP + phosphate[cytosol] + phosphate[cytosol] """,},'ucsd-rxns' : ['PIuabcpp',], 'protein-comments' : ["""NIL""","""(PstABCS is an ATP-dependent phosphate uptake system that is a member of the ATP-Binding Cassette
(ABC) Superfamily of transporters |CITS: [96381453]|. PstABCS is responsible for inorganic phosphate (Pi)
uptake under Pi starvation conditions. Inorganic phosphate is an essential component in cellular function
since phosphorylation of nucleic acids, lipids, sugars, and proteins are important for gene regulation and
signaling |CITS: [91054431]|. Based on sequence similarity, PstA and PstC are the membrane components
of the ABC transporter, while PstS is the periplasmic phosphate binding protein |CITS: [91054431]|, and
PstB is the ATP-binding component of the ABC transporter |CITS: [91054431]|. Whole cell transport
assay indicates that the Pst system has a Km of 0.20 μM |CITS: [82030542]|. Transcription
of the Pst system is induced by Pi starvation, as opposed to the Pit phosphate transport system that is
expressed regardless of Pi level |CITS: [91054431]|.)""",]},
'B3726' : {'ecocyc-rxns': {"""ABC-27-RXN""": """ATP + phosphate[periplasmic space] + H2O =ADP + phosphate[cytosol] + phosphate[cytosol] """,},'ucsd-rxns' : ['PIuabcpp',], 'protein-comments' : ["""(Protein topology in the inner membrane has been determined |CITS: [11867724]|.)""","""(PstABCS is an ATP-dependent phosphate uptake system that is a member of the ATP-Binding Cassette
(ABC) Superfamily of transporters |CITS: [96381453]|. PstABCS is responsible for inorganic phosphate (Pi)
uptake under Pi starvation conditions. Inorganic phosphate is an essential component in cellular function
since phosphorylation of nucleic acids, lipids, sugars, and proteins are important for gene regulation and
signaling |CITS: [91054431]|. Based on sequence similarity, PstA and PstC are the membrane components
of the ABC transporter, while PstS is the periplasmic phosphate binding protein |CITS: [91054431]|, and
PstB is the ATP-binding component of the ABC transporter |CITS: [91054431]|. Whole cell transport
assay indicates that the Pst system has a Km of 0.20 μM |CITS: [82030542]|. Transcription
of the Pst system is induced by Pi starvation, as opposed to the Pit phosphate transport system that is
expressed regardless of Pi level |CITS: [91054431]|.)""",]},
'B4481' : {'ecocyc-rxns': {"""FUC4NACTRANS-RXN""": """undecaprenyl N-acetyl-glucosaminyl-N-acetyl-mannosaminuronate pyrophosphate + dTDP-4-acetamido-4,6-dideoxy-D-galactose = undecaprenyl N-acetyl-glucosaminyl-N-acetyl-mannosaminuronate-4-acetamido-4,6-dideoxy-D-galactose pyrophosphate + dTDP""",},'ucsd-rxns' : ['AADDGT',], 'protein-comments' : ["""(The rffT gene encodes Fuc4NAc (4-acetamido-4,6-dideoxy-D-galactose) transferase, which catalyzes a
step in biosynthesis of lipid III during biosynthesis of enterobacterial common antigen (ECA)
|CITS: [2166030][11673418]|.
An rffT mutant exhibits a defect in lipid III biosynthesis |CITS: [2166030]|. A wecF/rffT mutant
exhibits several phenotypes that are indirect effects of outer membrane defects due to buildup of lipid II, including
increased transcription from the degP promoter, sensitivity to LamB or to bile salts, and stimulation of SigmaE
and Cpx signaling |CITS: [9811644]|. A wecF/rffT mutant shows a defect in production of a cyclic form of
enterobacterial common antigen that is water-soluble and found in wild type cells |CITS: [12618464]|. The
rff-726 mutation is an rffT allele |CITS: [2166030]| and exhibits a defect in biosynthesis of lipid II
|CITS: [3275612]| and lipid III |CITS: [2166030]|, but does not exhibit a defect in biosynthesis of lipid I
|CITS: [3275612]|. The rff-726 mutant exhibits a defect in enterobacterial common antigen (ECA) biosynthesis,
but shows biosynthesis of ECA intermediates including N-acetyl-D-mannosaminuronic acid |CITS: [3894334]|.
The rff genes have been characterized in Salmonella typhimurium |CITS: [783131][361690][3886625]|.
)""",]},
'B0642' : {'ecocyc-rxns': {"""LEUCINE--TRNA-LIGASE-RXN""": """tRNAleu + L-leucine + ATP -> L-leucyl-tRNAleu + diphosphate + AMP""",},'ucsd-rxns' : ['LEUTRS',], 'protein-comments' : ["""(Leucyl-tRNA synthetase (LeuRS) is a member of the family of aminoacyl tRNA synthetases, which interpret the
genetic code by covalently linking amino acids to their specific tRNA molecules. The reaction is driven by ATP
hydrolysis. Correct aminoacylation by LeuRS requires both an activation and an editing function |CITS: [10966471]|.
LeuRS belongs to the Class I aminoacyl tRNA synthetases; apart from sequence motifs within the active site, the
different enzymes show little similarity in their primary amino acid sequences |CITS: [7647112]|.
The CP1 (connective polypeptide 1) domain, which splits the nucleotide binding fold |CITS: [3306924]|, is required for
the editing function of LeuRS |CITS: [10828991][11331000][12186547][14705941][15110746]|. Crystal structures of
the editing domain in complex with non-cognate amino acids showed that amino acid discrimination is based on a
lock-and-key mechanism |CITS: [16277600]|.
)""",]},
'B1223' : {'ecocyc-rxns': {"""TRANS-RXN-26""": """H+[periplasmic space] + nitrite[cytosol] =H+[cytosol] + nitrite[periplasmic space] """,},'ucsd-rxns' : ['NO2t2rpp','NO3t7pp',], 'protein-comments' : ["""(NarK is a nitrite extrusion protein involved in anaerobic nitrate
respiration. Nitrate is the preferred electron acceptor for anaerobic
respiration in E. coli, resulting in reduction to nitrite, which is
either excreted or further reduced.
NarK was originally thought to act as a nitrate/nitrite antiporter
based on physiological studies of narK mutants |CITS: [91258310] [89338707]|.
However, nitrate transport experiments in whole cells demonstrated that
nitrate uptake is not affected by mutations in narK, but instead
affected nitrate utilisation due to a decreased ability to
excrete nitrite |CITS: [95020592]|. Nitrate/nitrite antiport activity
was not observable in whole cells. Transport experiments in proteoliposomes
using a nitrite fluorophore indicated that NarK mediates electrogenic
nitrite extrusion with a Km of approx 300 μM |CITS: [95020592]|. NarK
is a member of the major facilitator superfamily (MFS) of transporters
|CITS: [93040298]|, and probably functions as a proton/nitrite antiporter.
Expression of narK is regulated by nitrate and oxygen via the
regulatory proteins NarL and Fnr. Expression of narK is also
stimulated by nitrite |CITS: [93054319]|.)""",]},
'B0862' : {'ecocyc-rxns': {"""ABC-4-RXN""": """ATP + L-arginine[periplasmic space] + H2O =ADP + phosphate + L-arginine[cytosol] """,},'ucsd-rxns' : ['ARGabcpp',], 'protein-comments' : ["""NIL""","""(The ArtPMQJI arginine transporter is a member of the ATP Binding Cassette (ABC) transporter superfamily
|CITS: [98254124]|. ArtJ shows similarity to arginine-binding periplasmic protein components of other ABC
transporters. Expression studies show that ArtJ is localized to the periplasmic fractions of E. coli
and hybridization studies using radiolabeled arginine showed that part of the radioactivity co-eluted with
ArtJ, indicating that L-arginine is the natural substrate for ArtJ |CITS: [96111488]|. Furthermore, overexpression
of ArtJ resulted in stimulation of arginine uptake. In minimal medium, ArtJ was found in the periplasmic
extracts of E. coli but its presence was greatly diminished in high-arginine content medium
|CITS: [96111488]|. Sequence similarity, including a highly conserved ATP-binding consensus site, and
hydropathy analyses indicate that ArtP is highly homologous to the HisP ATP-binding protein of the
Histidine-LAO transporters (HisJQMP complexes) of S. typhimurium and E. coli . ArtQ
and ArtM are hydrophobic proteins and exhibit some homology to HisQ and HisM, membraneous
components of the Histidine-LAO ABC transport system, and to other ABC transporter integral membrane
proteins |CITS:[96111488]|. ArtQ and ArtM presumably function as integral membrane components and
couple the ATPase activity of ArtP to the transport of L-arginine across the inner membrane. ArtI exhibits
homology with a number of ABC transporter periplasmic binding proteins, but its substrate is not known
|CITS:[98254124]|.)""",]},
'B1732' : {'ecocyc-rxns': {"""RXN-8073""": """protoheme IX + H2O2 = heme d""","""CATAL-RXN""": """2 H2O2 = 2 H2O + O2""",},'ucsd-rxns' : ['CAT',], 'protein-comments' : ["""(The crystal structure of KatE has been reported |CITS: [7663946]|.
Review: |CITS: [8955627]|)""","""NIL""",]},
'B0894' : {'ecocyc-rxns': {"""DIMESULFREDUCT-RXN""": """dimethyl sulfoxide + H+ + menaquinol -> dimethylsulfide + H2O + menaquinone-8""",},'ucsd-rxns' : ['TMAOR1','DMSOR2','DMSOR1','TMAOR2',], 'protein-comments' : ["""(This subunit contains the active site and the molybdenum cofactor. |CITS: [91355180]|
DmsA contains a twin-arginine leader peptide which targets the protein to the membrane, although DmsA does not
appear to be exported to the periplasm. The leader peptide is also essential for expression of DmsA and stability of
the DmsAB dimer, and is cleaved between residues 45 and 46 |CITS: [3062312][10801884]|.
)""","""NIL""",]},
'B1533' : {'ecocyc-rxns': {"""RXN0-1924""": """L-cysteine[cytosol] =L-cysteine[periplasmic space] ""","""RXN0-1923""": """O-acetyl-L-serine[cytosol] =O-acetyl-L-serine[periplasmic space] """,},'ucsd-rxns' : ['ACSERtpp','CYStpp',], 'protein-comments' : ["""(YdeD is a major facilitator superfamily transporter involved in the efflux of O-acetylserine and Cysteine (metabolites of the Cysteine pathway).
YdeD acts independently of YfiK, an alternate O-acetylserine and Cysteine efflux permease.)""",]},
'B4240' : {'ecocyc-rxns': {"""TRANS-RXN-168""": """phosphoenolpyruvate + trehalose[periplasmic space] =trehalose 6-phosphate[cytosol] + pyruvate """,},'ucsd-rxns' : ['TREptspp',], 'protein-comments' : ["""(contains PTS Enzyme IIB and IIC domains)""","""(TreB, the trehalose PTS permease, belongs to the functional superfamily
of the phosphoenolpyruvate (PEP)-dependent, sugar transporting
phosphotransferase system (PTS). The PTS transports and simultaneously
phosphorylates its sugar substrates in a process called group
translocation. TreB together with IIAGlc
takes up exogenous trehalose, releasing the phosphate ester into
the cell cytoplasm in preparation for hydrolysis via phosphotrehalase
(TreA). Subsequent metabolism occurs primarily via glycolysis
|CITS: [8246840]| .
TreB, the Enzyme IITre complex, possesses
two domains in a single polypeptide chain with the domain order
IIB-IIC |CITS: [7608078]| . The IIB and IIC domains are homologous to the IIB
and IIC domains of PtsG, the glucose-specific PTS Enzyme II.
PtsG has been reported to possess 8 transmembrane α-helical
segments in its IIC domain. The IIB domain is localized to the
cytoplasmic side of the membrane, and it uses the glucose Enzyme
IIA to phosphorylate IIBTre. The overall
PTS-mediated phosphoryl transfer reaction, requiring the two general
energy coupling proteins of the PTS, Enzyme I and HPr, as well
as the three domains of the Enzyme II complex is:
PEP --> Enzyme I(his~~P)
--> HPr(his~~P)
--> IIA(his~~P) -->
IIB(cys~~P) -(IIC)-> trehalose-6-P.
TreB transports trehalose with micromolar affinity.
The tre operon is inducible in wild type E. coli K12
by the presence of low concentrations of trehalose. The treBC
operon contains the treB gene encoding the Enzyme IITre
and the treC gene encoding a phospho-trehalase that hydrolyzes
the α,α-glycosidic
bond in trehalose-6-phosphate |CITS: [8083158]| . The monocistronic treR
operon, encoding the repressor of the treBC operon is upstream
of the treBC operon and is transcribed in the same direction.
tre operon expression is under the control of the cyclic
AMP-cyclic AMP receptor protein (CRP) complex as well as that
of TreR. Metabolism of trehalose can occur either by a PTS-dependent
(low trehalose concentrations) or a PTS-independent (high trehalose
concentrations) mechanism. The latter process involves periplasmic
hydrolysis of trehalose to glucose.
)""",]},
'B0895' : {'ecocyc-rxns': {"""DIMESULFREDUCT-RXN""": """dimethyl sulfoxide + H+ + menaquinol -> dimethylsulfide + H2O + menaquinone-8""",},'ucsd-rxns' : ['TMAOR1','DMSOR2','DMSOR1','TMAOR2',], 'protein-comments' : ["""(This subunit contains four 4Fe-4S clusters and carries out
the electron-transfer process. |CITS: [91355180]|)""","""NIL""",]},
'B2037' : {'ecocyc-rxns': {"""TRANS-RXN-146""": """a lipopolysaccharide[cytosol] =a lipopolysaccharide[periplasmic space] """,},'ucsd-rxns' : ['O16AUNDtpp',], 'protein-comments' : ["""(RfbX, also known as WzxB, is a member of the Polysaccharide Transporter (PST) Family |CITS: [97419507]|.
It is believed to export O-antigen units across the cytoplasmic membrane following the synthesis
of O-antigen units in the cytoplasm |CITS: [96178979]|. On the periplasmic side, these repeating units
of O-antigen are then polymerized and ligated to the rest of the lipopolysaccharide (LPS) molecule,
completing the O-antigen lipopolysaccharide synthesis |CITS: [20044778]|. The completed LPS is then
translocated to the outer membrane, where O-antigen is displayed as the major cell surface antigen
|CITS: [96178979]|. Mutational analysis of the rfbX gene resulted in the accumulation of O-antigen
on the cytoplasmic side of the inner membrane, suggesting that the rfbX gene encodes a
flippase, responsible for the export of O-antigen units across the cytoplasmic membrane |CITS: [96178979]|.
Hydropathy analysis suggests that RfbX has 12 transmembrane segments |CITS: [96178979]|.)""",]},
'B3161' : {'ecocyc-rxns': {"""TRANS-RXN-142""": """H+[periplasmic space] + indole[periplasmic space] =H+[cytosol] + indole[cytosol] ""","""TRANS-RXN-76""": """L-tryptophan[periplasmic space] + H+[periplasmic space] =L-tryptophan[cytosol] + H+[cytosol] """,},'ucsd-rxns' : ['TRPt2rpp','INDOLEt2rpp',], 'protein-comments' : ["""(Mtr is one of three known transporters for tryptophan in E. coli,
the others being TnaB and AroP. Mtr is a high affinity transporter for
tryptophan (Km of about 2 μM) |CITS: [71014364]|, and is also able to transport
indole |CITS: [92011357]|.
Mtr is a member of the ArAAAP family of amino acid transporters and is
homologous to the TnaB and TyrP transporters of E. coli |CITS: [91216998]|.
Analysis of alkaline phosphatase and beta-galactosidase fusions have confirmed
that Mtr has an unusual topology with eleven TMS |CITS: [95113765]|.
Expression of the mtr gene is repressed by tryptophan via the Trp
repressor and induced by phenylalanine or tyrosine via the TyrR repressor
|CITS: [91258349] [91286199]|.)""",]},
'B4467' : {'ecocyc-rxns': {},'ucsd-rxns' : ['GLYCTO4','GLYCTO3','GLYCTO2',], 'protein-comments' : ["""(E. coli cells harboring a plasmid containing glcDEF have glycolate oxidase activity in crude cell extracts;
an insertion mutant in either glcD, glcE or glcF abolishes this activity |CITS: [8606183]|.)""",]},
'B0026' : {'ecocyc-rxns': {"""ISOLEUCINE--TRNA-LIGASE-RXN""": """tRNAile + L-isoleucine + ATP -> L-isoleucyl-tRNAile + diphosphate + AMP""",},'ucsd-rxns' : ['ILETRS',], 'protein-comments' : ["""(Isoleucyl-tRNA synthetase (IleRS) is a member of the family of aminoacyl-tRNA synthetases, which interpret the
genetic code by covalently linking amino acids to their specific tRNA molecules. The reaction is driven by ATP
hydrolysis. IleRS belongs to the Class I aminoacyl tRNA synthetases |CITS: [2203971][7647112]|.
IleRS contains two zinc atoms per active site |CITS: [8286369]|. One zinc atom bound near the N-terminal catalytic
core is important for amino acid binding and utilization |CITS: [7947832]|. The second zinc binding site has been
mapped near the C terminus of IleRS |CITS: [8051111]| and is required for the tRNA binding step in aminoacylation
|CITS: [7488160]|. The C-terminal peptide containing this site can complement the specific tRNA binding and
catalytic activity of the N-terminal domain in trans |CITS: [8672449][9184155]|. If separately expressed, the
three domains of IleRS can form an active complex and complement each other in trans |CITS: [1429621]|.
IleRS binds one molecule of tRNA per molecule of enzyme |CITS: [323006]|. A dispensable sequence interrupts the
nucleotide binding domain within IleRS |CITS: [3306924]|.
Specificity determinants within tRNAIle that are important for recognition by IleRS have been identified
|CITS: [789377][336087][411506][1726806][2023934][8199246][8114089]|. Residues within IleRS that interact with
tRNAIle have been identified |CITS: [7669778][8605884]|.
The reaction mechanism of IleRS has been studied |CITS: [6129973]|. Aminoacylation proceeds via the aminoacyl
adenylate pathway |CITS: [764868][323252]|.
Binding specificity of IleRS for various aliphatic amino acids and aminoalkyl adenylates has been determined; none of
the tested isoleucine analogs bind as tightly as isoleucine and isoleucinol-AMP itself
|CITS: [782880][795668][325520][3322383]|. Both amino acid discrimination and proofreading contribute to the
specificity of Ile charging onto tRNAIle |CITS: [3315663][3281834]|, and experimental data is consistent
with the existence of both a pre- and a post-transfer editing capability of the enzyme, depending on the amino acid
|CITS: [321008][329276][3297096][1720662]|.
Although valine is discriminated against at the amino acid recognition stage, IleRS misactivates valine at a significant
rate. A single point mutation, G56A, eliminates the ability to discriminate against valine, and valine is then
discriminated against by hydrolytic editing |CITS: [8146659]|.
The presence of misacylated tRNA is required for pre- and post-transfer editing |CITS: [14596614]|. The editing site
maps to the CP1 domain, an insertion that interrupts the Rossman fold nucleotide-binding domain |CITS: [7669778]|.
The editing response appears to be triggered by specific bases in the effector and does not require a tRNA-like
structure, active acceptor hydroxyl groups |CITS: [8610114]| or joining of the amino acid to the nucleic acid
|CITS: [11284704]|. The editing site is distinct from the active site for aminoacylation |CITS: [10889024]|.
Translocation of misactivated valine from the active site to the editing site is is required for editing
|CITS: [11782529][12515858]| and is dependent on tRNAIle |CITS: [10549284]|. Distinct residues within
the editing site are required for editing the misactivated adenylate form and the aninoacyl ester |CITS: [11864608]|.
Misactivated homocysteine undergoes pretransfer editing |CITS: [7024910]|.
Site-directed mutagenesis identified the isoleucine binding site |CITS: [3282306]|. Labeling studies with
pyridoxal-5'-phosphate identified residues that may be important for binding of the phosphates of ATP
|CITS: [8031903]|. An editing-deficient IleRS mutant strain has a growth yield advantage under specialized
conditions, generating "statistical proteins" containing norvaline |CITS: [15163798]|, but under most conditions, it has
a lower growth rate |CITS: [15647356]|.
Reviews: |CITS: [10966471][2183216][15677335]|
)""",]},
'B2276' : {'ecocyc-rxns': {"""NADH-DEHYDROG-A-RXN""": """ubiquinone-8 + NADH = ubiquinol-8 + NAD+""",},'ucsd-rxns' : ['NADH17pp','NADH18pp','NADH16pp',], 'protein-comments' : ["""(This subunit may function in proton translocation |CITS: [98256007]|.
NuoN is part of the inner membrane component of NADH dehydrogenase I |CITS: [7607227]|; it may interact with
quinones |CITS: [12718520]|.
)""","""(There is a cluster of 13 genes that code for NADH dehydrogenase I. Six of the subunits are peripheral proteins and
the other seven are very hydrophobic |CITS: [94178656] [98256007]|. Three-dimensional reconstruction of the
complex based on cryo-electron microscopy showed an L-shaped form with an integral membrane and a peripheral
arm |CITS: [9514725]|. A model of the spatial arrangement of the subunits and the possible functional mechanism of
proton pumping has been proposed |CITS: [12923180]|.)""",]},
'B0896' : {'ecocyc-rxns': {"""DIMESULFREDUCT-RXN""": """dimethyl sulfoxide + H+ + menaquinol -> dimethylsulfide + H2O + menaquinone-8""",},'ucsd-rxns' : ['TMAOR1','DMSOR2','DMSOR1','TMAOR2',], 'protein-comments' : ["""(This subunit anchors the A and B subunits to the membrane and stabilizes the catalytic subunits |CITS: [91355180]
[3062312]|. A glutamate residue, E87, was found to be important for menaquinol binding and oxidation
|CITS: [14757221]|.)""","""NIL""",]},
'B1215' : {'ecocyc-rxns': {"""KDO-8PSYNTH-RXN""": """D-arabinose 5-phosphate + H2O + phosphoenolpyruvate -> 3-deoxy-D-manno-octulosonate 8-P + phosphate""",},'ucsd-rxns' : ['KDOPS',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B2278' : {'ecocyc-rxns': {"""NADH-DEHYDROG-A-RXN""": """ubiquinone-8 + NADH = ubiquinol-8 + NAD+""",},'ucsd-rxns' : ['NADH17pp','NADH18pp','NADH16pp',], 'protein-comments' : ["""(This subunit may function in proton translocation. |CITS: [98256007]|
A C-terminally truncated fragment of NuoL can function as a Na+ pump |CITS: [12740360]|.
NuoL is part of the inner membrane component of NADH dehydrogenase I |CITS: [7607227]|.
)""","""(There is a cluster of 13 genes that code for NADH dehydrogenase I. Six of the subunits are peripheral proteins and
the other seven are very hydrophobic |CITS: [94178656] [98256007]|. Three-dimensional reconstruction of the
complex based on cryo-electron microscopy showed an L-shaped form with an integral membrane and a peripheral
arm |CITS: [9514725]|. A model of the spatial arrangement of the subunits and the possible functional mechanism of
proton pumping has been proposed |CITS: [12923180]|.)""",]},
'B2279' : {'ecocyc-rxns': {"""NADH-DEHYDROG-A-RXN""": """ubiquinone-8 + NADH = ubiquinol-8 + NAD+""",},'ucsd-rxns' : ['NADH17pp','NADH18pp','NADH16pp',], 'protein-comments' : ["""(The two membrane-embedded acidic residues Glu36 and Glu72 of NuoK are required for high rates of ubiquinone
reduction |CITS: [14730982]|. Analysis of site-directed mutants in conserved residues of NuoK confirmes that NuoK
is important for NDH-1 activity |CITS: [15996109]|.
NuoK is part of the inner membrane component of NADH dehydrogenase I |CITS: [7607227]|.
)""","""(There is a cluster of 13 genes that code for NADH dehydrogenase I. Six of the subunits are peripheral proteins and
the other seven are very hydrophobic |CITS: [94178656] [98256007]|. Three-dimensional reconstruction of the
complex based on cryo-electron microscopy showed an L-shaped form with an integral membrane and a peripheral
arm |CITS: [9514725]|. A model of the spatial arrangement of the subunits and the possible functional mechanism of
proton pumping has been proposed |CITS: [12923180]|.)""",]},
'B4468' : {'ecocyc-rxns': {},'ucsd-rxns' : ['GLYCTO4','GLYCTO3','GLYCTO2',], 'protein-comments' : ["""(E. coli cells harboring a plasmid containing glcDEF have glycolate oxidase activity in crude cell extracts;
an insertion mutant in either glcD, glcE or glcF abolishes this activity |CITS: [8606183]|.)""",]},
'B3679' : {'ecocyc-rxns': {},'ucsd-rxns' : ['INOSTt4pp',], 'protein-comments' : ["""(The YidK protein is an uncharacterised member of the
SSS superfamily of sodium dependent solute transporters |CITS: [94304911]|.
Based on sequence similarity, YidK may function as a sodium-driven
metabolite uptake system.)""",]},
'B0428' : {'ecocyc-rxns': {"""HEMEOSYN-RXN""": """protoheme IX + trans, trans-farnesyl diphosphate + H2O = heme o + diphosphate""",},'ucsd-rxns' : ['HEMEOS',], 'protein-comments' : ["""(The CyoE protein, heme O synthase, catalyzes the synthesis of heme O, which is essential for the
catalytic fuctions of the cytochrome bo oxidase complex |CITS: [1336371][8253713]|.
At one time it was thought that CyoE was a fifth subunit of the cytochrome bo oxidase, but it was shown that a
28 kDa polypeptide which co-purifies with the cytochrome bo oxidase complex appears even in a cyoE
deletion strain |CITS: [8262927]|.
)""",]},
'B2441' : {'ecocyc-rxns': {"""ETHAMLY-RXN""": """ethanolamine = acetaldehyde + ammonia""",},'ucsd-rxns' : ['ETHAAL',], 'protein-comments' : ["""(EutB codes for the larger subunit, which probably serves in
a regulatory function. |CITS: [PenningtonBiochemSocTrans9-447]
[84214916]|)""","""NIL""",]},
'B2440' : {'ecocyc-rxns': {"""ETHAMLY-RXN""": """ethanolamine = acetaldehyde + ammonia""",},'ucsd-rxns' : ['ETHAAL',], 'protein-comments' : ["""(EutC codes for the smaller subunit, which is the probable
catalytic subunit carrying the ethanolamine and adenosylcobalamin
binding sites. |CITS: [PenningtonBiochemSocTrans9-447] [84241706]|)""","""NIL""",]},
'B2378' : {'ecocyc-rxns': {"""PALMITOTRANS-RXN""": """KDO2-lipid IVA + palmitoleoyl-ACP = KDO2-(palmitoleoyl)-lipid IVA + acyl carrier protein""",},'ucsd-rxns' : ['EDTXS3',], 'protein-comments' : ["""NIL""",]},
'B1489' : {'ecocyc-rxns': {"""RXN0-4181""": """cyclic bis(3' -> 5') dimeric GMP + H2O -> linear dimeric GMP""","""3.1.4.17-RXN""": """H2O + a nucleoside 3',5'-cyclic phosphate -> a nucleoside-5'-phosphate""",},'ucsd-rxns' : ['PDE1',], 'protein-comments' : ["""(Dos acts a direct sensor of oxygen; the protein has an N-terminal heme-binding PAS domain and a C-terminal
phosphodiesterase domain |CITS: [10704219]|. Conformational changes within the N-terminal domain regulate the
enzymatic activity of the C-terminal domain |CITS: [10704219]|. Dos exhibits cAMP phosphodiesterase activity
|CITS: [11970957]|. The ferrous form is enzymatically active and the ferric form is not |CITS: [11970957]|. Under
different assay conditions, Dos exhibits c-di-GMP-specific phosphodiesterase activity, but no cAMP-dependent
phosphodiesterase activity |CITS: [15995192]|.
Dos forms a homotetramer |CITS: [11970957]|, but appears as a dimer in the crystal structure |CITS: [14982921]
[15005609]|. The C-terminal region is responsible for tetramerization |CITS: [14551206]|.
Binding of O2, CO, and NO has been studied in detail |CITS: [10704219][14612459][14612459]|. The
physical characteristics of the heme-binding domain are examined in detail |CITS: [10704219][11939776][12080073]
[12198316][12271121][12437964][12767236][14612459]|. Binding to heme is not necessary for tetramerization or for
enzymatic activity |CITS: [14551206]|. The Asp40 residue appears to play a role in the electronic structure of the
haem iron; mutations in Asp40 abolish catalytic activity |CITS: [15373839]|.
Residues His77 |CITS: [11970957][12080073]| and Met95 coordinate the heme group |CITS: [12080073]|.
Coordination by Met95 appears to be indirect, probably water-mediated |CITS: [14622266]|. When O2
or CO is bound, the heme-Met95 interaction is disrupted, causing a conformational change |CITS: [12080073]|.
Mg2+ is required for activity |CITS: [11970957]| and appears to bind at residues His590 and His594
|CITS: [14551206]|.
Dos: "direct oxygen sensor" |CITS: [10704219]|.
Review: |CITS: [16411738]|)""","""NIL""",]},
'B3630' : {'ecocyc-rxns': {"""RXN0-5121""": """glucosyl-heptosyl2-KDO2-lipid A + ATP = glucosyl-heptosyl2-KDO2-lipid A-phosphate + ADP""",},'ucsd-rxns' : ['HEPK1',], 'protein-comments' : ["""(The lipopolysaccharide of E. coli K-12 consists of two major components:
the hydrophobic lipid A moiety inserted into the outer membrane and the
phosphorylated core oligosaccharide |CITS:[12045108]|. E. coli K-12
does not produce O antigen to attach to the LPS core due to a defect in the
rfb gene cluster which can be complemented with genes from a second,
independent rfb mutant to produce an O16 type O antigen |CITS:[7517391]|.
E. coli K-12 may have two major pathways for LPS biosynthesis. One
generates LPS cores suitable for O antigen attachment, and a second generates
lipooligosaccharides (LOS) with modifications to the core structure which prevent
O antigen attachment |CITS:[1385388]|.
The WaaP protein is a lipopolysaccharide (LPS) kinase; it is required for the addition
of phosphate to O-4 of the heptose I residue in the lipopolysaccharide core
|CITS:[1348243],[9756860],[11069912]|. This modification appears to be critical for the
stability of the outer membrane.
Assays using WaaP from E. coli strain F470 reveal Mg2+ is
required for WaaP activity, and the optimum pH is between 8.0 and 9.0
|CITS:[11069912]|. Also, WaaP activity is partially dependent upon an intact
waaG in order to phosphorylate the HepI residue in F470 |CITS:[10986272]|.
waaP+ reversed the deep rough phenotype of a
waaGPBO deletion mutant |CITS:[1348243]|. Mutation of the waaP
gene causes hypersensitivity to novobiocin and sodium dodecyl sulfate (and
generally, hydrophobic antibiotics and detergents) |CITS:[9756860]|.
Reviews: |CITS:[12045108],[9791168],[7504166]|)""",]},
'B1927' : {'ecocyc-rxns': {"""ALPHA-AMYL-RXN""": """a 1,4-α-D-glucan = maltodextrin""",},'ucsd-rxns' : ['AAMYL',], 'protein-comments' : ["""NIL""",]},
'B2662' : {'ecocyc-rxns': {"""GABATRANSAM-RXN""": """α-ketoglutarate + 4-aminobutyrate = L-glutamate + succinate semialdehyde""",},'ucsd-rxns' : ['ABTA',], 'protein-comments' : ["""(The gabT gene was identified in a search for mutants that have lost the ability to utilize 4-aminobutyrate (GABA) as
a nitrogen source |CITS: [374339]|. Regulation of the operon containing gabT has been studied extensively
|CITS: [9512707], [11251833], [11532138], [12446648], [14731280]|. gabT was also identified in a screen for genes
which are activated by self-produced extracellular signals |CITS: [10200310], [11418561], [14612251]|.
Crystal structures of the free and inhibitor-bound enzyme have been reported |CITS: [15323550]|.)""","""NIL""",]},
'B3992' : {'ecocyc-rxns': {"""THIFIS-RXN""": """ThiS-COAMP + L-cysteine = ThiS-COSH + L-alanine + AMP""","""THIFAMP-RXN""": """ThiS protein + ATP = ThiS-COAMP + diphosphate""",},'ucsd-rxns' : ['THZPSN',], 'protein-comments' : ["""(The ThiF protein catalyzes the adenylation of the ThiS protein as part of the formation of the thiazole moiety during
thiamin biosynthesis |CITS: [99311269][98298179]|. ThiS and ThiF form a covalently linked protein-protein conjugate
as an essential intermediate of this reaction |CITS: [11438688]|.
Crystal structures of ThiF have been solved at 2.75 and 2.95 A resolution and provide insight into the nucleotide
specificity and interactions with ThiS |CITS: [15896804]|.)""",]},
'B2687' : {'ecocyc-rxns': {},'ucsd-rxns' : ['RHCCE',], 'protein-comments' : ["""(LuxS is involved in biosynthesis of autoinducer, the hormone-like signal that mediates cell-cell communication during quorum sensing, the response to increased cell density |CITS: [9990077]|. LuxS is the synthase that catalyzes formation of autoinducer 2 (AI-2), which is an acylated homoserine lactone, by cleavage of S-ribosylhomocysteine |CITS: [11489131]|. Recycling of S-adenosylhomocysteine via LuxS-mediated AI-2 formation may have metabolic significance |CITS: [11932438]|.
A luxS mutant exhibits altered expression of 242 genes, compared to wild type |CITS: [11514505]|. A luxS mutant has been examined by large-scale phenotypic assay |CITS: [12897016]|.
The DH5alpha strain has a luxS mutation that prevents autoinducer production, whereas the MG1655 strain produces autoinducer |CITS: [9990077]|.
A crystal structure of Bacillus subtilis LuxS is presented at 1.6 A resolution |CITS: [11553770]|. Bacillus subtilis LuxS is homodimeric |CITS: [11553770]|.
LuxS is involved in regulation of pathogenicity genes in enterohemorrhagic and enteropathogenic E. coli strains |CITS: [10611361], [11489873], [11972776], [12810266], [12847292]|. AI-2 production in an E. coli luxS mutant is functionally complemented by LuxS of Borrelia burgdorferi |CITS: [12117917], [12704164]|, Streptococcus mutans |CITS: [12654815]|, Bacillus anthracis |CITS: [12819077]|, Porphyromonas gingivalis |CITS: [11882711]|, Mannheimia haemolytica A1 |CITS: [11786252]|, Porphyromonas gingivalis |CITS: [11292769]|, Helicobacter pylori |CITS: [10816463]|, Vibrio harveyi |CITS: [9990077]|, or E. coli O157:H7 |CITS: [9990077]|.
Regulation has been described |CITS: [11591692], [12107143]|. Transcription of luxS is induced by acetate |CITS: [11591692]| or by acidic pH |CITS: [12107143]|.
Review: |CITS: [12949525]|.
)""",]},
'B3835' : {'ecocyc-rxns': {"""2-OCTAPRENYLPHENOL-HYDROX-RXN""": """2 2-octaprenylphenol + O2 = 2 2-octaprenyl-6-hydroxyphenol""",},'ucsd-rxns' : ['OPHHX',], 'protein-comments' : ["""(ubiB mutants contains no detectable ubiquinone |CITS: [9422602]| and accumulate octaprenylphenol
|CITS: [4897112][10960098]|.)""",]},
'B1270' : {'ecocyc-rxns': {"""BTUR2-RXN""": """ATP + cobinamide + H2O = phosphate + diphosphate + adenosylcobinamide""","""COBALADENOSYLTRANS-RXN""": """ATP + cob(I)alamin + H2O = coenzyme B12 + PPPi""",},'ucsd-rxns' : ['CBIAT','CBLAT',], 'protein-comments' : ["""(This protein is comparable to the cobA polypeptide of
Salmonella.)""",]},
'B3833' : {'ecocyc-rxns': {"""ADOMET-DMK-METHYLTRANSFER-RXN""": """demethylmenaquinone-8 + S-adenosyl-L-methionine = menaquinone-8 + S-adenosyl-L-homocysteine""","""2-OCTAPRENYL-METHOXY-BENZOQ-METH-RXN""": """2-octaprenyl-6-methoxy-1,4-benzoquinone + S-adenosyl-L-methionine = 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinone + S-adenosyl-L-homocysteine""",},'ucsd-rxns' : ['AMMQLT8','OMBZLM',], 'protein-comments' : ["""(UbiE mutants have been characterized. |CITS: [71136273] [93074269]|
Regulation has been described |CITS: [10960098]|. The ubiE, yigP, and ubiB genes form an operon |CITS: [10960098]|.)""",]},
'B1276' : {'ecocyc-rxns': {"""ACONITATEDEHYDR-RXN""": """citrate = cis-aconitate + H2O""","""ACONITATEHYDR-RXN""": """cis-aconitate + H2O = isocitrate""",},'ucsd-rxns' : ['ACONTa','ACONTb',], 'protein-comments' : ["""NIL""",]},
'B2937' : {'ecocyc-rxns': {"""AGMATIN-RXN""": """H2O + agmatine = urea + putrescine""",},'ucsd-rxns' : ['AGMT',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B3962' : {'ecocyc-rxns': {"""PYRNUTRANSHYDROGEN-RXN""": """NAD+ + NADPH = NADH + NADP+""",},'ucsd-rxns' : ['NADTRHD',], 'protein-comments' : ["""(E. coli contains both a soluble and a membrane-bound proton-translocating pyridine nucleotide
transhydrogenase. The soluble pyridine nucleotide transhydrogenase is the sthA gene product; its primary
physiological role appears to be the reoxidation of NADPH |CITS: [11731130][14660605]|. The membrane-bound
proton-translocating transhydrogenase is the pntAB gene product; PntAB is a major source of NADPH
|CITS: [14660605]|. The two transhydrogenases are also distinguished by the stereospecificity of the reducing
equivalents transfer. SthA is a BB-specific transhydrogenase, while PntAB is AB-specific.
SthA contains noncovalently bound FAD and is present in a form consisting of seven or eight monomers
|CITS: [99121046]|.
Moderate overexpression of SthA allows an increased maximal growth rate of a phosphoglucose isomerase mutant
|CITS: [11731130]|, and a pgi sthA double mutant is not viable |CITS: [14660605]|. These phenotypes may be
due to the ability of SthA to restore the cellular redox balance under conditions of excess NADPH formation
|CITS: [11731130][14660605]|.
Transcription of sthA is downregulated by growth on glycerol |CITS: [14660605]|.
)""","""NIL""",]},
'B2938' : {'ecocyc-rxns': {"""ARGDECARBOX-RXN""": """L-arginine = CO2 + agmatine""",},'ucsd-rxns' : ['ARGDCpp',], 'protein-comments' : ["""(Biosynthetic arginine decarboxylase undergoes reversible
association and dissociation depending on buffer conditions. |CITS:
[73149257]| The enzyme exists as a homotetramer in the presence of
Mg++ and pyridoxal phosphate. |CITS: [85163236]|
The monomeric form of the enzyme is found as a mixture of Mr
71,000 and Mr 75,500 polypeptides. The 75,500-Mr form is a precursor
to the 71,000-Mr form, which is found in the periplasmic space. This
may explain why exogenous arginine is more easily converted to
putrescine than arginine formed endogenously. |CITS: [85163236]|
)""","""NIL""",]},
'B1278' : {'ecocyc-rxns': {"""UNDECAPRENYL-DIPHOSPHATASE-RXN""": """undecaprenyl diphosphate + H2O -> undecaprenyl phosphate + phosphate""","""RXN0-4461""": """diacylglycerol pyrophosphate = diacylglycerol phosphate + phosphate""","""PGPPHOSPHA-RXN""": """an L-1-phosphatidylglycerol-phosphate + H2O = an L-1-phosphatidyl-glycerol + phosphate""",},'ucsd-rxns' : ['PAPA181pp','PGPP180pp','PGPP161pp','PGPP181','PGPP180','PAPA160','PAPA161','PGPP120pp','PGPP141','PGPP140','PGPP160pp','PGPP120','PAPA140','PAPA141','PAPA120pp','PAPA160pp','PGPP161','PGPP160','PAPA141pp','PAPA161pp','UDCPDP','UDCPDPpp','PAPA180','PAPA181','PGPP141pp','PGPP140pp','PAPA120','PGPP181pp','PAPA140pp','PAPA180pp',], 'protein-comments' : ["""(The main physiological activity of PgpB may be its diacylglycerol pyrophosphate (DGPP) phosphatase activity.
Phosphatidate (PA), lyso-PA, and phosphatidylglycerophosphate are alternative substrates for the enzyme
|CITS: [8940025]|. PgpB is unusual in that it appears to be located in both the outer and cytoplasmic membranes. Its
activity varies according to the subcellular location. PGP phosphatase activity is higher in the cytoplasmic
membrane, while PA and LPA phosphatase activities are higher in the outer membrane |CITS: [2846511]|.
A pgpB null mutant has no obvious growth defect |CITS: [1309518]|. Simultaneous inactivation of pgpB,
bacA, and ybjG is lethal. Depletion of BacA in the triple mutant strain causes changes in cell
morphology and lysis. Overexpression of pgpB, yeiU, bacA, and ybjG leads to increased
undecaprenyl pyrophosphate (C55PP) phosphatase activity in crude membrane extracts. Expression of
C55PP phosphatase activity from any one of the three genes pgpB, bacA, and ybjG
appears to be sufficient for synthesis of undecaprenyl phosphate and survival |CITS: [15778224]|.)""",]},
'B3360' : {'ecocyc-rxns': {"""PABSYNMULTI-RXN""": """L-glutamine + chorismate = p-aminobenzoate + L-glutamate + pyruvate""","""PABASYN-RXN""": """L-glutamine + chorismate = 4-amino-4-deoxychorismate + L-glutamate""",},'ucsd-rxns' : ['ADCS',], 'protein-comments' : ["""(Component II provides the glutamine amidotransferase
activity.)""","""(Before the multienzyme character of this complex was known,
a single protein was thought to carry out the reaction of
para-aminobenzoate synthesis. It was known (now incorrectly)
as para-aminobenzoate synthase. This enzyme forms the
intermediate aminodeoxychorismate.
)""","""NIL""",]},
'B1377' : {'ecocyc-rxns': {"""RXN0-2481""": """hydrophilic solute or ion < 600 Da[extracellular space] =hydrophilic solute or ion < 600 Da[periplasmic space] """,},'ucsd-rxns' : ['Htex','LEUtex','ALAALAtex','LYStex','ORNtex','O2Stex','UMPtex','GAMAN6Ptex','UDPACGALtex','INDOLEtex','3AMPtex','ACtex','GALBDtex','XTSNtex','THMtex','TRPtex','SERtex','CRNtex','SO4tex','ARGtex','ETHAtex','23CGMPtex','CLtex','ACSERtex','METSOX2tex','ACMANAtex','NOtex','DGSNtex','UDPGtex','23DAPPAtex','GLYCtex','MELIBtex','SO2tex','12PPDStex','GALURtex','23CAMPtex','GLUtex','DGMPtex','GSNtex','THYMtex','GLYBtex','NMNtex','GLCNtex','FE2tex','12PPDRtex','DALAtex','ALAtex','Zn2tex','HCINNMtex','ACGAL1Ptex','TSULtex','THMDtex','CGLYtex','DOPAtex','GTHRDtex','AGMtex','G3PStex','PSCLYStex','HOMtex','GBBTNtex','DMStex','HG2tex','PItex','IDONtex','GLCtex','TYRtex','MOBDtex','ASNtex','ACGALtex','NO3tex','NAtex','PACALDtex','PPPNtex','DSERtex','ACMUMtex','PPALtex','HIStex','DINStex','TCYNTtex','SULFACtex','OCTAtex','CD2tex','URAtex','GALCTtex','TUNGStex','SO3tex','METDtex','TMAOtex','CYANtex','MSO3tex','TMAtex','GALCTNLtex','ALLtex','PYRtex','D-LACtex','BUTtex','XMPtex','MMETtex','5DGLCNtex','ALLTNtex','G3PCtex','CYStex','GLYCAtex','MNtex','G3PEtex','ASO3tex','TYRPtex','GLYtex','L-LACtex','FORtex','PNTOtex','ETOHtex','SPMDtex','HPPPNtex','GDPtex','BALAtex','FRULYStex','TARTRtex','3GMPtex','MNLtex','DCMPtex','AMPtex','ACGAtex','ACACtex','SUCCtex','FALDtex','PEAMNtex','SUCRtex','UDPGALtex','PPAtex','PROtex','XANtex','PPTtex','ASPtex','HXAtex','SKMtex','HYXNtex','TREtex','CO2tex','PROGLYtex','MALtex','ILEtex','GLCUR1Ptex','UREAtex','DAPtex','GLNtex','CSNtex','PTRCtex','XYLtex','O2tex','DAMPtex','G3PGtex','3PEPTtex','VALtex','AKGtex','METtex','ASCBtex','SBTtex','3CMPtex','GLYC2Ptex','GLYALDtex','G6Ptex','NO2tex','PSERtex','CYTDtex','H2tex','MANGLYCtex','DUMPtex','LYXtex','34dhpactex','R5Ptex','ARBtex','GAL1Ptex','FRUURtex','MG2tex','METSOX1tex','TAURtex','GALTtex','UDPGLCURtex','CYNTtex','23CCMPtex','G1Ptex','GLCRtex','IMPtex','RMNtex','DHAtex','GTPtex','FUCtex','ANHGMtex','GLYCLTtex','GALtex','CITtex','23CUMPtex','LCTStex','H2O2tex','OROTtex','DCAtex','NACtex','ACALDtex','CYSDtex','G3PItex','ISETACtex','ACGAM1Ptex','INSTtex','ABUTtex','GTHOXtex','DMSOtex','F6Ptex','GALCTNtex','26DAHtex','MAN6Ptex','GAMtex','GLYC3Ptex','GLCURtex','NI2tex','DIMPtex','THRPtex','MANtex','GMPtex','CU2tex','THRtex','XYLUtex','DTMPtex','TYMtex','4PEPTtex','ADEtex','RIBtex','H2Otex','ETHSO3tex','CA2tex','BUTSO3tex','3UMPtex','CUtex','4HOXPACDtex','NH4tex','UACGAMtex','Ktex','FE3tex','MALDtex','FRUtex','PHEtex','FUMtex','N2Otex','H2Stex','CMPtex','DDGLCNtex','COBALT2tex','CHLtex',], 'protein-comments' : ["""(ompN is a quiescent porin gene. Cloning and over expression of ompN revealed a porin with functional properties (single-channel conductance) closely
resembling those of OmpC.)""",]},
'B2836' : {'ecocyc-rxns': {"""RXN-5741""": """octanoate + acyl carrier protein + ATP = octanoyl-ACP + AMP + diphosphate""","""ACYLGPEACYLTRANS-RXN""": """an acyl-ACP + a 2-acyl-sn-glycero-3-phosphoethanolamine = acyl carrier protein + an L-1-phosphatidyl-ethanolamine""","""ACYLACPSYNTH-RXN""": """ATP + a fatty acid + acyl carrier protein = AMP + diphosphate + an acyl-ACP""",},'ucsd-rxns' : ['2AGPEAT181','2AGPEAT180','AACPS8','AACPS9','AACPS4','AACPS5','AACPS6','AACPS7','AACPS1','AACPS2','AACPS3','2AGPEAT120','2AGPGAT120','2AGPGAT141','2AGPGAT140','2AGPEAT161','2AGPEAT160','2AGPGAT160','2AGPGAT161','2AGPEAT141','2AGPEAT140','2AGPGAT181','2AGPGAT180',], 'protein-comments' : ["""(The protein contains bound ACP. |CITS: [91310656][89214178]|
Based on sequence similarity, Aas has been predicted to be a hydroxycinnamate-CoA ligase |CITS: [12952533]|.)""",]},
'B2552' : {'ecocyc-rxns': {"""R621-RXN""": """2 nitric oxide + 2 O2 + NAD(P)H = 2 NO3- + NAD(P)+ + H+""","""1.5.1.34-RXN""": """5,6,7,8-tetrahydropteridine + NAD(P)+ = 6,7-dihydropteridine + NAD(P)H""",},'ucsd-rxns' : ['NODOy','NODOx',], 'protein-comments' : ["""NIL""",]},
'B4069' : {'ecocyc-rxns': {"""4-COUMARATE--COA-LIGASE-RXN""": """coenzyme A + 4-coumarate + ATP -> coumaroyl-CoA + diphosphate + AMP""","""PROPIONATE--COA-LIGASE-RXN""": """coenzyme A + propionate + ATP = propionyl-CoA + diphosphate + AMP""","""ACETATE--COA-LIGASE-RXN""": """coenzyme A + acetate + ATP = acetyl-CoA + diphosphate + AMP""",},'ucsd-rxns' : ['ACS',], 'protein-comments' : ["""(Acs appears to be more likely than PrpE to catalyze the first step in the propionate metabolism pathway
|CITS: [12473114]|.
Based on sequence similarity, Acs has been predicted to be a hydroxycinnamate-CoA ligase |CITS: [12952533]|.
Regulation has been described |CITS: [12473114], [14563880], [14651625]|. Gene expression is observed during
growth on acetate or propionate |CITS: [12473114]|.)""",]},
'B2661' : {'ecocyc-rxns': {"""SUCCSEMIALDDEHYDROG-RXN""": """succinate semialdehyde + NADP+ + H2O = NADPH + succinate""",},'ucsd-rxns' : ['SSALy',], 'protein-comments' : ["""(The gabD gene was identified in a search for mutants that have lost the ability to utilize 4-aminobutyrate (GABA) as
a nitrogen source |CITS: [374339]|. Regulation of the operon containing gabD has been studied extensively
|CITS: [9512707], [11251833], [11532138], [14731280]|.)""",]},
'B1385' : {'ecocyc-rxns': {"""PHENDEHYD-RXN""": """H2O + NAD+ + phenylacetaldehyde = NADH + phenylacetate""",},'ucsd-rxns' : ['ALDD19x',], 'protein-comments' : ["""NIL""","""(Phenylacetaldehyde dehydrogenase is a dimer in solution |CITS: [97263463]|. The enzyme is inducible
|CITS: [3309152]|.
E. coli K-12 is capable of growth on 2-phenylethylamine as the sole carbon and
energy source. 2-Phenylethylamine is degraded in two steps, an amine oxidase
activity and a phenylacetaldehyde dehydrogenase activity. Phenylacetaldehyde
dehydrogenase is NAD dependent and oxidizes only phenylacetaldehyde-like
aromatic aldehydes. |CITS: [97263463] [88009860]|
Based on sequence similarity, FeaB is predicted to be an aminobutyraldehyde dehydrogenase and a
succinate-semialdehyde dehydrogenase |CITS: [12952533]|.
feaB: 2-phenylethylamine catabolism |CITS: [9043126]|
)""",]},
'B3281' : {'ecocyc-rxns': {"""SHIKIMATE-5-DEHYDROGENASE-RXN""": """NADP+ + shikimate = NADPH + 3-dehydro-shikimate""",},'ucsd-rxns' : ['SHK3Dr',], 'protein-comments' : ["""NIL""",]},
'B2563' : {'ecocyc-rxns': {"""HOLO-ACP-SYNTH-RXN""": """apo-[acyl-carrier protein] + coenzyme A = adenosine-3',5'-bisphosphate + acyl carrier protein""",},'ucsd-rxns' : ['ACPS1',], 'protein-comments' : ["""(The acpS gene encodes holo-[ACP] synthase, which transfers the 4-phosphopantetheine
moiety of CoA to the apo-ACP to form holo-ACP, the active
form of the carrier in lipid synthesis |CITS: [7559576], [4872726], [7016860]|.
The enzyme is an AcpS homodimer |CITS: [7559576]|.
The acpS gene is essential for viability |CITS: [1537799], [1537800]|. An acpS mutant exhibits growth dependence on supplementation of the media with high levels of pantothenate |CITS: [7016860]|. Decreased holo-ACP abundance does not affect the rate of incorporation of oleic acid into phospholipid |CITS: [6378892]|. A conditional acpS mutant (MP4 strain) exhibits an abnormally low ratio of holo-ACP to apo-ACP under permissive as well as restrictive conditions, whereas the ratio of phospholipid to protein content is similar to wild type, indicating that the holo-ACP to apo-ACP ratio is not critical for the maintenance of lipid abundance |CITS: [6317688]|. This conditional acpS1 mutation from the MP4 strain specifies a G4D change, which decreases enzyme efficiency by 5-fold |CITS: [10625633]|. The heat sensitivity of an acpS1 mutant is suppressed by overproduction of YhhU |CITS: [10625633]|. Suppressors of acpS reduction-of-function mutations include lon mutations |CITS: [1537800]|.
AcpS is a member of a 4'-phosphopantetheinyl transferase (P-pant transferase, or PPTase) protein family (including E. coli EntD, E. coli o195 protein, and Bacillus subtilis Sfp) that shares two conserved motifs but shares relatively low sequence identity overall |CITS: [8939709]|. The phenotype of an E. coli acpS mutant is functionally complemented by Streptococcus pneumoniae AcpS |CITS: [10903317]|, Bacillus subtilis AcpS (encoded by ydcB) |CITS: [11489886]|, Bacillus subtilis Sfp |CITS: [11489886]|, or Bacillus brevis Gsp |CITS: [11489886]|.
Regulation has been described |CITS: [8971718]|.)""","""NIL""",]},
'B1308' : {'ecocyc-rxns': {"""THIOSULFATE-SULFURTRANSFERASE-RXN""": """hydrogen cyanide + thiosulfate = thiocyanate + sulfite""",},'ucsd-rxns' : ['CYANSTpp',], 'protein-comments' : ["""(PspE exhibits thiosulfate sulfurtransferase (rhodanese) activity |CITS: [11997041]|.
PspE is periplasmic |CITS: [1324873]|. PspE has a signal peptide that is cleaved from the mature protein |CITS: [9868784]|.
Multi-copy overexpression of the psp operon increases survival of stress caused by n-hexane treatment |CITS: [9493373]|.
PspE has similarity to the dark-inducible Din1 protein of radish |CITS: [9559559]|. The corresponding psp locus of Yersinia enterocolitica is virulence-related |CITS: [11136463]|.
Regulation has been described |CITS: [1712397], [9344746], [9512522], [9878422], [9987127], [9493373], [1717346], [8606168], [7596833], [8134371], [7921245]|. The psp operon shows induction upon phage infection, temperature increase, or exposure to ethanol, osmotic shock |CITS: [1712397]|, or the organic solvents n-hexane or cyclooctane |CITS: [9493373]|. Induction is mediated by sigma54, PspB, PspC |CITS: [1717346]|, PspF |CITS: [8606168]|, and IHF |CITS: [7596833]|. Transcription is induced by conditions that cause stress related to energy depletion |CITS: [8134371]|. Treatment with the drugs diazaborine or cerulenin, which inhibit synthesis of fatty acids and phospholipids, or treatment with globomycin, which disrupts lipoprotein processing, causes transcriptional induction of pspA |CITS: [7921245]|. Transcription is repressed by by PspA and by the heat shock (sigma32-dependent) system |CITS: [1717346]|. The pspE gene is also transcribed from a second promoter |CITS: [1712397]|.
PspE: phage shock protein |CITS: [1712397]|.
Review: |CITS: [9159513]|.)""",]},
'B2039' : {'ecocyc-rxns': {"""DTDPGLUCOSEPP-RXN""": """α-D-glucose 1-phosphate + dTTP = dTDP-D-glucose + diphosphate""",},'ucsd-rxns' : ['G1PTT',], 'protein-comments' : ["""NIL""",]},
'B4067' : {'ecocyc-rxns': {"""RXN0-5111""": """glycolate[periplasmic space] =glycolate[cytosol] ""","""RXN0-1981""": """acetate[periplasmic space] =acetate[cytosol] """,},'ucsd-rxns' : ['GLYCLTt4pp','ACt4pp',], 'protein-comments' : ["""(The YjcG protein is an acetate/glycolate permease in the Solute:Sodium Symporter (SSS) Family
(TC:2.A.21). The gene yjcG is cotranscribed with acs, a gene encoding an acetyl coenzyme A
synthetase, which is involved in the scavenging of acetate |CITS:[14563880]|. YjcG has been found as a
dimer in the inner membrane |CITS:[16079137]|.)""",]},
'B4169' : {'ecocyc-rxns': {"""NACMURLALAAMI-RXN""": """EC# 3.5.1.28""",},'ucsd-rxns' : ['AGM3PApp','AGM4PApp',], 'protein-comments' : ["""(E. coli contains three N-acetylmuramyl-L-alanine amidases named AmiA, B, and C involved in cell division
by splitting the murein septum. They accomplish this by removing the peptide moiety from N-acetylmuramic acid,
removing crosslinks |CITS:[11454209]|.
AmiB is believed to be transported to the periplasm by the Sec system |CITS:[12787348][12787347]|. It is predicted
to have a signal peptide from residues 1 to 22, an unknown domain from residues 23 to 253, and an amidase domain
from residues 254 to 445 |CITS:[12787347]|.
Separation of daughter cells during division is reduced in amidase mutants, with the exception of amiB,
resulting in chaining of cells. Deletion of multiple amidases, including amiB, leads to increases in chain length
and relative number of chains formed. The triple amidase mutant is less sensitive to the combined activities of the
antibiotics aztreonam and bulgecin |CITS:[11454209]|.
)""",]},
'B2303' : {'ecocyc-rxns': {"""H2NTPEPIM-RXN""": """7,8-dihydroneopterin 3'-triphosphate = dihydromonapterin-triphosphate""",},'ucsd-rxns' : ['DHPTPE',], 'protein-comments' : ["""NIL""","""(Dihydroneopterin triphosphate 2'-epimerase has been known in E. coli for some time. The epimerase reaction
yields dihydromonapterin triphosphate, from which L-monapterin is produced after successive dephosphorylation
and oxidation. L-monapterin is the major pterin in E. coli. |CITS: [97326109][97158693][76062517]|
However, a folX deletion mutant shows no detectable growth defect on complete and minimal medium. The
physiological roles of the epimerase and its metabolic product thus remain unknown |CITS: [9651328]|.
A crystal structure of FolX has been solved at 2.9 A resolution. Two tetramers associate head-to-head to form the
active enzyme complex |CITS: [99306033]|.
)""",]},
'B2262' : {'ecocyc-rxns': {"""NAPHTHOATE-SYN-RXN""": """O-succinylbenzoyl-CoA = coenzyme A + 1,4-dihydroxy-2-naphthoate""",},'ucsd-rxns' : ['NPHS',], 'protein-comments' : ["""NIL""",]},
'B0194' : {'ecocyc-rxns': {"""PROLINE--TRNA-LIGASE-RXN""": """tRNApro + L-proline + ATP -> L-prolyl-tRNApro + diphosphate + AMP""",},'ucsd-rxns' : ['PROTRS',], 'protein-comments' : ["""(Prolyl-tRNA synthetase (ProRS) is a member of the family of aminoacyl-tRNA synthetases, which interpret the
genetic code by covalently linking amino acids to their specific tRNA molecules. The reaction is driven by ATP
hydrolysis. ProRS belongs to the Class II aminoacyl tRNA synthetases, which share three regions of homology
|CITS: [2203971][1852601]|.
ProRS of E. coli B is a dimer in solution |CITS: [4886431]|.
Specificity determinants within tRNAPro that are important for recognition by ProRS have been
identified |CITS: [7493319][7522561][8643363][7870582][8127693][9383472][11112540][12903242]|. Specificity
determinants and residues within ProRS that are important for catalytic activity have been investigated
|CITS: [9062123][11112540]|.
Many aminoacyl tRNA synthetases have been shown to have editing functions. ProRS misactivates alanine, but has
both a pre-transfer editing function, hydrolyzing the non-cognate amino acid before transfer to tRNAPro,
and a post-transfer editing function that deacetylates mischarged Ala-tRNAPro |CITS: [10922054]|.
The C433 residue is critical for the post-transfer editing function |CITS: [10922054]|. ProRS contains a large insertion
domain between motifs 2 and 3 of the class II aminoacyl tRNA synthetases; this domain is independently folded and
plays a role in the editing functions |CITS: [12033945][14530268]|.
ProRS exhibits a natural level of mischarging with cysteine, resulting in Cys-tRNAPro, which is not edited
by the enzyme. The kcat/Km for proline is 369-fold higher than for cysteine
|CITS: [12130657]|.
Review: |CITS: [10966471]|)""","""NIL""",]},
'B4136' : {'ecocyc-rxns': {"""DSBDC-RXN""": """DsbDreduced + DsbCoxidized = DsbDoxidized + DsbCreduced""","""DSBD-RXN""": """DsbGoxidized + DsbDreduced = DsbGreduced + DsbDoxidized""",},'ucsd-rxns' : ['DSBDR','DSBDR','TDSR1','TDSR2',], 'protein-comments' : ["""(The crystal structure of DsbD has been determined to a resolution of 2.85 angstroms |CITS:[15057279]|.)""","""NIL""",]},
'B3431' : {'ecocyc-rxns': {"""3.2.1.33-RXN""": """EC# 3.2.1.33""",},'ucsd-rxns' : ['GLDBRAN2',], 'protein-comments' : ["""(GlgX is a glycogen debranching enzyme |CITS: [8576033]|. Based on sequence similarity, GlgX has been predicted to be an isoamylase |CITS: [12952533]|.
The enzyme activity has been characterized |CITS: [779849]|. The enzyme shows a small amount of activity toward glycogen itself |CITS: [779849]|.
GlgX has similarity to glycogen branching enzyme, and to glucan hydrolases and transferases |CITS: [2975249]|. GlgX has similarity to protein from Rhizobium tropici |CITS: [11208782]|.
Regulation has been described |CITS: [779849], [2975249], [8576033]|.)""",]},
'B3477' : {'ecocyc-rxns': {"""ABC-20-RXN""": """Ni2+[periplasmic space] + ATP + H2O =Ni2+[cytosol] + ADP + phosphate """,},'ucsd-rxns' : ['NI2uabcpp',], 'protein-comments' : ["""NIL""","""(The NikABCDE ATP-dependent nickel (II) uptake system is a member of the ATP-Binding Cassette (ABC)
Superfamily of transporters |CITS: [96381453]|. The Nik system exhibits significant sequence similarity to
the components of other ABC transporters for dipeptides or oligopeptides |CITS: [95020649]|. Based on
sequence similarity, NikA is the periplasmic binding protein, NikB and NikC are the membrane components,
and NikD and NikE are the ATP-binding components of the ABC transporter. The nickel-binding
properties of the protein have been studied by monitoring the quenching of intrinsic protein fluorescence
|CITS: [95172074]|. NikA binds one atom of nickel per molecule of protein with a Kd of less
than 0.1 μM. The transporter's high specificity for nickel ion has also been demonstrated by
high-performance immobilized-metal-ion affinity chromatography |CITS:[95172074]|. The structure of NikA
has been determined to a resolution of 1.8 angstroms showing that it binds FeEDTA(H2O)
with very high affinity. It also binds the nickel ion associated with a metallophore which is at least similar
to EDTA |CITS:[16011372]|. Insertional mutation in the nik operon severely reduces nickel transport
ability |CITS:[95020649]|. Nickel is an important cofactor in a variety of enzymatic reactions in prokaryotes
|CITS:[20112624]|. However, nickel at high intracellular concentrations is toxic because it can catalyze the
formation of reactive forms of oxygen that can damage cellular constituents |CITS: [20112624]|. Because of
the toxicity of nickel, the synthesis of the Nik system is tightly controlled by nickel concentration. At high
nickel concentrations (0.3 mM) synthesis of Nik is completely repressed by the protein NikR
|CITS:[20112624]|. Expression of NikABCDE corresponds to expression of NiFe hydrogenases for which
nickel is a cofactor. Mutation and LacZ fusion experiments show that nitrate, via the activity of the NarLX
two-component system, represses expression of nikABCDE considerably. NikABCDE is
upregulated by FNR under anaerobic conditions |CITS:[16159764]|.
)""",]},
'B0451' : {'ecocyc-rxns': {"""TRANS-RXN-149""": """ammonia[periplasmic space] =ammonia[cytosol] """,},'ucsd-rxns' : ['NH4tpp',], 'protein-comments' : ["""(The AmtB transporter is responsible for uptake of either ammonium or
ammonia. Disruption of the amtB gene impairs growth on ammonium
only under acidic growth conditions, and this defect could be complemented
by the cloned amtB gene |CITS: [98284052]|. Whole cell transport
experiments have shown that AmtB mediates transport of the ammonium
analogue, methylammonium and have suggested that transport is dependent
on rapid metabolism of the transported substrate |CITS: [98284052]|.
Whether AmtB mediates transport of ammonium ions or the uncharged species,
ammonia, remains unclear. The energy coupling mechanism is also unclear.
Amt has been proposed to mediate ammonia uniport in an energy independent,
non-concentrative process |CITS: [98284052]|, but homologues of AmtB in other
organisms have been proposed to function as ammonium/proton symporters
|CITS: [96214991]|. AmtB is a member of the Amt family of ammonium/ammonia
transporters.
The amtB forms an operon with the glnK gene, and expression
of this operon occurs under nitrogen-limiting conditions and is
dependent on the NtrC regulatory protein |CITS: [97000355]|.
GlnK and AmtB have been shown to directly interact after ammonium shock.
This reversible sequestration of GlnK by AmtB is rapidly responsive to μM
concentrations of ammonium. The deuridylylated form of GlnK has been shown
to be sequestered by AmtB and to inhibit transport of ammonium by AmtB.
Deletion or mutation of amtB was shown to prevent deuridylylation of GlnK.
The internal glutamine pool, which is increased upon rapid increases in
ammonium availability to nitrogen-limited cells, is responsible for deuridylylation
of GlnK due to its interaction with uridylyltransferase. From these results it has
been suggested that AmtB acts as a sensor of external ammonium concentration
as part of the Ntr system |CITS:[14668330]|.
Imported
ammonia/ammonium is rapidly metabolised to glutamine and glutamate.
The crystal structure has been resolved in two forms at 1.8 and 2.1 A |CITS:[15563598]|. A 12 A resolution projection map of AmtB was determined by cryoelectron microscopy, and
high-resolution topographs were acquired using atomic force microscopy. As determined by
both techniques, AmtB was found to be trimeric in the native cell membrane |CITS:[15568015]|.)""",]},
'B0904' : {'ecocyc-rxns': {"""TRANS-RXN-1""": """formate[cytosol] =formate[periplasmic space] """,},'ucsd-rxns' : ['FORt2pp','FORtppi',], 'protein-comments' : ["""(FocA is a putative formate transporter, possibly involved in both
formate uptake and efflux. Disruption of the focA gene confers
resistance to hypophosphite, a toxic formate analogue |CITS: [94293770]|.
focA mutants were also shown to be associated with increased
intracellular levels of formate, decreased hypophosphite uptake, and
decreased excretion of formate |CITS: [94293770]|. FocA may therefore
function as a bidirectional formate transporter, responsible for
regulating the intracellular formate pool. The energetics of FocA-mediated
formate transport remain unclear.
FocA is a member of the FNT family of formate and nitrite transporters
|CITS: [99184734]|. Analysis of alkaline phosphatase fusions has indicated
that FocA contains six transmembrane segments |CITS: [94293770]|. The
focA gene is encoded in an anaerobically-induced operon with pflA
and pflB, encoding pyruvate-formate lyase |CITS: [94293770]|, a
second formate transporter (FocB?) may function under aerobic conditions.)""",]},
'B2129' : {'ecocyc-rxns': {},'ucsd-rxns' : ['GLYBabcpp','CHLabcpp',], 'protein-comments' : ["""(ATP-binding component of ABC transporter)""","""(YehX, YehW, YehY, YehZ are uncharacterized members
of the ABC superfamily of transporters |CITS: [99091701]|.
YehX is the putative ATP binding component, YehW and YehY
are the membrane components, and YehZ is the putative
periplasmic binding protein. Based on sequence similarity
they probably function together as an ATP-dependant
osmoprotection transporter. The yehX, yehW,
yehY, and yehZ genes are located
within a single operon.
Osmotic shock and entry into stationary phase induced transcription of the yehZYXW operon,
which was dependent upon σs |CITS:[15251200]|.)""",]},
'B0902' : {'ecocyc-rxns': {"""TDCEACT1-RXN""": """2-ketobutyrate formate-lyase/pyruvate formate-lyase 4, inactive + reduced flavodoxin + S-adenosyl-L-methionine -> 5'-deoxyadenosine + 2-ketobutyrate formate-lyase / pyruvate formate-lyase 4 + oxidized flavodoxin""","""1.97.1.4-A-RXN""": """pyruvate formate-lyase (inactive) + reduced flavodoxin + S-adenosyl-L-methionine -> 5'-deoxyadenosine + L-methionine + pyruvate formate-lyase + oxidized flavodoxin""",},'ucsd-rxns' : ['PFL','PFL','PFL','OBTFL','OBTFL','OBTFL',], 'protein-comments' : ["""NIL""",]},
'B0903' : {'ecocyc-rxns': {"""PYRUVFORMLY-RXN""": """formate + acetyl-CoA = pyruvate + coenzyme A""","""KETOBUTFORMLY-RXN""": """2-oxobutanoate + coenzyme A = propionyl-CoA + formate""",},'ucsd-rxns' : ['PFL','PFL','OBTFL','OBTFL',], 'protein-comments' : ["""(Pyruvate formate-lyase catalyzes the non-oxidative cleavage
of pyruvate to acetyl-CoA and formate in anaerobically growing cells.
The enzyme converts between inactive and active forms. The active
form contains an organic free radical, sensitive to oxygen, which is
essential for catalysis. The reaction is reversible and employs a
'ping-pong mechanism'. The enzyme is also active with 2-ketobutyrate,
but pyruvate is the preferred substrate.|CITS: [91064082] [75112170] [98143432]|)""","""NIL""","""NIL""",]},
'B3734' : {'ecocyc-rxns': {"""ATPSYN-RXN""": """H+[cytosol] + H2O + ATP =H+[periplasmic space] + phosphate + ADP """,},'ucsd-rxns' : ['ATPS4rpp','ATPS4rpp',], 'protein-comments' : ["""NIL""","""(The alpha subunit plays an essential role in the catalytic mechanism of the
enzyme and in the binding and coupling between the F-1 and F-O complexes. The
alpha-subunit also contains an adenine-specific binding site which is
noncatalytic, nonregulatory and not essential for enzyme assembly in vitro. Its
function has not yet been determined. The alpha subunit complex is a homotrimer.
|CITS: [89034048]|)""","""(The F-1 complex of ATP synthase contains the catalytic sites. The complex
consists of five subunits, each of which is required for activity.
|CITS: [90303438] [89372792]|)""","""(The enzyme is made up of two subcomplexes, the F-1 complex and the F-O complex.
There are eight total subunits all required for activity. The F-1 complex is
the catalytic unit. The F-O complex anchors the F-1 complex to the membrane
and also forms the proton channel. |CITS: [89123355] [90303438] [93252965]|)""",]},
'B2287' : {'ecocyc-rxns': {"""NADH-DEHYDROG-A-RXN""": """ubiquinone-8 + NADH = ubiquinol-8 + NAD+""",},'ucsd-rxns' : ['NADH17pp','NADH18pp','NADH16pp',], 'protein-comments' : ["""(This subunit contains the N2 4Fe-4S cluster. |CITS: [93389724][98256007][12975362]|
Point mutations in NuoB have been analyzed; the Tyr114 and Tyr139 residues appear to be protonated upon
reduction of the 4Fe-4S cluster, and a double mutant retains only 20% activity |CITS: [12446673]|.
NuoB is part of the connecting fragment of NADH dehydrogenase I |CITS: [7607227]|.)""","""(This complex is thought to connect the soluble fragment of NADH dehydrogenase I to the inner membrane
components |CITS: [7607227]|.)""","""(There is a cluster of 13 genes that code for NADH dehydrogenase I. Six of the subunits are peripheral proteins and
the other seven are very hydrophobic |CITS: [94178656] [98256007]|. Three-dimensional reconstruction of the
complex based on cryo-electron microscopy showed an L-shaped form with an integral membrane and a peripheral
arm |CITS: [9514725]|. A model of the spatial arrangement of the subunits and the possible functional mechanism of
proton pumping has been proposed |CITS: [12923180]|.)""",]},
'B1015' : {'ecocyc-rxns': {"""TRANS-RXN-118A""": """Li+[periplasmic space] + L-proline[periplasmic space] =Li+[cytosol] + L-proline[cytosol] ""","""TRANS-RXN-118""": """Na+[periplasmic space] + L-proline[periplasmic space] =Na+[cytosol] + L-proline[cytosol] """,},'ucsd-rxns' : ['PROt4pp','PPAt4pp',], 'protein-comments' : ["""(PutP is a sodium/proline symporter responsible for the uptake of proline. Mutations in putP
decrease proline transport and can be complemented by the cloned putP gene |CITS:[86174353]|.
The PutP protein has been purified, reconstituted in proteoliposomes, and shown to mediate proline
transport in the presence of a sodium or lithium ion gradient |CITS:[98359785],[86140003]|. Kinetic analysis
has shown that PutP binds proline with a Km of approx 2 μM and sodium with a Km of approx 700
μM |CITS:[98359785]|. Sodium and proline are transported by PutP with a stoichiometry of 1:1
|CITS:[86140003]|. PutP is a member of the SSS family of sodium/solute transporters |CITS:[94304911]|.
The principle role of PutP is uptake of proline for proline utilization and protein synthesis. Genetic and
spectroscopic analyses indicate that PutP consists of 13 transmembrane (TMs) helices with the
N-terminus on the periplasmic side of membrane and the C-terminus facing the cytoplasm
|CITS:[10769140][9756872]|. PutP has been found as a dimer in the inner membrane |CITS:[16079137]|.
The transport activity of PutP is associated with charge translocation |CITS:[15476811]|.
Sodium ion and/or proline individually or together induce a charge displacement and conformational
alteration through the binding process at the cytoplasmic face of the protein |CITS:[10769140]|.
Reviewed in |CITS:[12354616],[9693722],[11248195]|.
)""",]},
'B1014' : {'ecocyc-rxns': {"""RXN-821""": """L-proline + FAD = pyrroline 5-carboxylate + FADH2""","""PYRROLINECARBDEHYDROG-RXN""": """pyrroline 5-carboxylate + NAD+ + 2 H2O = L-glutamate + NADH""",},'ucsd-rxns' : ['P5CD','PROD2',], 'protein-comments' : ["""(The PutA protein is a bifunctional enzyme as well as a transcriptional repressor of the put (proline utilization) regulon,
belonging to the PutA family. The proline dehydrogenase activity resides in the amino terminal 669 amino acids of
PutA; a truncated protein retains proline dehydrogenase and DNA binding activity, but lacks membrane association and 1-pyrroline-5-carboxylate dehydrogenase activity |CITS: [12009917]|. The amino-terminal 47 residues contain the dimerization domain and the specific DNA binding activity |CITS: [15155740]|.
Crystal structures of the amino-terminal proline dehydrogenase domain have been reported
|CITS: [11717519][12514740][15449943]|.
put = "proline utilization" |CITS: [7006756]|)""","""NIL""","""NIL""",]},
'B2241' : {'ecocyc-rxns': {"""GLYC3PDEHYDROG-RXN""": """sn-glycerol-3-phosphate + ubiquinone-8 = dihydroxy-acetone-phosphate + ubiquinol-8""",},'ucsd-rxns' : ['G3PD7','G3PD6','G3PD5',], 'protein-comments' : ["""NIL""","""(The GlpABC enzyme is loosely associated with the cell membrane. A functional two subunit form, GlpAC, has been
isolated, and it is assumed that the third subunit (GlpB) is responsible for membrane anchoring.
The GlpA subunit contains noncovalently bound FAD, and the GlpC subunit is thought to bind flavin mononucleotide
|CITS: [3286606]|.
The GlpB subunit contains two iron-sulfur clusters, and does not contain any transmembrane helices, so
the mechanism by which it acts as the membrane anchor for the complex is not clear
|CITS: [3286606][7576488]|.
Please note: reference |CITS: [6363389]| and reference |CITS: [3286606]| utilize different terminologies for the
members of the glpACB operons. The former names the genes A,B,C, while the later names them A,C and B,
respectively. Throughout this discussion we have used the nomenclature of the later.
This three-subunit enzyme converts glycerol-3-phosphate to dihydroxyacetone phosphate (DHAP) using
electron acceptors other than oxygen, and functions mostly under anaerobic conditions.
The anaerobic dehydrogenase protein complex is encoded by the glpACB operon,
and is regulated by glycerol and catabolite repression |CITS: [6363389]|.
The reducing equivalents are passed through a simple electron transport chain which terminates with
fumarate or nitrate as the electron acceptor |CITS:[82007833]|.
Expression of glpABC (along with other members of the glp regulon |CITS: [825019]| is repressed by
GlpR and induced by glycerol-3-phosphate. Optimal intracellular levels of glycerol-3-phosphate are maintained for
biosynthesis of phospholipids. The glpTQ operon, which encodes glycerol-3-phosphate transporter and
phosphodiesterase is adjacent to glpABC. The two operons are divergently transcribed; the operators to
which GlpR binds overlap the ,glpA promoter |CITS: [9179845]|.
)""",]},
'B3479' : {'ecocyc-rxns': {"""ABC-20-RXN""": """Ni2+[periplasmic space] + ATP + H2O =Ni2+[cytosol] + ADP + phosphate """,},'ucsd-rxns' : ['NI2uabcpp',], 'protein-comments' : ["""NIL""","""(The NikABCDE ATP-dependent nickel (II) uptake system is a member of the ATP-Binding Cassette (ABC)
Superfamily of transporters |CITS: [96381453]|. The Nik system exhibits significant sequence similarity to
the components of other ABC transporters for dipeptides or oligopeptides |CITS: [95020649]|. Based on
sequence similarity, NikA is the periplasmic binding protein, NikB and NikC are the membrane components,
and NikD and NikE are the ATP-binding components of the ABC transporter. The nickel-binding
properties of the protein have been studied by monitoring the quenching of intrinsic protein fluorescence
|CITS: [95172074]|. NikA binds one atom of nickel per molecule of protein with a Kd of less
than 0.1 μM. The transporter's high specificity for nickel ion has also been demonstrated by
high-performance immobilized-metal-ion affinity chromatography |CITS:[95172074]|. The structure of NikA
has been determined to a resolution of 1.8 angstroms showing that it binds FeEDTA(H2O)
with very high affinity. It also binds the nickel ion associated with a metallophore which is at least similar
to EDTA |CITS:[16011372]|. Insertional mutation in the nik operon severely reduces nickel transport
ability |CITS:[95020649]|. Nickel is an important cofactor in a variety of enzymatic reactions in prokaryotes
|CITS:[20112624]|. However, nickel at high intracellular concentrations is toxic because it can catalyze the
formation of reactive forms of oxygen that can damage cellular constituents |CITS: [20112624]|. Because of
the toxicity of nickel, the synthesis of the Nik system is tightly controlled by nickel concentration. At high
nickel concentrations (0.3 mM) synthesis of Nik is completely repressed by the protein NikR
|CITS:[20112624]|. Expression of NikABCDE corresponds to expression of NiFe hydrogenases for which
nickel is a cofactor. Mutation and LacZ fusion experiments show that nitrate, via the activity of the NarLX
two-component system, represses expression of nikABCDE considerably. NikABCDE is
upregulated by FNR under anaerobic conditions |CITS:[16159764]|.
)""",]},
'B3478' : {'ecocyc-rxns': {"""ABC-20-RXN""": """Ni2+[periplasmic space] + ATP + H2O =Ni2+[cytosol] + ADP + phosphate """,},'ucsd-rxns' : ['NI2uabcpp',], 'protein-comments' : ["""NIL""","""(The NikABCDE ATP-dependent nickel (II) uptake system is a member of the ATP-Binding Cassette (ABC)
Superfamily of transporters |CITS: [96381453]|. The Nik system exhibits significant sequence similarity to
the components of other ABC transporters for dipeptides or oligopeptides |CITS: [95020649]|. Based on
sequence similarity, NikA is the periplasmic binding protein, NikB and NikC are the membrane components,
and NikD and NikE are the ATP-binding components of the ABC transporter. The nickel-binding
properties of the protein have been studied by monitoring the quenching of intrinsic protein fluorescence
|CITS: [95172074]|. NikA binds one atom of nickel per molecule of protein with a Kd of less
than 0.1 μM. The transporter's high specificity for nickel ion has also been demonstrated by
high-performance immobilized-metal-ion affinity chromatography |CITS:[95172074]|. The structure of NikA
has been determined to a resolution of 1.8 angstroms showing that it binds FeEDTA(H2O)
with very high affinity. It also binds the nickel ion associated with a metallophore which is at least similar
to EDTA |CITS:[16011372]|. Insertional mutation in the nik operon severely reduces nickel transport
ability |CITS:[95020649]|. Nickel is an important cofactor in a variety of enzymatic reactions in prokaryotes
|CITS:[20112624]|. However, nickel at high intracellular concentrations is toxic because it can catalyze the
formation of reactive forms of oxygen that can damage cellular constituents |CITS: [20112624]|. Because of
the toxicity of nickel, the synthesis of the Nik system is tightly controlled by nickel concentration. At high
nickel concentrations (0.3 mM) synthesis of Nik is completely repressed by the protein NikR
|CITS:[20112624]|. Expression of NikABCDE corresponds to expression of NiFe hydrogenases for which
nickel is a cofactor. Mutation and LacZ fusion experiments show that nitrate, via the activity of the NarLX
two-component system, represses expression of nikABCDE considerably. NikABCDE is
upregulated by FNR under anaerobic conditions |CITS:[16159764]|.
)""",]},
'B1866' : {'ecocyc-rxns': {"""ASPARTATE--TRNA-LIGASE-RXN""": """tRNAasp + L-aspartate + ATP -> L-aspartyl-tRNAasp + diphosphate + AMP""",},'ucsd-rxns' : ['ASPTRS',], 'protein-comments' : ["""(Aspartyl-tRNA synthetase (AspRS) is a member of the family of aminoacyl-tRNA synthetases, which interpret the
genetic code by covalently linking amino acids to their specific tRNA molecules. The reaction is driven by ATP
hydrolysis. AspRS belongs to the Class II aminoacyl tRNA synthetases, which share three regions of homology
|CITS: [2203971]|.
The enzyme is a dimer in solution |CITS: [2129559]|. Crystal structures of AspRS have been determined and allow
modelling of specific interactions with the tRNA and the reaction mechanism |CITS: [10562565][10873442][11566892]|.
The tls-1 allele of aspS consists of a P555S mutation in the highly conserved proline residue of motif 3.
It has no significant effect on substrate binding, but may affect the active site |CITS: [9171418]|. Specific interactions
of AspRS with tRNA(Asp) were deduced from the crystal structures and by mutagenesis of the tRNA substrate
|CITS: [12649491]|. The L45 loop within the OB-fold domain of AspRS appears to be responsible for
anticodon recognition |CITS: [12766171]|. Mutations that allow charging of an amber tRNA(Asp) with aspartate mostly
localize to the anticodon binding domain of AspRS, although some are far from the anticodon binding domain
|CITS: [15289581]|.
Review: |CITS: [8955904][10966471]|)""","""NIL""",]},
'B4088' : {'ecocyc-rxns': {"""ABC-28-RXN""": """ATP + D-ribose[periplasmic space] + H2O =ADP + phosphate + D-ribose[cytosol] ""","""ABC-42-RXN""": """D-allose[periplasmic space] + ATP + H2O =D-allose[cytosol] + ADP + phosphate """,},'ucsd-rxns' : ['ALLabcpp','RIBabcpp',], 'protein-comments' : ["""NIL""","""(The AlsABC transporter belongs to the ATP-binding Cassette (ABC)
Superfamily |CITS: [94272333]|. It is responsible for the uptake of D-allose, an
all-cis hexose that can be used by E. coli as a sole carbon
source |CITS: [98062191]|. Deletion of the als genes resulted in an inability
to grow on D-allose |CITS: [98062191]|. AlsB is a periplasmic protein that binds
D-allose with a Kd of 0.33μM, as determined by
fluorescence spectroscopy |CITS: [98062191]|. Based on sequence similarity, AlsA
is the ATP-binding component, and AlsC is the membrane
component of the ABC transporter |CITS: [99165783]|. The AlsABC system also
transports ribose at low affinity |CITS: [98062191]|. Complementation analysis of
als mutants showed that the cloned als genes could
restore growth on ribose minimal media |CITS: [98062191]|. Analysis of
β-galactosidase transcriptional fusions suggest that AlsR is a
negative regulator of alsABC, and transcription of
alsR is regulated by allose |CITS: [98062191]|.)""",]},
'B0261' : {'ecocyc-rxns': {"""HOMOCYSTEINE-S-METHYLTRANSFERASE-RXN""": """L-homocysteine + S-adenosyl-L-methionine = L-methionine + S-adenosyl-L-homocysteine""","""MMUM-RXN""": """S-methyl-L-methionine + L-homocysteine = 2 L-methionine""",},'ucsd-rxns' : ['HCYSMT','HCYSMT2',], 'protein-comments' : ["""(MmuM is an S-methylmethionine: homocysteine methyltransferase |CITS: [99102233], [10026151]| involved in S-methylmethionine utilization |CITS: [99102233]|.
A mmuM metE metH triple mutant shows inability to grow on S-methylmethionine, in contrast to a metE metH double mutant or to wild type |CITS: [99102233]|.
MmuM has similarity to Arabidopsis thaliana HMT-1 and HMT-2 proteins, production of which functionally complements phenotypes of an E. coli mmuM mutant |CITS: [10747987]|. MmuM has similarity to Astragalus bisulcatus selenocysteine methyltransferase |CITS: [10026151]|.
Overproduction and purification of the enzyme is described |CITS: [10026151]|.
Regulation has been described |CITS: [99102233]|. Protein abundance is decreased in the presence of methionine, but not S-methylmethionine |CITS: [99102233]|.)""",]},
'B0914' : {'ecocyc-rxns': {"""3.6.3.39-RXN""": """a lipopolysaccharide[cytosol] + H2O + ATP =a lipopolysaccharide[out] + phosphate + ADP """,},'ucsd-rxns' : ['PA141abcpp','PA120abcpp','PE160abcpp','PA181abcpp','PE120abcpp','PG160abcpp','PG180abcpp','PE180abcpp','PA160abcpp','PE161abcpp','PGP140abcpp','PA161abcpp','PE181abcpp','LIPACabcpp','PA180abcpp','PG141abcpp','PG120abcpp','K2L4Aabcpp','PGP180abcpp','PG161abcpp','COLIPAabcpp','PG140abcpp','PE140abcpp','PGP141abcpp','PGP160abcpp','PG181abcpp','LIPAabcpp','PGP120abcpp','PA140abcpp','PGP161abcpp','PGP181abcpp','PE141abcpp',], 'protein-comments' : ["""(MsbA is a member of the ATP Binding Cassette (ABC) Superfamily of transporters
|CITS:[96381453]|. MsbA is a membrane protein that also possesses a cytoplasmic
ATP-binding domain. Its ability to bind ATP has been demonstrated with an
ATP-agarose column |CITS:[96405645]|. It is believed to export core lipid A and
possibly glycerophospholipid molecules across the inner membrane.
msbA-deficient strains were shown to cause the accumulation of
hexa-acylated lipid A species and glycerophospholipids within the inner
membrane. Lipid A serves as a hydrophobic membrane anchor for the
lipopolysaccharide, which is a major component of the outer leaflet of the outer
membranes of Gram-negative bacteria |CITS:[98241619]|. MsbA was shown to
be essential for the translocation of lipopolysaccharides across the inner membrane.
Studies using spheroblasts found that lipopolysaccharides synthesized
de novo co-fractionated with the outer membranes in a MsbA-dependent
fashion |CITS:[15576375]|. MsbA has also been shown to transport
N-acetyl-glucosamine, a precursor of lipopolysaccharides. A msbA
mutant showed N-acetyl-glucosamine accumulation in the inner membrane.
Translocation of N-acetyl-glucosamine to the outer membrane was restored
by transformation with a plasmid containing the wild-type msbA gene
|CITS:[96405645]|.
The structure of the homodimeric MsbA lipopolysaccharide ABC transporter
has been examined using site-directed spin labeling and electron paramagnetic
resonance spectroscopy |CITS:[15890883]|. X-ray crystallographic analysis of
MsbA has also been performed in Salmonella typhimurium |CITS:[15890884]|.
The activity of MsbA as a multidrug transporter has been examined by heterologous
expression in a lipopolysaccharide-less lactococcal model. Expression of MsbA
conferred increased resistance to erythromycin, ethidium, and Hoechst 33342
|CITS:[16159769]|.
MsbA shares sequence similarity with Mdr1 a human multidrug resistance protein |CITS:[93172962]|.
)""",]},
'B0511' : {'ecocyc-rxns': {},'ucsd-rxns' : ['ALLTNt2rpp',], 'protein-comments' : ["""(The YbbW protein is an uncharacterized member of the
NCS1 family of purine and pyrimidine transporters
|CITS: [99184734]|. Based on sequence similarity,
YbbW may function as a proton-driven allantoin uptake
system. Supporting this notion, the downstream gene
from ybbW encodes a putative allantoinase enzyme.)""",]},
'B0512' : {'ecocyc-rxns': {"""ALLANTOINASE-RXN""": """H2O + allantoin = allantoate""",},'ucsd-rxns' : ['ALLTN',], 'protein-comments' : ["""(AllB has similarity to HyuA |CITS: [11092864]|.)""","""NIL""",]},
'B3370' : {'ecocyc-rxns': {},'ucsd-rxns' : ['FRULYSt2pp','PSCLYSt2pp',], 'protein-comments' : ["""(FrlA is an uncharacterized member of the APC superfamily of amino acid transporters |CITS:[20391827]|. Based on
the activities of FrlB and FrlD, FrlA is suggested to transport fructoselysine, which can be utilized as a carbon source
|CITS: [12147680]|. The function of FrlA has not been experimentally determined.
An frlA mutant is unable to grow on 20mM fructoselysine or psicoselysine as the sole source of carbon
|CITS: [14641112]|.
FrlA: "fructoselysine" |CITS: [12147680]|.)""",]},
'B0849' : {'ecocyc-rxns': {},'ucsd-rxns' : ['RNDR2b','RNDR3b','RNDR1b','GRXR','PAPSR2','RNDR4b',], 'protein-comments' : ["""NIL""","""(Glutaredoxins are ubiquitous proteins that catalyze the reduction of disulfides via reduced glutathione (GSH).
Escherichia coli has three glutaredoxins (Grx1, Grx2, and Grx3) containing the classic dithiol active site
CPYC, and a fourth one which contains a monothiol (CGFS) potential active site |CITS: [15833738]|.
The glutaredoxins act as a cofactor enabling intracellular redox reactions through a disulfide/dithiol
enzymatic mechanism involving the active site cysteines. They are used as a
hydrogen donor for the glutathione(GSH)-dependent synthesis of deoxyribonucleotides
by ribonucleotide reductase and reduces specific cysteine residues in
ribonucleotide reductase.
Glutaredoxin are also a hydrogen donor for the reduction of adenosine 3'-phosphate 5'-phosphosulfate
and methionine sulfoxide.
In addition, glutaredoxins also catalyzes GSH-disulfide oxidoreduction reactions with low molecular weight
substrates. |CITS: [79151138] [91242463] [93003075]| There are two additional
glutaredoxins in E. coli whose physiological roles have not been fully
determined. |CITS: [95024051]|)""",]},
'B0517' : {'ecocyc-rxns': {"""R165-RXN""": """(S)-ureidoglycolate + NAD(P)+ = oxalureate + NAD(P)H""",},'ucsd-rxns' : ['URDGLYCD',], 'protein-comments' : ["""NIL""",]},
'B0516' : {'ecocyc-rxns': {"""ALLANTOICASE-RXN""": """allantoate + H2O = (S)-ureidoglycolate + urea""",},'ucsd-rxns' : ['ALLTAMH',], 'protein-comments' : ["""NIL""",]},
'B3903' : {'ecocyc-rxns': {"""RHAMNISOM-RXN""": """L-rhamnose = rhamnulose""","""LYXISOM-RXN""": """L-lyxose = L-xylulose""",},'ucsd-rxns' : ['RMI','LYXI',], 'protein-comments' : ["""NIL""",]},
'B3902' : {'ecocyc-rxns': {"""RHAMNULPALDOL-RXN""": """rhamnulose-1-phosphate = lactaldehyde + dihydroxy-acetone-phosphate""",},'ucsd-rxns' : ['RMPA',], 'protein-comments' : ["""NIL""","""(Rhamnulose-1-phosphate aldolase is a class II aldolase,
which contains 2 grams of zinc per mole of enzyme. The metal is
required by the enzyme subunits to form the active tetramer. The
enzyme has been crystallized. |CITS: [74173401] [69155179]|)""",]},
'B0067' : {'ecocyc-rxns': {"""ABC-32-RXN""": """ATP + thiamine[periplasmic space] + H2O =ADP + phosphate + thiamine[cytosol] """,},'ucsd-rxns' : ['THMabcpp',], 'protein-comments' : ["""NIL""","""(The ABC transporter ThiBPQ was functionally characterized in Salmonella typhimurium where it is
required for the uptake of thiamine and thiamine pyrophosphate |CITS:[9535878]|. Its ortholog in
E. coli, SfuABC, has not been functionally characterized yet but presumably also function in
thiamine uptake. thiB (sfuA) encodes periplasmic thiamine binding protein. thiP
(sfuB) encodes inner membrane permease, and thiQ(sfuC) encodes
energy-transducing ATPase.
)""",]},
'B1865' : {'ecocyc-rxns': {"""RXN0-384""": """dATP + H2O = dAMP + diphosphate""",},'ucsd-rxns' : ['NTPP5','DNTPPA',], 'protein-comments' : ["""NIL""",]},
'B3907' : {'ecocyc-rxns': {"""TRANS-RXN-112""": """H+[periplasmic space] + L-rhamnose[periplasmic space] =H+[cytosol] + L-rhamnose[cytosol] """,},'ucsd-rxns' : ['LYXt2pp','RMNtpp',], 'protein-comments' : ["""(RhaT is the sole transporter for rhamnose in E. coli and functions as a rhamnose/proton symporter.
rhaT mutants were unable to utilise or transport rhamnose, and this defect could be complemented by the
cloned rhaT gene |CITS: [92202251]|. Studies in membrane vesicles have shown that RhaT can transport
rhamnose with moderate affinity (20-40 μM) and that rhamnose transport is coupled with proton transport
|CITS: [93207538]|. RhaT is the prototype member of the RhaT family of transporters. Analysis of RhaT-BlaZ fusions
has indicated that the RhaT protein contains 10 transmembrane segments |CITS: [94086487]|. Expression of
rhaT is induced by rhamnose in a process involving RhaS and RhaT |CITS: [96303522]|.)""",]},
'B0063' : {'ecocyc-rxns': {"""RXN0-5116""": """L-ribulose + ATP -> L-ribulose-5-phosphate + ADP""",},'ucsd-rxns' : ['XYLK','RBK_L1','XYLK2',], 'protein-comments' : ["""(Ribulokinase catalyzes the phosphorylation of L-ribulose to L-ribulose-5-phosphate, the second step in the
L-arabinose degradation pathway.
The araBAD operon and its gene products were first studied in E. coli B |CITS: [13829634]|. The
E. coli B ribulokinase has been crystallized |CITS: [67134324]|, and its subunit structure was determined
|CITS: [70179415]|. The enzyme uses four 2-ketopentoses (L- and D-ribulose, L- and D-xylulose) with similar
catalytic activity. In addition, L-arabitol and ribitol can serve as substrates |CITS: [11747300]|. In the absence of
sugar substrates, the enzyme exhibits a low ATPase activity |CITS: [11747300]|.
The sequence of the E. coli B enzyme is 98% identical to the E. coli K-12 enzyme.)""","""NIL""",]},
'B3904' : {'ecocyc-rxns': {"""RHAMNULOKIN-RXN""": """rhamnulose + ATP -> rhamnulose-1-phosphate + ADP""",},'ucsd-rxns' : ['RMK',], 'protein-comments' : ["""(Rhamnulokinase catalyzes the second step of rhamnose degradation, the phosphorylation of rhamnulose.
Rhamnulokinase is a monomer in solution |CITS: [16674975]|. Crystal structures of rhamnulokinase as an apo- and
holo-enzyme have been determined and show that the enzyme belongs to the hexokinase-hsp70-actin superfamily.
A catalytic mechanism has been proposed |CITS: [16674975]|.
The enzyme was first identified in E. coli B |CITS: [13416205]|.)""",]},
'B0155' : {'ecocyc-rxns': {"""RXN0-2501""": """chloride[periplasmic space] + H+[cytosol] =chloride[cytosol] + H+[periplasmic space] """,},'ucsd-rxns' : ['CLt3_2pp',], 'protein-comments' : ["""(EriC is a homologue of ClC chloride channels. The transporter mediates a chloride:proton antiport
reaction (a secondary carrier type transport reaction) in which two Cl- exchange for
one H+ |CITS:[14985752]|. The crystal structure of EriC has been determined to a
resolution of 3.5 angstroms. Eric exists as a homodimer of two monomers, each of which contains
a pore and selectivity filter mediated by its antiparallel conformation |CITS:[11796999]|. Analysis
of the crystal structure at resolution of 2.5 angstroms of Eric bound to a Fab fragment revealed that
gating occurs independently within each monomer and is pH-dependent |CITS:[12649487]|.
Electrophysiological experiments reveal that mutation of the gating residue eliminates the pH
dependence of the transporter |CITS:[14985752]|.)""",]},
'B3909' : {'ecocyc-rxns': {"""TRANS-RXN-113""": """H+[periplasmic space] + 2-dehydro-3-deoxy-D-gluconate[periplasmic space] =H+[cytosol] + 2-dehydro-3-deoxy-D-gluconate[cytosol] """,},'ucsd-rxns' : ['GLCURt2rpp','DDGLCNt2rpp',], 'protein-comments' : ["""(KdgT is a probable 2-keto-3-deoxy-D-gluconate (KDG) uptake system.
The cloned kdgT gene increased uptake of KDG and to a lesser
extent glucuronate |CITS: [85054564]| and could complement the
KDG transport defect in kdgT mutants. KDG transport has been
shown in whole cells and membrane vesicles to be via proton symport
|CITS: [77157151]|. KdgT is the prototype representative of the KdgT
family of KDG transporters. Expression of kdgT is inducible
by KDG and is under the control of the KdgR repressor |CITS: [74090271]|.
Imported KDG is subsequently degraded to pyruvate and triose-phosphate.)""",]},
'B3908' : {'ecocyc-rxns': {"""SUPEROX-DISMUT-RXN""": """2 H+ + 2 O2- = H2O2 + O2""",},'ucsd-rxns' : ['SPODM',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B2841' : {'ecocyc-rxns': {"""TRANS-RXN-10""": """H+[periplasmic space] + α-L-arabinose[periplasmic space] =H+[cytosol] + α-L-arabinose[cytosol] """,},'ucsd-rxns' : ['ARBt2rpp',], 'protein-comments' : ["""(AraE is an arabinose/proton symporter responsible for the uptake
of arabinose. Studies in membrane vesicles have shown that AraE
can transport L-arabinose with low affinity (140-320 μM) and
arabinose transport is coupled with proton transport
|CITS: [82205973]|. The AraE protein has been overproduced and
reconstituted in liposomes as a arabinose/proton symporter
|CITS: [86230078]|. AraE is a member of the major facilitator
superfamily (MFS) of transporters |CITS: [93040298]|.
Arabinose is the sole inducer of araE expression
|CITS: [82205973]|, which is controlled by the AraC regulator.
Imported arabinose is catabolised to xylulose-5-phosphate and
thence via the pentose phosphate pathway.)""",]},
'B1479' : {'ecocyc-rxns': {"""MALIC-NAD-RXN""": """NAD+ + malate = NADH + CO2 + pyruvate""",},'ucsd-rxns' : ['ME1',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B0154' : {'ecocyc-rxns': {"""GSAAMINOTRANS-RXN""": """glutamate-1-semialdehyde = 5-amino-levulinate""",},'ucsd-rxns' : ['G1SAT',], 'protein-comments' : ["""(Glutamate-1-semialdehyde aminotransferase catalyzes the pyridoxal 5'-phosphate-dependent reaction which
converts GSA to delta-aminolevulinate (ALA). ALA is the first committed precursor of porphyrin biosynthesis
|CITS: [91258321]|. The enzyme is homodimeric |CITS: [2045363]|.
HemL forms a tight complex with glytamyl-tRNA reductase, the preceding enzyme in the pathway, suggesting
metabolic channeling of the highly reactive intermediate glutamate-1-semialdehyde |CITS: [15757895]|.
Transcription of hemL is regulated by Mg2+ and PhoP |CITS: [12813061]|.)""","""NIL""",]},
'B0638' : {'ecocyc-rxns': {"""RIBAZOLEPHOSPHAT-RXN""": """α-ribazole-5'-P + H2O = α-ribazole + phosphate""",},'ucsd-rxns' : ['RZ5PP',], 'protein-comments' : ["""(In Salmonella, the cobC gene encodes an enzyme in the cobalamin biosynthetic pathway
|CITS: [95014494][ColiSalII]|.)""",]},
'B0684' : {'ecocyc-rxns': {},'ucsd-rxns' : ['RNTR3c','RNTR3c','FLDR','RNTR4c','RNTR4c','RNTR1c','RNTR1c','RNTR2c','RNTR2c',], 'protein-comments' : ["""(Flavodoxins are small, acidic electron transfer proteins which contain FMN as a prosthetic group. They are only
able to accept and donate electrons. Flavodoxin is an important member of the multi-enzyme complexes that are
involved in the activation of anaerobic nucleoside reductase and pyruvate-formate lyase. Flavodoxins are
functionally interchangeable with ferredoxins, but some enzymes are specific for one or the other. E. coli has
at least two flavodoxins |CITS: [91154129][95050480][93194782]|.
FldA is essential under both aerobic and anaerobic growth conditions |CITS: [10714981]|. The essential role for
flavodoxin 1 under aerobic conditions is in the MEP pathway for isoprenoid biosynthesis
(|FRAME: NONMEVIPP-PWY|) |CITS: [15978585]|.
Crystal and solution structures of FldA have been solved |CITS: [9416602][9119004]|.)""","""NIL""",]},
'B0103' : {'ecocyc-rxns': {"""DEPHOSPHOCOAKIN-RXN""": """dephospho-CoA + ATP = coenzyme A + ADP""",},'ucsd-rxns' : ['DPCOAK',], 'protein-comments' : ["""(Dephospho-CoA kinase catalyzes the final step in coenzyme-A biosynthesis |CITS: [21189301]|. The enzyme
appeared to be a monomer in solution |CITS: [21189301]|; subsequent analysis of the crystal structure, where it
appears as a trimer, led to the discovery that the presence of sulfate ions stabilizes a trimeric state in solution as well.
The biological role of the trimeric form is unclear |CITS: [12538896]|.
Crystal structures of the enzyme have been solved |CITS: [12538896][16021622]|.)""",]},
'B0159' : {'ecocyc-rxns': {"""ADENOSYLHOMOCYSTEINE-NUCLEOSIDASE-RXN""": """S-adenosyl-L-homocysteine + H2O -> S-ribosyl-L-homocysteine + adenine""",},'ucsd-rxns' : ['AHCYSNS','5DOAN','MTAN',], 'protein-comments' : ["""(The mtn gene encodes 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase |CITS: [9524204]|.
The enzyme catalyzes glycosidic bond cleavage in S-adenosylhomocysteine and 5'-methylthioadenosine
substrates, with a higher Vmax toward 5'-methylthioadenosine |CITS: [3911944]|. The enzyme activity
has been characterized in detail |CITS: [782530][3911944][8941345][9746359]|.
An mtn mutant is auxotrophic for biotin due to the accumulation of 5'-deoxyadenosine, which inhibits biotin
synthase activity |CITS: [15911379]|.
Crystal structures of the enzyme bound to adenine (1.9 Å resolution) |CITS: [11591349]|, formycin A
(2.2 Å resolution) |CITS: [12496243]|, and 5'-methylthiotubercidin (2.0 Å resolution) |CITS: [12496243]|
are presented, and the implications of the structures with respect to catalysis are discussed
|CITS: [11591349][12496243]|. Additional crystal structures of the wild-type and mutant enzymes have been
determined, allowing analysis of the conformational motions occuring during the catalytic cycle
|CITS: [15746096][16109423]|. The enzyme is dimeric |CITS: [11591349]|.
Mtn has potential as a drug target |CITS: [8941345]|.)""","""NIL""",]},
'B1640' : {'ecocyc-rxns': {"""RXN0-4621""": """1,6-anhMurNAc + ATP = MurNAc-6-P + ADP""",},'ucsd-rxns' : ['ANHMK',], 'protein-comments' : ["""(AnmK is one of the enzymes responsible for the recycling of murein. Anhydro-N-acetylmuramic acid
(anhMurNAc) is produced by the cleavage of muropeptide by NagZ (between the GlcNAc and the anhMurNAc
moieties) and AmpD (between the anhMurNAc and peptide moieties), and AnmK catalyzes the hydrolysis of the
1,6-anhydro bond and simultaneous posphorylation of anhMurNAc to N-acetylmuramate 6-phosphate. An
etherase then cleaves the ether bond between the GlcNAc and D-lactate moieties of N-acetylmuramate
6-phosphate |CITS: [15901686]|.
In an anmK null mutant, anhMurNAc does not accumulate inside the cell, although no other enzyme activity
that is able to modify anhMurNAc can be detected. When anhMurNAc can not be phosphorylated, it is lost into the
medium instead |CITS: [15901686]|.)""",]},
'B3012' : {'ecocyc-rxns': {"""RXN0-4281""": """methylglyoxal + NADPH -> acetol + NADP+""","""RXN0-1941""": """ethyl-2-methylacetoacetate + NADPH = ethyl-(2R)-methyl-(3S)-hydroxybutanoate + NADP+""","""1.1.1.274-RXN""": """NADPH + 2,5-didehydro-D-gluconate = 2-dehydro-D-gluconate + NADP+""",},'ucsd-rxns' : ['ALR2','DKGLCNR1',], 'protein-comments' : ["""(DkgA has been shown to have a stereoselective beta-keto ester reductase |CITS: [11934293]| and
methylglyxoal reductase |CITS: [16077126]| activity.
The dkgA gene was reported to encode 2,5-diketo-D-gluconate reductase (25DKGR) A, one of two 25DKG
reductases in E. coli. The enzyme uses NADPH as the preferred electron donor. It is thought to be involved
in ketogluconate metabolism |CITS: [99357626]|. The specific activity of the enzyme towards 2,5-diketo-D-gluconate
was reported to be almost 1000-fold lower than its activity towards methylglyoxal |CITS: [16077126]|.
Expression of dkgA is not increased in response to methylglyoxal |CITS: [16077126]|.)""",]},
'B2799' : {'ecocyc-rxns': {"""GLYCOLALDREDUCT-RXN""": """NAD+ + ethylene glycol = glycolaldehyde + NADH""","""LACTALDREDUCT-RXN""": """NADH + lactaldehyde = NAD+ + propane-1,2-diol""",},'ucsd-rxns' : ['LCARS',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B4139' : {'ecocyc-rxns': {"""ASPARTASE-RXN""": """L-aspartate = fumarate + ammonia""",},'ucsd-rxns' : ['ASPT',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B1900' : {'ecocyc-rxns': {"""ABC-2-RXN""": """H2O + α-L-arabinose[periplasmic space] + ATP =α-L-arabinose[cytosol] + phosphate + ADP """,},'ucsd-rxns' : ['ARBabcpp',], 'protein-comments' : ["""NIL""","""(The AraFGH arabinose transporter is a member of the ATP Binding Cassette (ABC) transporter superfamily.
Expression of all three components was necessary to complement high-affinity arabinose transport in an
araFGH knockout strain |CITS: [89255061]| Membrane vesicle studies have shown that there are
two main arabinose uptake systems in E. coli: the low affinity proton-driven AraE transporter and a
high affinity ATP-driven system utilizing AraF as a binding protein |CITS:[82205973]|. The AraF binding
protein has been purified, crystallized and its high resolution structure shown to bind arabinose
|CITS:[78070158]|. Based on sequence similarity, AraH is the membrane component and AraG is the
ATP-binding component of this ABC transporter |CITS: [88062740]|.)""",]},
'B2797' : {'ecocyc-rxns': {"""THREDEHYD-RXN""": """L-threonine -> 2-oxobutanoate + ammonia""","""4.3.1.17-RXN""": """L-serine -> pyruvate + ammonia""",},'ucsd-rxns' : ['SERD_L','THRD_L',], 'protein-comments' : ["""NIL""",]},
'B2796' : {'ecocyc-rxns': {"""TRANS-RXN-71""": """H+[periplasmic space] + L-serine[periplasmic space] =H+[cytosol] + L-serine[cytosol] """,},'ucsd-rxns' : ['SERt2rpp',], 'protein-comments' : ["""(SdaC is a probable serine uptake system, likely to function as a serine/proton
symporter. Expression of the cloned sdaC resulted in an increased rate
of serine uptake and this uptake was insensitive to threonine |CITS: [94298831]|.
SdaC likely corresponds to the threonine-insensitive serine/proton symport system
described in a nhaB mutant |CITS: [93054369]|. This sytem was suggested
to be a high affinity serine-specific transporter with a Km of 5-6 μM. SdaC
is a member of the STP family of amino acid transporters, and is homologous to
the threonine/serine transporter TdcC.
The sdaC is part of an operon which includes the sdaB gene, encoding
a serine deaminase |CITS: [94298831]|. SdaB has been suggested to have a degradative,
energy-providing role, implying that serine imported via SdaC is used primarily
for energy production. Resistance of a sdaC mutant to colicin V has revealed that SdaC is an inner
membrane receptor for this peptide antibiotic |CITS:[15743941]|.)""",]},
'B0841' : {'ecocyc-rxns': {"""UNDECAPRENYL-DIPHOSPHATASE-RXN""": """undecaprenyl diphosphate + H2O -> undecaprenyl phosphate + phosphate""",},'ucsd-rxns' : ['UDCPDP','UDCPDPpp',], 'protein-comments' : ["""(YbjG is similar to a bacitracin resistance protein BcrC of Bacillus licheniformis. Disruption of ybjG
causes increased bacitracin sensitivity, and overexpression causes increased resistance to bacitracin
|CITS: [10498733][15778224]|. ybjG was also identified as a lactoperoxidase-thiocyanate system-inducible
gene |CITS: [15748988]|.
Simultaneous inactivation of ybjG, bacA, and pgpB is lethal. Depletion of BacA in the triple mutant
strain causes changes in cell morphology and lysis. Overexpression of ybjG, yeiU, bacA, and
pgpB leads to increased undecaprenyl pyrophosphatase (C55PP) activity in crude membrane
extracts. Expression of C55PP activity from one of the three genes ybjG, bacA, and
pgpB appears to be sufficient for synthesis of undecaprenyl phosphate and survival |CITS: [15778224]|.
ybjG expression is increased in an evgS1 mutant and may be directly regulated by PhoP
|CITS: [15126461]|.)""",]},
'B1277' : {'ecocyc-rxns': {"""GTP-CYCLOHYDRO-II-RXN""": """3 H2O + GTP -> diphosphate + 2,5-diamino-6-(ribosylamino)-4-(3H)-pyrimidinone 5'-phosphate + formate""",},'ucsd-rxns' : ['GTPCII2',], 'protein-comments' : ["""(GTP cyclohydrolase II catalyzes the generation of a pyrimidine derivative, the first committed step in riboflavin
biosynthesis. GTP cyclohydrolase II is distinct from GTP cyclohydrolase I, which is part of the folic acid biosynthesis
pathway. The enzyme also catalyzes a reaction that produces GMP as approximately 10% of the product
|CITS: [11301327]|. The catalytic mechanism and kinetics of the enzyme have been studied
|CITS: [8320220][11301327][11553632][16115872]|.
Crystal structures of GTP cyclohydrolase II alone and in complex with a GTP analogue have been determined
|CITS: [16115872]|.
Expression of ribA, the gene encoding GTP cyclohydrolase II |CITS: [8320220]|, is inducible by paraquat and
other superoxide-generating compounds and is dependent on SoxS |CITS: [8709966]|.
ribA: "riboflavin")""","""NIL""",]},
'B0425' : {'ecocyc-rxns': {"""2-DEHYDROPANTOATE-REDUCT-RXN""": """L-pantoate + NADP+ = 2-dehydropantoate + NADPH""",},'ucsd-rxns' : ['DPR',], 'protein-comments' : ["""(In both E. coli and S. typhimurium, the reaction
can also be carried out by the IlvC enzyme, acetohydroxy acid
isomeroreductase. |CITS: [83082612] [98389700]|)""",]},
'B1200' : {'ecocyc-rxns': {"""2.7.1.121-RXN""": """dihydroxy-acetone + phosphoenolpyruvate -> dihydroxy-acetone-phosphate + pyruvate""",},'ucsd-rxns' : ['DHAPT',], 'protein-comments' : ["""(The K subunit is similar to the N-terminal half of ATP-dependent dihydroxyacetone kinase of
Citrobacter freundii and eukaryotes.
It exists in holoenzyme as a homodimer, consisting of two six-stranded mixed beta-sheets
surrounded by nine alpha-helices and a beta-ribbon.)""","""(Dihydroxyacetone kinase, which is composed of three subunits: DhaK, DhaL, and DhaM, functions similarly to a
phosphotrasferase system (PTS) in that it utilizes phosphoenolpyruvate as a phosphoryl donor. It differs in not being
involved in transport. Other dihydroxyacetone kinases found in other bacteria, animals, and plants utilize ATP.
Two of the subunits, DhaK and DhaL, are homologous to the ATP-dependent dihydroxyacetone kinases. Another
subunit, DhaM is homologous to certain components of PTS: to a domain of EI, to HPr, and to the AB domains of EII.
The product of this reaction, dihydroxyacetone phosphate, is also formed by a flavin-dependent oxidation of
glycerol-3-phosphate. Dihydroxyacetone phosphate is further metabolized through the glycolytic pathway.)""",]},
'B2150' : {'ecocyc-rxns': {"""ABC-18-RXN""": """ATP + β-D-galactose[periplasmic space] + H2O =ADP + phosphate + β-D-galactose[cytosol] """,},'ucsd-rxns' : ['GALabcpp','GLCabcpp',], 'protein-comments' : ["""NIL""","""(MglABC is a beta-methylgalactoside transport system that is a member of the ATP-Binding Cassette (ABC) Superfamily
of transporters |CITS: [96381453]|. Based on sequence similarity, mglB encodes the galactose-binding component,
mglC encodes the integral membrane component, and mglA encodes the ATP-binding component of the ABC
transporter. Insertional mutations in each gene indicate that all three components are necessary for beta-methylgalactoside
transport function |CITS: [83082637]|. Complementation experiments show that mlg genes cloned into a plasmid
vector are able to complement the transport functions of the mglA, mglB, and mglC mutants
|CITS: [82239395]|. MglB, but not MglA or MglC, was found to also serve as the galactose chemoreceptor in E. coli
|CITS: [83082637]|. mglB mutants eliminate the chemotactic function in E. coli; however, mglA and
MglC mutants exhibit normal galactose taxis but defective galactoside uptake activities |CITS: [87286407] [83082637]|.)""",]},
'B0421' : {'ecocyc-rxns': {"""GPPSYN-RXN""": """dimethylallyl-pyrophosphate + Δ3-isopentenyl-PP = diphosphate + geranyl-PP""","""FPPSYN-RXN""": """geranyl-PP + Δ3-isopentenyl-PP = diphosphate + trans, trans-farnesyl diphosphate""",},'ucsd-rxns' : ['DMATT','GRTT',], 'protein-comments' : ["""(The subunit structure is unknown.)""",]},
'B0420' : {'ecocyc-rxns': {"""DXS-RXN""": """pyruvate + D-glyceraldehyde-3-phosphate = CO2 + 1-deoxy-D-xylulose 5-phosphate""",},'ucsd-rxns' : ['DXPS',], 'protein-comments' : ["""(The enzyme 1-deoxy-D-xylulose 5-phosphate (DXP) synthase, probably a Dxs homodimer |CITS: [10648511]|, acts in the mevalonate-independent pathway of isopentenyl diphosphate biosynthesis, in thiamin biosynthesis, and pyridoxal biosynthesis |CITS: [9371765]|.
Overproduction of Dxs affects flux through the pathway under some circumstances |CITS: [11180061], [11120644], [10803894]|. Dxs has been overproduced and purified |CITS: [10648511]|.
Dxs has similarity to transketolases |CITS: [9482846]|. An H49Q mutation, at a residue located within a region conserved among transketolase enzymes, eliminates DXP synthase activity |CITS: [11708793]|. Production of Rhodobacter capsulatus 1-deoxy-D-xylulose 5-phosphate synthase B functionally complements viability of an E. coli FH11 dxs mutant |CITS: [11114895]|.)""","""NIL""",]},
'B2155' : {'ecocyc-rxns': {"""RXN0-1721""": """ferric dihydroxybenzoylserine[extracellular space] =ferric dihydroxybenzoylserine[periplasmic space] """,},'ucsd-rxns' : ['FE3DHBZStonex',], 'protein-comments' : ["""(Cir is a member of the Outer Membrane Receptor (OMR) family of porins. Cir is a TonB dependent iron-siderophore
complex uptake receptor. The substrate spectrum of Cir is very similar to that of Fiu. Cir transports monomers, dimer,
and linear trimers of 2,3-dihydorxybenzoylserine. |CITS: [2139424]| In addition Cir is a receptor for colicins IA, IB,
and V and microcins E492, H47, and M. |CITS: [12423780]|)""",]},
'B2154' : {'ecocyc-rxns': {"""GLYOXII-RXN""": """S-lactoyl-glutathione + H2O = glutathione + D-lactate""","""S-FORMYLGLUTATHIONE-HYDROLASE-RXN""": """S-formylglutathione + H2O = formate + glutathione""",},'ucsd-rxns' : ['SFGTHi',], 'protein-comments' : ["""(YeiG is a promiscuous serine hydrolase; its highest specific activity is with the substrate S-formylglutathione.
Sulfhydryl inhibitors affect enzymatic activity |CITS: [16567800]|. A general esterase activity of YeiG was first
discovered in a high-throughput screen of purified proteins |CITS: [15808744]|.
YeiG also has significant activity with the substrate lactoylglutathione, an intermediate of the detoxification of
methylglyoxal. It may thus represent a cytoplasmic equivalent of glyoxalase II, which may be involved in the
detoxification of endogenous methylglyoxal |CITS: [16567800]|.
YeiG has similarity to S-formylglutathione hydrolases of Arabidopsis, S. cerevisiae, human, and a
paralog, FrmB |CITS: [16567800]|.
yeiG is expressed constitutively in both the wild type and frmB deletion background. Under normal
growth conditions, neither a yeiG deletion mutant nor a frmB yeiG double mutant have a detectable
growth defect. Addition of 0.4 mM formaldehyde to the growth medium had no effect on the yeiG single mutant,
while the growth rate of the double mutant drops to 43% of wild type |CITS: [16567800]|. Site-directed yeiG
mutants were used to define residues important for catalytic activity |CITS: [16567800]|.)""","""NIL""",]},
'B2010' : {'ecocyc-rxns': {"""3.4.16.4-RXN""": """D-alanyl-D-alanine + H2O = 2 D-alanine""",},'ucsd-rxns' : ['MDDCP2pp','MDDCP1pp','MDDCP5pp','MDDCP4pp','MDDCP3pp',], 'protein-comments' : ["""(DacD, also called penicillin-binding protein (PBP6b), is a D-alanyl-D-alanine carboxypeptidase and penicillin-binding protein with sequence
similarity to DacA(PBP5) and DacC(PBP6) |CITS: [8955390]|.
Deletion of eight penicillin binding proteins, including DacD among them, still leaves cells
viable |CITS: [10383966]|. Overexpression of DacA in early exponential growth leads to cell
lysis |CITS: [11325933]|.)""",]},
'B0417' : {'ecocyc-rxns': {"""THI-P-KIN-RXN""": """thiamine-phosphate + ATP = thiamine diphosphate + ADP""",},'ucsd-rxns' : ['TMPK',], 'protein-comments' : ["""(The subunit structure is unknown.)""",]},
'B0429' : {'ecocyc-rxns': {"""CYT-UBIQUINOL-OXID-RXN""": """ubiquinol-8 + O2 = ubiquinone-8 + 2 H2O""",},'ucsd-rxns' : ['CYTBO3_4pp',], 'protein-comments' : ["""(CyoD is subunit IV of the cytochrome bo terminal oxidase complex encoded by cyoABCDE.
Although this subunit's function is unknown, it is necessary for a functional enzyme. |CITS: [ColiSalII]|
The CyoD polypeptide contains three transmembrane helices |CITS: [2165491]|.
Deletion and cross-linking studies have suggested that subunit IV interacts with subunits I and III |CITS: [8663126]|,
which is confirmed by the crystal structure of the entire cytochrome bo terminal oxidase complex that has been
determined at 3.5 A resolution |CITS: [11017202]|.)""","""NIL""",]},
'B2835' : {'ecocyc-rxns': {},'ucsd-rxns' : ['2AGPG141tipp','2AGPG120tipp','2AGPG181tipp','2AGPE181tipp','2AGPE120tipp','2AGPA161tipp','2AGPA120tipp','2AGPG180tipp','2AGPE161tipp','2AGPE160tipp','2AGPG160tipp','2AGPG161tipp','2AGPE140tipp','2AGPA140tipp','2AGPA160tipp','2AGPE141tipp','2AGPA141tipp','2AGPA181tipp','2AGPG140tipp','2AGPA180tipp','2AGPE180tipp',], 'protein-comments' : ["""(LplT is a major facilitator superfamily (MFS) protein that acts as a flippase for transbilayer movement of
lysophospholipids. Mutation experiments and
transporter assays have determined LplT is responsible for the facilitated diffusion of lysophospholipids to
the cytoplasmic portion of the inner membrane providing substrate for the bifunctional enzyme
2-acyl-GPE acyltransferase/acyl-ACP synthetase (Aas). lplT forms an operon with the aas
gene |CITS:[15661733]|.)""",]},
'B2421' : {'ecocyc-rxns': {"""ACSERLY-RXN""": """O-acetyl-L-serine + hydrogen sulfide = L-cysteine + acetate""",},'ucsd-rxns' : ['CYSS',], 'protein-comments' : ["""(Cysteine synthase B is one of two isozymes in E. coli that catalyze the formation of L-cysteine from
O-acetyl-L-serine and sulfide |CITS: [colisalII]|. Unlike cysteine synthase A, cysteine synthase B does not form a
complex with serine acetyltransferase |CITS: [16546401]|. Both isozymes can also catalyze the reverse reaction,
mobilizing sulfur from cysteine and providing it for Fe-S cluster synthesis in vitro. This reaction can be driven
by removing the sulfide product or by dithiothreitol adding to the aminoacrylate |CITS: [8663055]|.
Cysteine synthase B can also use thiosulfate in place of sulfide, producing S-sulfocysteine |CITS: [12640465]|.
The broad substrate specificity of cysteine synthase was exploited for the synthesis of unnatural L-α-amino
acids |CITS: [12640465]|. Initial synthesis rates of nonproteinaceous amino acids have been determined
|CITS: [16546401]|.
Crystal structures of CysM have been solved at 2.1 and 2.7 Å resolution |CITS: [15952768]|.)""","""NIL""",]},
'B3737' : {'ecocyc-rxns': {"""ATPSYN-RXN""": """H+[cytosol] + H2O + ATP =H+[periplasmic space] + phosphate + ADP """,},'ucsd-rxns' : ['ATPS4rpp','ATPS4rpp',], 'protein-comments' : ["""(The c subunit of the F0 complex of ATP synthase is absolutely required for proton translocation and is also
necessary for binding of the F-1 complex. This is the subunit affected by the
inhibitor dicyclohexylcarbodiimide. The stoichiometry of the subunits has not
been fully resolved. Values have been obtained ranging from 10 to 18.
|CITS: [93147708] [92329454] [92041957] [90303438]|
The initiating methionine is cleaved |CITS: [9868784]|.)""","""NIL""","""(The F-O complex of ATP synthase functions as the proton channel and consists of
three subunits. All are required for a functional F-O complex. The F-O complex
is membrane-bound. |CITS: [90303438] [93147708]|)""","""(The enzyme is made up of two subcomplexes, the F-1 complex and the F-O complex.
There are eight total subunits all required for activity. The F-1 complex is
the catalytic unit. The F-O complex anchors the F-1 complex to the membrane
and also forms the proton channel. |CITS: [89123355] [90303438] [93252965]|)""",]},
'B3040' : {'ecocyc-rxns': {"""RXN0-16""": """Mn2+[periplasmic space] =Mn2+[cytoplasm] ""","""RXN0-14""": """Cu2+[periplasmic space] =Cu2+[cytoplasm] ""","""RXN0-12""": """Zn2+[periplasmic space] =Zn2+[cytoplasm] ""","""RXN0-10""": """Cd2+[periplasmic space] =Cd2+[cytoplasm] ""","""TRANS-RXN-8""": """Fe2+[periplasmic space] =Fe2+[cytosol] ""","""TRANS-RXN-141A""": """Co2+[periplasmic space] =Co2+[cytosol] """,},'ucsd-rxns' : ['CD2tpp','MN2tpp','ZN2tpp','CU2tpp','COBALT2tpp','FE2tpp',], 'protein-comments' : ["""(ZupT is a member of the ZIP family of divalent metal cation transporters, and is predicted to have 8
transmembrane domains. Transporter assays along with mutation and complementation studies indicate that
ZupT transports zinc,
cadmium, copper |CITS:[11790762]|, iron, cobalt, and manganese into the cell. ZupT is expressed
constitutively at a low level as a monocistronic transcript |CITS:[15716430]|.)""",]},
'B1611' : {'ecocyc-rxns': {"""FUMHYDR-RXN""": """malate = fumarate + H2O""",},'ucsd-rxns' : ['FUM',], 'protein-comments' : ["""(One of three isozymes in E. coli, fumarase C is a Class II fumarase. Fumarase C is dissimilar to fumarase A
and B.)""","""NIL""",]},
'B3041' : {'ecocyc-rxns': {"""DIOHBUTANONEPSYN-RXN""": """D-ribulose-5-phosphate = 3,4-dihydroxy-2-butanone-4-P + formate""",},'ucsd-rxns' : ['DB4PS',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B4290' : {'ecocyc-rxns': {"""RXN0-2261""": """ferric dicitrate[extracellular space] =ferric dicitrate[cytosol] ""","""ABC-9-RXN""": """ATP + ferric dicitrate[periplasmic space] + H2O =ADP + phosphate + ferric dicitrate[cytosol] """,},'ucsd-rxns' : ['FE3DCITabcpp',], 'protein-comments' : ["""(Periplasmic substrate binding component of the iron dicitrate ABC transporter)""","""(FecBCDE is an ATP Binding Cassette (ABC) citrate-dependent iron (III) transport system. Sequence
homology and hydropathy analyses indicate that FecB is the periplasmic binding protein, FecC and FecD
are integral membrane proteins and FecE is the ATP-binding protein |CITS: [88227855]|. Mutation and
induction studies indicate that exogenous ferric citrate induces the expression of fec transport genes
through a signaling mechanism which does not require ferric citrate to enter the cytoplasm |CITS: [82004187]|.
|CITS:[81116964]|, or to cross the outer membrane into the periplasmic space |CITS: [95246736]|. Rather,
induction of fec transport genes is a function of FecA-ferric citrate binding and is coupled through
the TonB, ExbB and ExbD proteins independent of their role in uptake |CITS:[95246736]|.)""","""NIL""",]},
'B0832' : {'ecocyc-rxns': {"""RXN0-11""": """glutathione[periplasmic space] + ATP + H2O =glutathione[cytoplasm] + ADP + phosphate """,},'ucsd-rxns' : ['GTHRDabcpp',], 'protein-comments' : ["""(inner membrane component of glutathione ABC transporter)""","""(The GsiABCD glutathione transporter is a member of the ATP Binding Cassette (ABC) superfamily
of transporters. Based on sequence similarity, GsiA is predicted to be the ATP-binding component, GsiB
is predicted to be the periplasmic binding component, and GsiC and GsiD are predicted to be inner
membrane components. Mutation of any component impairs the ability of E. coli to transport the
glutathione molecule into the cell. Expression of the cloned genes in their respective mutants restores their
ability to transport glutathione. Transport by the glutathione ABC transporter is one of two known
mechanisms for salvage of glutathione excreted from the cell. The other involves hydrolysis of glutathione
by γ-glutamyl transpeptidase in the periplasm to yield glutamic acid and cysteinylglycine which
can be taken back into the cell |CITS:[16109926]|.)""",]},
'B0830' : {'ecocyc-rxns': {"""RXN0-11""": """glutathione[periplasmic space] + ATP + H2O =glutathione[cytoplasm] + ADP + phosphate """,},'ucsd-rxns' : ['GTHRDabcpp',], 'protein-comments' : ["""(periplasmic binding component of glutathione ABC transporter)""","""(The GsiABCD glutathione transporter is a member of the ATP Binding Cassette (ABC) superfamily
of transporters. Based on sequence similarity, GsiA is predicted to be the ATP-binding component, GsiB
is predicted to be the periplasmic binding component, and GsiC and GsiD are predicted to be inner
membrane components. Mutation of any component impairs the ability of E. coli to transport the
glutathione molecule into the cell. Expression of the cloned genes in their respective mutants restores their
ability to transport glutathione. Transport by the glutathione ABC transporter is one of two known
mechanisms for salvage of glutathione excreted from the cell. The other involves hydrolysis of glutathione
by γ-glutamyl transpeptidase in the periplasm to yield glutamic acid and cysteinylglycine which
can be taken back into the cell |CITS:[16109926]|.)""",]},
'B0831' : {'ecocyc-rxns': {"""RXN0-11""": """glutathione[periplasmic space] + ATP + H2O =glutathione[cytoplasm] + ADP + phosphate """,},'ucsd-rxns' : ['GTHRDabcpp',], 'protein-comments' : ["""(inner membrane component of glutathione ABC transporter)""","""(The GsiABCD glutathione transporter is a member of the ATP Binding Cassette (ABC) superfamily
of transporters. Based on sequence similarity, GsiA is predicted to be the ATP-binding component, GsiB
is predicted to be the periplasmic binding component, and GsiC and GsiD are predicted to be inner
membrane components. Mutation of any component impairs the ability of E. coli to transport the
glutathione molecule into the cell. Expression of the cloned genes in their respective mutants restores their
ability to transport glutathione. Transport by the glutathione ABC transporter is one of two known
mechanisms for salvage of glutathione excreted from the cell. The other involves hydrolysis of glutathione
by γ-glutamyl transpeptidase in the periplasm to yield glutamic acid and cysteinylglycine which
can be taken back into the cell |CITS:[16109926]|.)""",]},
'B3018' : {'ecocyc-rxns': {"""1-ACYLGLYCEROL-3-P-ACYLTRANSFER-RXN""": """a 1-acyl-sn-glycerol-3P + an acyl-ACP -> an L-phosphatidate + acyl carrier protein""",},'ucsd-rxns' : ['AGPAT120','AGPAT140','AGPAT141','AGPAT160','AGPAT161','AGPAT180','AGPAT181',], 'protein-comments' : ["""NIL""",]},
'B1288' : {'ecocyc-rxns': {"""RXN0-2145""": """trans-Δ3-cis-Δ5-dodecenoyl-ACP + NADPH = NADP+ + cis-Δ5-dodecenoyl-ACP""","""ENOYL-ACP-REDUCT-NADPH-RXN""": """an acyl-ACP + NADP+ = NADPH + a trans-Δ2-enoyl-acyl-ACP""","""ENOYL-ACP-REDUCT-NADH-RXN""": """an acyl-ACP + NAD+ -> NADH + a trans-Δ2-enoyl-acyl-ACP""",},'ucsd-rxns' : ['EAR121y','EAR121x','EAR120x','EAR120y','EAR140x','EAR140y','EAR141y','EAR141x','EAR80x','EAR80y','EAR161y','EAR161x','EAR160x','EAR160y','EAR100x','EAR100y','EAR60x','EAR60y','EAR181y','EAR181x','EAR180x','EAR180y','EAR40x','EAR40y',], 'protein-comments' : ["""(The FabI protein is an enoyl acyl carrier protein reductase which catalyzes an essential step in fatty acid
biosynthesis.
|CITS: [93123967] [94164884]|
Inhibitors of FabI have been identified |CITS: [15105103][14736233]|.)""",]},
'B0839' : {'ecocyc-rxns': {},'ucsd-rxns' : ['MDDCP2pp','MDDCP1pp','MDDCP5pp','MDDCP4pp','MDDCP3pp',], 'protein-comments' : ["""(DacC is a penicillin-binding protein that is required for proper cell morphology and provides
some resistance to penicillin |CITS: [1447130][12354237][6215397]|. It is one of four DD-carboxypeptidase
low-molecular weight PBPs in Escherichia coli (along with PBP4, PBP6 and DacD) that modify
peptidoglycans through the removal of the terminal D-alanine from pentapeptide side chains |CITS:[368033]|,
|CITS:[8955390]|.
The carboxy-terminus of DacC is capable of forming an alpha helix and interacts with
membranes chiefly through hydrophobic forces |CITS: [9371419][9858668]|.
Deletion of this membrane-anchoring portion of the protein produces soluble DacC. Whereas
overexpression of native DacC results in membrane vesicles in the cystoplasm, overexpression
of this soluble variant yields inclusion bodies. Both forms of DacC can be purified with
Procion rubine MX-B and subsequently bind stoichiometrically with penicillin |CITS: [1447130]|.
Despite being part of a family of D-alanine carboxypeptidases, DacC lacks detectable activity
against bisacetyl-L-lysine-D-alanyl-D-alanine and other test substrates |CITS: [1447130]|.
Deletions in dacC are viable, though slightly penicillin sensitive |CITS: [6215397]|.
dacC dacA double mutants are viable, though they show defects in morphology and cell division
when bolA, which is required for dacC expression on entry to stationary phase, is overexpressed |CITS: [3903044][12354237][2684651]|.
A complete deletion of dacA-D is also viable, as is a strain lacking eight of the known penicillin-binding protein genes,
dacC among them |CITS: [8955390][10383966]|. Overexpression of DacC allows cell division in ftsI23 mutants, but leads to cell
lysis during early exponential growth |CITS: [2254246][11325933]|.)""",]},
'B2223' : {'ecocyc-rxns': {},'ucsd-rxns' : ['ACACt2pp','HEXt2rpp','BUTt2rpp',], 'protein-comments' : ["""(No information about this protein was found by a literature search conducted on June 13, 2005.
)""",]},
'B3605' : {'ecocyc-rxns': {"""L-LACTDEHYDROGFMN-RXN""": """a quinone + lactate = a hydroquinone + pyruvate""",},'ucsd-rxns' : ['L-LACD3','L-LACD2',], 'protein-comments' : ["""NIL""",]},
'B4193' : {'ecocyc-rxns': {"""RXN0-2461""": """phosphoenolpyruvate + L-ascorbate[periplasmic space] =L-ascorbate-6-phosphate[cytosol] + pyruvate """,},'ucsd-rxns' : ['ASCBptspp',], 'protein-comments' : ["""(SgaT is required for the ability to utilize L-ascorbate as the carbon source under anaerobic growth
conditions |CITS: [12644495]|.
UlaA "utilization of L-ascorbate" |CITS: [11741871]| Contains a PTS Enzyme IIC domain.)""","""(SgaTBA, a putative PTS permease, belongs to the functional superfamily
of the phosphoenolpyruvate (PEP)-dependent, sugar transporting
phosphotransferase system (PTS). The PTS transports and simultaneously
phosphorylates its sugar substrates in a process called group
translocation. SgaTBA presumably takes up an exogenous sugar,
releasing the phosphate ester into the cell cytoplasm in preparation
for metabolism |CITS: [8246840]| . The overall PTS-mediated phosphoryl transfer
reaction, requiring the two general energy coupling proteins of
the PTS, Enzyme I and HPr, as well as the three domains of the
Enzyme II complex is:
PEP --> Enzyme I(his~~P)
--> HPr(his~~P)
--> IIA(his~~P) -->
IIB(cys~~P) -(IIC)-> sugar-P.
The sga operon encodes SgaT, an integral membrane putative
transporter protein with 12 putative transmembrane α-helical
spanners that might function as a PTS Enzyme IIC; SgaB, the putative
Enzyme IIBSga, and SgaA, the putative Enzyme
IIASga |CITS: [REIZERGENOMESCITECH153]|. SgaB is homologous to the IIB
domains of the lactose-cellobiose PTS permease family. SgaA is
homologous to the IIA domains/proteins of the fructose-mannitol
PTS permease family. Little is known regarding the function of
these enzymes or expression of the sga operon in which
the encoding genes are found. However, the sga genes may
allow metabolism and interconversion of pentose and hexose phosphate
esters |CITS: [9274005]| .
Deletion mutation studies |CITS:[12644495]| indicate that all three components
are necessary for the uptake and utiliztion of L-ascorbate in vivo as well as for the
phosphorylation of L-ascorbate in vitro.)""",]},
'B4192' : {'ecocyc-rxns': {},'ucsd-rxns' : ['ASCBPL',], 'protein-comments' : ["""(UlaG is required for the ability to utilize L-ascorbate as the sole carbon source under anaerobic growth conditions
|CITS: [12644495]|. The enzyme was suggested to be a cytoplasmic L-ascorbate 6-phosphate lactonase
|CITS: [12644495]|. Phosphodiesterase activity of UlaG was discovered in a high-throughput screen of purified
proteins |CITS: [15808744]|.
Expression of ulaG is negatively regulated by UlaR |CITS: [12374842]|.)""",]},
'B3600' : {'ecocyc-rxns': {"""MANNPDEHYDROG-RXN""": """mannitol-1-phosphate + NAD+ = D-fructose-6-phosphate + NADH""",},'ucsd-rxns' : ['M1PD',], 'protein-comments' : ["""(The protein has been purified as both a monomer and an
apparent dimer. Current thinking is that the protein is active in the
monomeric state and the dimer of 22K peptides resulted from
proteolysis. |CITS: [90254197] [85006766]|)""",]},
'B4194' : {'ecocyc-rxns': {"""RXN0-2461""": """phosphoenolpyruvate + L-ascorbate[periplasmic space] =L-ascorbate-6-phosphate[cytosol] + pyruvate """,},'ucsd-rxns' : ['ASCBptspp',], 'protein-comments' : ["""(UlaB "utilization of L-ascorbate" |CITS: [11741871]| Contains a PTS Enzyme IIB domain.)""","""(SgaTBA, a putative PTS permease, belongs to the functional superfamily
of the phosphoenolpyruvate (PEP)-dependent, sugar transporting
phosphotransferase system (PTS). The PTS transports and simultaneously
phosphorylates its sugar substrates in a process called group
translocation. SgaTBA presumably takes up an exogenous sugar,
releasing the phosphate ester into the cell cytoplasm in preparation
for metabolism |CITS: [8246840]| . The overall PTS-mediated phosphoryl transfer
reaction, requiring the two general energy coupling proteins of
the PTS, Enzyme I and HPr, as well as the three domains of the
Enzyme II complex is:
PEP --> Enzyme I(his~~P)
--> HPr(his~~P)
--> IIA(his~~P) -->
IIB(cys~~P) -(IIC)-> sugar-P.
The sga operon encodes SgaT, an integral membrane putative
transporter protein with 12 putative transmembrane α-helical
spanners that might function as a PTS Enzyme IIC; SgaB, the putative
Enzyme IIBSga, and SgaA, the putative Enzyme
IIASga |CITS: [REIZERGENOMESCITECH153]|. SgaB is homologous to the IIB
domains of the lactose-cellobiose PTS permease family. SgaA is
homologous to the IIA domains/proteins of the fructose-mannitol
PTS permease family. Little is known regarding the function of
these enzymes or expression of the sga operon in which
the encoding genes are found. However, the sga genes may
allow metabolism and interconversion of pentose and hexose phosphate
esters |CITS: [9274005]| .
Deletion mutation studies |CITS:[12644495]| indicate that all three components
are necessary for the uptake and utiliztion of L-ascorbate in vivo as well as for the
phosphorylation of L-ascorbate in vitro.)""",]},
'B4197' : {'ecocyc-rxns': {"""LXULRU5P-RXN""": """L-ribulose-5-phosphate = L-xylulose-5-phosphate""",},'ucsd-rxns' : ['X5PL3E',], 'protein-comments' : ["""(UlaE: "utilization of L-ascorbate" |CITS: [11741871]|.)""",]},
'B3603' : {'ecocyc-rxns': {"""TRANS-RXN-104""": """H+[periplasmic space] + lactate[periplasmic space] =H+[cytosol] + lactate[cytosol] """,},'ucsd-rxns' : ['D-LACt2pp','L-LACt2rpp','GLYCLTt2rpp',], 'protein-comments' : ["""(LctP is a probable lactate/proton symporter responsible for the
uptake of L-lactate. The lctP gene is located in a lactate-inducible
operon with the lctD and lctR genes encoding a lactate
dehydrogenase and a regulatory protein, respectively |CITS: [94012541]|.
Disruption of the lct operon decreased lactate transport, which
could be restored by complementation with the cloned lctP gene
|CITS: [94012541]|. LctP is the archetypal member of the Lct family of
transporters.
)""",]},
'B0160' : {'ecocyc-rxns': {"""DGTPTRIPHYDRO-RXN""": """H2O + dGTP -> PPPi + deoxyguanosine""",},'ucsd-rxns' : ['NTPTP1','NTPTP2',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B4198' : {'ecocyc-rxns': {"""RIBULPEPIM-RXN""": """L-ribulose-5-phosphate = D-xylulose-5-phosphate""",},'ucsd-rxns' : ['RBP4E',], 'protein-comments' : ["""(The operon encoding SgaE is required for fermentation of L-ascorbate |CITS: [11741871]| . UlaF: "utilization of L-ascorbate" |CITS: [11741871]|
)""",]},
'B2935' : {'ecocyc-rxns': {"""1TRANSKETO-RXN""": """D-ribose-5-phosphate + D-xylulose-5-phosphate = D-sedoheptulose-7-phosphate + D-glyceraldehyde-3-phosphate""","""2TRANSKETO-RXN""": """D-erythrose-4-phosphate + D-xylulose-5-phosphate = D-fructose-6-phosphate + D-glyceraldehyde-3-phosphate""",},'ucsd-rxns' : ['TKT2','TKT1',], 'protein-comments' : ["""(TktA is responsible for the major transketolase activity in E.
coli, and TktB is responsible for the minor transketolase activity
|CITS: [8396116]|.
TktA has been reported to be homodimeric |CITS: [7607225]|. TktA and/or
TktB binds to zinc |CITS: [11985624]|.
The activity of purified recombinant enzyme has been studied in vitro
|CITS: [7607225]|. Superoxide inhibits transketolase by oxidation of
the 1, 2-dihydroxyethyl thiamine pyrophosphate |CITS: [9933617]|.
Mutations have been described |CITS: [4902809], [4597996]|.
Overproduction of TktA increases the amount of carbon channeled into
aromatic amino acid biosynthesis |CITS: [8987689]|. Overproduction of
TktB causes increased transketolase activity and suppresses the tktA
mutant phenotype |CITS: [8396116]|. A tktA tktB double mutant exhibits
auxotrophy for pyridoxine (or 4-hydroxy-L-threonine or glycolaldehyde),
and aromatic amino acids and vitamins |CITS: [7928977]|. Transketolase has been utilized in metabolic engineering |CITS: [8953718], [9630954], [11375660], [12790643], [7993080], [10397840], [10514257]|.
TktA has 49.5% identity to Rhodobacter sphaeroides transketolase,
46.8% identity to Saccharomyces cerevisiae transketolase, and
28.9% identity to human transketolase |CITS: [8241274]|.
Regulation has been described |CITS: [8241274], [8600350]|. TktA
abundance is affected by the SOS inducer and mutagen
7-methoxy-2-nitronaphtho[2,1-b]furan (R7000) |CITS: [8600350]|.
Review: |CITS: [8572885]|.)""","""NIL""",]},
'B3608' : {'ecocyc-rxns': {"""GLYC3PDEHYDROGBIOSYN-RXN""": """sn-glycerol-3-phosphate + NAD(P)+ = dihydroxy-acetone-phosphate + NAD(P)H + H+""",},'ucsd-rxns' : ['G3PD2',], 'protein-comments' : ["""(The enzyme catalyzes the NAD(P)H-dependent reduction of the glycolytic intermediate
dihydroxyacetone-phosphate to produce glycerol-3-phosphate, a precursor for the biosynthesis of phospholipids
|CITS: [79109670]|.
The enzyme was first isolated by Kito and Pizer |CITS: [4389388]|, and was later purified to homogeneity and
investigated by Edgar and Bell |CITS: [355254][28326]|. The enzyme is strongly inhibited in vitro by
glycerol-3-P, and it was shown that this inhibition does not involve association or dissociation. A mutant version of
the protein which is resistant to feedback inhibition is known |CITS: [240817]|.
The enzyme is constitutively produced, and is present in the cell in low amounts. It was calculated that on average
only about 1000 molecules are present per cell |CITS: [355254]|.
GpsA did not show dehydrogenase activity in a high-throughput screen of purified proteins |CITS: [15808744]|.
)""","""NIL""",]},
'B0166' : {'ecocyc-rxns': {"""TETHYDPICSUCC-RXN""": """H2O + tetrahydrodipicolinate + succinyl-CoA = N-succinyl-2-amino-6-ketopimelate + coenzyme A""",},'ucsd-rxns' : ['THDPS',], 'protein-comments' : ["""NIL""","""(Tetrahydrodipicolinate succinylase catalyzes the formation of N-succinyl-2-amino-6-ketopimelate from
succinyl-CoA and tetrahydrodipicolinate, and is a key enzyme
in the E. coli lysine biosynthetic pathway.
It was purified 1900-fold from crude extracts and was shown to be homogeneous.
The Stokes radius of the enzyme and its sedimentation constant were 35 A and 4.7 (S20,w),
providing molecular weights of 68 and 72 kDa, respectively, indicating that the enzyme is a homodimer.
Tetrahydrodipicolinate succinylase was shown to be a sulfhydryl enzyme, and catalyzes a reversible reaction.
The equilibrium lies predominantly in favor of product formation in physiological pH |CITS: [6365916]|.)""",]},
'B2704' : {'ecocyc-rxns': {"""TRANS-RXN-169""": """phosphoenolpyruvate + D-sorbitol[periplasmic space] =D-sorbitol-6-phosphate[cytosol] + pyruvate """,},'ucsd-rxns' : ['SBTptspp',], 'protein-comments' : ["""(contains a PTS Enzyme IIA domain)""","""(GutABE, the glucitol PTS permease, belongs to the functional superfamily
of the phosphoenolpyruvate (PEP)-dependent, sugar transporting
phosphotransferase system (PTS). The PTS transports and simultaneously
phosphorylates its sugar substrates in a process called group
translocation. GutAB takes up exogenous glucitol, releasing the
phosphate ester into the cell cytoplasm in preparation for oxidation
to fructose-6-P and subsequent metabolism, primarily via glycolysis
|CITS: [94066914]|.
GutABE comprises the Enzyme IIGut complex. The
enzyme possesses a split IIC domain unlike all other characterized Enzyme
II complexes of the PTS |CITS: [94066914]|. GutA is a (putative) 4 TMS integral
membrane protein of 187 amino acyl residues. GutE is a larger protein of
319 residues that includes the hydrophilic IIB domain fused to a
hydrophobic (putative) 4 TMS domain |CITS: [97035393]|. GutB is the hydrophilic IIA
domain. Thus, the integral membrane IIC constituent of the glucitol
permease is split in half and encoded by two distinct genes, gutA and gutE.
gutB and gutE, respectively, encode the IIA and IIB constituents.
The IIB domain of GutE and the IIA (GutB) protein are localized to the
cytoplasmic side of the membrane. The overall PTS-mediated phosphoryl
transfer reaction, requiring the two general energy coupling proteins of
the PTS, Enzyme I and HPr, as well as the three domains of the Enzyme II
complex is:
PEP --> Enzyme I(his~~P)
--> HPr(his~~P)
--> IIA(his~~P) -->
IIB(cys~~P) -(IIC)-> glucitol-6-P.
GutABE transports glucitol with low micromolar affinities.
The gut operon is inducible in wild type E. coli K12
by the presence of exogenous glucitol. The gut operon
(gutABDMRQ) contains the gutA, gutB and gutE genes,
encoding the Enzyme IIGut complex, and the
gutD gene encoding glucitol-6-P dehydrogenase that oxidizes
glucitol-6-P to fructose-6-P. GutM and GutR are positive and
negative transcriptional regulators of gut operon expression,
respectively |CITS: [89094828]|. The function of GutQ is not known |CITS: [89094828]|. gut
operon expression is under the control of the cyclic AMP-cyclic
AMP receptor protein (CRP) complex.
)""",]},
'B2705' : {'ecocyc-rxns': {"""SORB6PDEHYDROG-RXN""": """D-sorbitol-6-phosphate + NAD+ = D-fructose-6-phosphate + NADH""",},'ucsd-rxns' : ['SBTPD',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B2702' : {'ecocyc-rxns': {"""TRANS-RXN-169""": """phosphoenolpyruvate + D-sorbitol[periplasmic space] =D-sorbitol-6-phosphate[cytosol] + pyruvate """,},'ucsd-rxns' : ['SBTptspp',], 'protein-comments' : ["""(Membrane topology predictions using experimentally determined C terminus
locations indicate that SrlA has 3 transmembrane helices and the C-terminus is
located in the cytoplasm |CITS:[15044727]|.
Cotains PTS enzyme IIC1 domain.)""","""(GutABE, the glucitol PTS permease, belongs to the functional superfamily
of the phosphoenolpyruvate (PEP)-dependent, sugar transporting
phosphotransferase system (PTS). The PTS transports and simultaneously
phosphorylates its sugar substrates in a process called group
translocation. GutAB takes up exogenous glucitol, releasing the
phosphate ester into the cell cytoplasm in preparation for oxidation
to fructose-6-P and subsequent metabolism, primarily via glycolysis
|CITS: [94066914]|.
GutABE comprises the Enzyme IIGut complex. The
enzyme possesses a split IIC domain unlike all other characterized Enzyme
II complexes of the PTS |CITS: [94066914]|. GutA is a (putative) 4 TMS integral
membrane protein of 187 amino acyl residues. GutE is a larger protein of
319 residues that includes the hydrophilic IIB domain fused to a
hydrophobic (putative) 4 TMS domain |CITS: [97035393]|. GutB is the hydrophilic IIA
domain. Thus, the integral membrane IIC constituent of the glucitol
permease is split in half and encoded by two distinct genes, gutA and gutE.
gutB and gutE, respectively, encode the IIA and IIB constituents.
The IIB domain of GutE and the IIA (GutB) protein are localized to the
cytoplasmic side of the membrane. The overall PTS-mediated phosphoryl
transfer reaction, requiring the two general energy coupling proteins of
the PTS, Enzyme I and HPr, as well as the three domains of the Enzyme II
complex is:
PEP --> Enzyme I(his~~P)
--> HPr(his~~P)
--> IIA(his~~P) -->
IIB(cys~~P) -(IIC)-> glucitol-6-P.
GutABE transports glucitol with low micromolar affinities.
The gut operon is inducible in wild type E. coli K12
by the presence of exogenous glucitol. The gut operon
(gutABDMRQ) contains the gutA, gutB and gutE genes,
encoding the Enzyme IIGut complex, and the
gutD gene encoding glucitol-6-P dehydrogenase that oxidizes
glucitol-6-P to fructose-6-P. GutM and GutR are positive and
negative transcriptional regulators of gut operon expression,
respectively |CITS: [89094828]|. The function of GutQ is not known |CITS: [89094828]|. gut
operon expression is under the control of the cyclic AMP-cyclic
AMP receptor protein (CRP) complex.
)""",]},
'B3568' : {'ecocyc-rxns': {"""ABC-33-RXN""": """ATP + D-xylose[periplasmic space] + H2O =ADP + phosphate + D-xylose[cytosol] """,},'ucsd-rxns' : ['XYLabcpp',], 'protein-comments' : ["""NIL""","""(XylFGH is a D-xylose transporter belonging to the ATP Binding Cassette (ABC) Superfamily
|CITS: [96381453]|. D-xylose is the most abundant sugar in nature after glucose, and it can be utilized
by E. coli as a sole carbon source and metabolized through the pentose phosphate pathway
|CITS: [98336901]|. Sequence homology analysis suggests that XylG is the ATP-binding protein,
XylF is the periplasmic substrate-binding protein |CITS: [96117780]|, and XylH is the membrane
component of the ABC transport system |CITS: [94316500]|. The binding affinity of the receptor protein,
XylF, was studied using a mutant of xylE, which encodes the other D-Xylose transport system
in E. coli. The Km of XylF was determined to be in the range of 0.2-4 μM,
indicating that XylF is a high-affinity D-xylose transport system |CITS: [96117780]|. Transposon
mutagenesis studies suggest that XylFGH can also transport D-ribose in E.coli cells lacking
the high affinity RbsABC ribose transport system |CITS: [98336901]|.)""",]},
'B2701' : {'ecocyc-rxns': {},'ucsd-rxns' : ['MLTGY3pp','MLTGY4pp','MLTGY1pp','MLTGY2pp',], 'protein-comments' : ["""(MltB is one of three (along with MltA and Slt70) major lytic endotransglycosylases expressed in
Escherichia coli. MltA and MltB are expressed as membrane-bound lipoproteins. Expression
of MltB in cells grown in the presence of H-3 palmitate followed by SDS-PAGE analysis resulted in
fluorographic visualization of a labeled band corresponding to the 36 kDa mass of MltB, demonstrating
the lipoprotein character of MltB. Additionally, in the presence of globomycin, an inhibitor of the
lipoprotein signal peptidase, a larger protein, the prolipoprotein form of MltB, was found to accumulate.
Overexpression of mltB resulted in a 55-fold increase in murein hydrolase activity in the membrane
fraction and subsequent cell lysis. Membrane fractionation followed by sucrose-density-gradient
centrifugation indicated that most of the induced hydrolytic activity was located in the outer and
intermediate membrane fractions. A deletion of the mltB gene showed no obvious phenotype
|CITS:[746170]|, while a triple mltA, mltB, and slt70 mutant resulted in a 72%
reduction in murein turnover |CITS:[10572120]|.)""",]},
'B3565' : {'ecocyc-rxns': {"""XYLISOM-RXN""": """D-xylose = xylulose""",},'ucsd-rxns' : ['XYLI1','XYLI2',], 'protein-comments' : ["""(An amber mutation has been generated |CITS: [12853150]|.)""","""NIL""",]},
'B4208' : {'ecocyc-rxns': {"""RXN0-5130""": """H+[periplasmic space] + D-serine[periplasmic space] =H+[cytosol] + D-serine[cytosol] ""","""TRANS-RXN-62B""": """H+[periplasmic space] + glycine[periplasmic space] =H+[cytosol] + glycine[cytosol] ""","""TRANS-RXN-62A""": """H+[periplasmic space] + D-alanine[periplasmic space] =H+[cytosol] + D-alanine[cytosol] """,},'ucsd-rxns' : ['DSERt2pp','BALAt2pp','ALAt2pp','GLYt2pp','DALAt2pp',], 'protein-comments' : ["""(CycA is a transporter involved in the uptake of glycine, serine
and alanine. Mutants defective in cycA show decreased transport
of glycine, D-serine and D-alanine and are resistant to D-cycloserine
inhibition |CITS: [95202071] [74011087]|. Deletion mutation studies indicate that beta-alanine uptake rates are significantly reduced in cycA mutant strains and that uptake activity can be restored through plasmid expression of cycA |CITS:[15221223]|.CycA is a member of the
APC superfamily of amino acid transporters and is likely to function
as a proton/serine, alanine or glycine symporter.)""",]},
'B3567' : {'ecocyc-rxns': {"""ABC-33-RXN""": """ATP + D-xylose[periplasmic space] + H2O =ADP + phosphate + D-xylose[cytosol] """,},'ucsd-rxns' : ['XYLabcpp',], 'protein-comments' : ["""NIL""","""(XylFGH is a D-xylose transporter belonging to the ATP Binding Cassette (ABC) Superfamily
|CITS: [96381453]|. D-xylose is the most abundant sugar in nature after glucose, and it can be utilized
by E. coli as a sole carbon source and metabolized through the pentose phosphate pathway
|CITS: [98336901]|. Sequence homology analysis suggests that XylG is the ATP-binding protein,
XylF is the periplasmic substrate-binding protein |CITS: [96117780]|, and XylH is the membrane
component of the ABC transport system |CITS: [94316500]|. The binding affinity of the receptor protein,
XylF, was studied using a mutant of xylE, which encodes the other D-Xylose transport system
in E. coli. The Km of XylF was determined to be in the range of 0.2-4 μM,
indicating that XylF is a high-affinity D-xylose transport system |CITS: [96117780]|. Transposon
mutagenesis studies suggest that XylFGH can also transport D-ribose in E.coli cells lacking
the high affinity RbsABC ribose transport system |CITS: [98336901]|.)""",]},
'B3566' : {'ecocyc-rxns': {"""ABC-33-RXN""": """ATP + D-xylose[periplasmic space] + H2O =ADP + phosphate + D-xylose[cytosol] """,},'ucsd-rxns' : ['XYLabcpp',], 'protein-comments' : ["""NIL""","""(XylFGH is a D-xylose transporter belonging to the ATP Binding Cassette (ABC) Superfamily
|CITS: [96381453]|. D-xylose is the most abundant sugar in nature after glucose, and it can be utilized
by E. coli as a sole carbon source and metabolized through the pentose phosphate pathway
|CITS: [98336901]|. Sequence homology analysis suggests that XylG is the ATP-binding protein,
XylF is the periplasmic substrate-binding protein |CITS: [96117780]|, and XylH is the membrane
component of the ABC transport system |CITS: [94316500]|. The binding affinity of the receptor protein,
XylF, was studied using a mutant of xylE, which encodes the other D-Xylose transport system
in E. coli. The Km of XylF was determined to be in the range of 0.2-4 μM,
indicating that XylF is a high-affinity D-xylose transport system |CITS: [96117780]|. Transposon
mutagenesis studies suggest that XylFGH can also transport D-ribose in E.coli cells lacking
the high affinity RbsABC ribose transport system |CITS: [98336901]|.)""",]},
'B3731' : {'ecocyc-rxns': {"""ATPSYN-RXN""": """H+[cytosol] + H2O + ATP =H+[periplasmic space] + phosphate + ADP """,},'ucsd-rxns' : ['ATPS4rpp','ATPS4rpp',], 'protein-comments' : ["""(The epsilon subunit appears to play an important role in coupling the catalytic
site events with proton translocation in association with the gamma subunit.
The coupling involves conformational changes and probable translocations of one
or both subunits. This subunit is also required for binding of the F-1 complex
to the F-O complex. |CITS: [96216373] [90303438]|)""","""(The F-1 complex of ATP synthase contains the catalytic sites. The complex
consists of five subunits, each of which is required for activity.
|CITS: [90303438] [89372792]|)""","""(The enzyme is made up of two subcomplexes, the F-1 complex and the F-O complex.
There are eight total subunits all required for activity. The F-1 complex is
the catalytic unit. The F-O complex anchors the F-1 complex to the membrane
and also forms the proton channel. |CITS: [89123355] [90303438] [93252965]|)""",]},
'B3560' : {'ecocyc-rxns': {"""GLYCINE--TRNA-LIGASE-RXN""": """tRNAgly + glycine + ATP -> glycyl-tRNAgly + diphosphate + AMP""",},'ucsd-rxns' : ['GLYTRS',], 'protein-comments' : ["""NIL""","""(Glycyl-tRNA synthetase (GlyRS) is a member of the family of aminoacyl-tRNA synthetases, which interpret the
genetic code by covalently linking amino acids to their specific tRNA molecules. The reaction is driven by ATP
hydrolysis. GlyRS belongs to the Class II aminoacyl tRNA synthetases, which share three regions of homology
|CITS: [2203971][1852601]|.
GlyRS is a tetramer consisting of two α and two β subunits. Both subunits are required for catalytic activity
|CITS: [4923123][6992865]|. An enzyme in which the α and β subunits are fused into a single polypeptide
chain is catalytically active |CITS: [3009467]|.
Specificity determinants within tRNAGly that are important for recognition by GlyRS have been
identified |CITS: [167016][2068095][7664744][9171287]|. The tRNA binding site is located in the β subunit of
GlyRS |CITS: [6374618]|.
Review: |CITS: [10966471]|)""",]},
'B2708' : {'ecocyc-rxns': {"""DARAB5PISOM-RXN""": """D-arabinose 5-phosphate = D-ribulose-5-phosphate""",},'ucsd-rxns' : ['A5PISO',], 'protein-comments' : ["""(gutQ encodes the second of two D-arabinose 5-phosphate isomerases (API) in E. coli. Its
biochemical properties are very similar to those of KdsD, the first identified D-arabinose 5-phosphate isomerase.
Strains containing single mutations in either the kdsD or gutQ genes are viable and have a functional
LPS. A kdsD gutQ double mutant strain required the addition of exogenous arabinose 5-phosphate for viability
|CITS: [16199563]|.
GutQ has previously been shown to have a sugar isomerase (SIS) domain |CITS: [10203754]| and a predicted ATP
binding site |CITS: [2134185]|.
GutQ has similarity to of E. coli K1 KpsF, which plays a role in polysialic acid capsule expression
|CITS: [9383150]|.
Regulation has been described |CITS: [2134185]|.)""","""NIL""",]},
'B3607' : {'ecocyc-rxns': {"""CYSSYNMULTI-RXN""": """L-serine + acetyl-CoA + hydrogen sulfide = L-cysteine + coenzyme A + acetate""","""SERINE-O-ACETTRAN-RXN""": """L-serine + acetyl-CoA = O-acetyl-L-serine + coenzyme A""",},'ucsd-rxns' : ['SERAT',], 'protein-comments' : ["""NIL""","""(Serine acetyltransferase is a hexamer (dimer of trimers) of CysE |CITS: [10617639]|. A crystal structure has been
solved at 2.2 A resolution; the structure reveals the mechanism of feedback inhibition by cysteine and suggests a
reaction mechanism for O-acetylation of serine by the enzyme |CITS: [15231846]|.
A cysE mutant shows an enhanced rate of biofilm formation |CITS: [15516574]|.)""","""(Serine O-acetyl transferase is associated in a bifunctional complex with O-acetyl serine (thiol) lyase A
(O-acetylserine sulfhydrolase A) |CITS: [88009872] [91099514]|. The complex dissociates in the presence of
O-acetylserine, the product of the serine-O-acetyltransferase-catalyzed reaction |CITS: [ColiSalII] [91099514]
[88009872]|.
)""",]},
'B3371' : {'ecocyc-rxns': {"""RXN0-963""": """fructoselysine-6-phosphate + H2O = β-D-glucose-6-phosphate + L-lysine""",},'ucsd-rxns' : ['FRULYSDG',], 'protein-comments' : ["""(Fructoselysine 6-phosphate deglycase, which acts in fructoselysine degradation, is a FrlB dodecamer
|CITS: [12147680]|. The fructoselysine 6-phosphate deglycase reaction is reversible in vitro, but is catalyzed
in the direction of formation of glucose 6-phosphate and lysine in vivo |CITS: [12147680]|. A detailed reaction
mechanism is discussed |CITS: [12147680]|.
Fructoselysine 6-phosphate deglycase activity is undetectable when cells are grown on glucose; stationary phase
extract of cells grown on fructoselysine or psicoselysine have a deglycase activity of 20 nmol/min per mg of protein
|CITS: [14641112]|.
An frlA mutant is unable to grow on 20mM fructoselysine or psicoselysine as the sole source of carbon
|CITS: [14641112]|.
FrlB: "fructoselysine" |CITS: [12147680]|.)""","""NIL""",]},
'B3634' : {'ecocyc-rxns': {"""PANTEPADENYLYLTRAN-RXN""": """pantetheine 4'-phosphate + ATP = dephospho-CoA + diphosphate""",},'ucsd-rxns' : ['PTPATi',], 'protein-comments' : ["""(The coaD (kdtB) gene product had been thought to be involved in lipopolysaccharide assembly as a
cytidylyltransferase. However, recent investigations have shown that the enzyme encoded by this gene does not
have any activity with the putative lipopolysaccharide substrate, but instead encodes the pantetheine-phosphate
adenylyltransferase in CoA biosynthesis. |CITS: [99221637][99410451]|
A mutant does not grow in complex media |CITS: [11361082]|; CoaA is thus an attractive potential antimicrobial drug
target |CITS: [12142426]|. Inhibitors of the enzyme have been found and tested |CITS: [12750020]|.
The enzyme has been crystallized, and the catalytic mechanism and substrate interactions have been characterized
|CITS: [99221637][99263343][11812124][12837781]|.)""","""NIL""",]},
'B4195' : {'ecocyc-rxns': {"""RXN0-2461""": """phosphoenolpyruvate + L-ascorbate[periplasmic space] =L-ascorbate-6-phosphate[cytosol] + pyruvate """,},'ucsd-rxns' : ['ASCBptspp',], 'protein-comments' : ["""(UlaC: "utilization of L-ascorbate" |CITS: [11741871]|. Contains a PTS Enzyme IIA domain.)""","""(SgaTBA, a putative PTS permease, belongs to the functional superfamily
of the phosphoenolpyruvate (PEP)-dependent, sugar transporting
phosphotransferase system (PTS). The PTS transports and simultaneously
phosphorylates its sugar substrates in a process called group
translocation. SgaTBA presumably takes up an exogenous sugar,
releasing the phosphate ester into the cell cytoplasm in preparation
for metabolism |CITS: [8246840]| . The overall PTS-mediated phosphoryl transfer
reaction, requiring the two general energy coupling proteins of
the PTS, Enzyme I and HPr, as well as the three domains of the
Enzyme II complex is:
PEP --> Enzyme I(his~~P)
--> HPr(his~~P)
--> IIA(his~~P) -->
IIB(cys~~P) -(IIC)-> sugar-P.
The sga operon encodes SgaT, an integral membrane putative
transporter protein with 12 putative transmembrane α-helical
spanners that might function as a PTS Enzyme IIC; SgaB, the putative
Enzyme IIBSga, and SgaA, the putative Enzyme
IIASga |CITS: [REIZERGENOMESCITECH153]|. SgaB is homologous to the IIB
domains of the lactose-cellobiose PTS permease family. SgaA is
homologous to the IIA domains/proteins of the fructose-mannitol
PTS permease family. Little is known regarding the function of
these enzymes or expression of the sga operon in which
the encoding genes are found. However, the sga genes may
allow metabolism and interconversion of pentose and hexose phosphate
esters |CITS: [9274005]| .
Deletion mutation studies |CITS:[12644495]| indicate that all three components
are necessary for the uptake and utiliztion of L-ascorbate in vivo as well as for the
phosphorylation of L-ascorbate in vitro.)""",]},
'B2499' : {'ecocyc-rxns': {"""AIRS-RXN""": """ATP + 5-phosphoribosyl-N-formylglycineamidine -> ADP + phosphate + 5-aminoimidazole ribonucleotide""",},'ucsd-rxns' : ['PRAIS',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B0604' : {'ecocyc-rxns': {"""5.3.4.1-RXN""": """a protein with incorrect disulfide bonds = a protein with correct disulfide bonds""","""DISULFOXRED-RXN""": """a protein with reduced sulfide groups = a protein with oxidized disulfide bonds""",},'ucsd-rxns' : ['TDSR2','DSBGGT',], 'protein-comments' : ["""NIL""","""NIL""","""NIL""",]},
'B3642' : {'ecocyc-rxns': {"""OROPRIBTRANS-RXN""": """orotidine-5'-phosphate + diphosphate = 5-phosphoribosyl 1-pyrophosphate + orotate""",},'ucsd-rxns' : ['ORPT',], 'protein-comments' : ["""NIL""","""(This enzyme is at a low level in E. coli strains W1485 and its daughters
W3110 and MG1655 because of a mutation in the upstream gene affecting
transcription of pyrE. |CITS: [93273707]|)""",]},
'B3028' : {'ecocyc-rxns': {"""RXN0-271""": """NADPH + a quinone = NADP+ + a hydroquinone""","""NADPH-DEHYDROGENASE-(QUINONE)-RXN""": """an acceptor + NADPH = a reduced acceptor + NADP+""",},'ucsd-rxns' : ['NADPHQR2','NADPHQR3','NADPHQR4',], 'protein-comments' : ["""NIL""","""(The MdaB quinone reductase is specific for NADPH and is most active with quinone derivatives and ferricyanide
|CITS: [8611590]|. YgiN is able to reoxidize menadiol that has been reduced by MdaB quinone reductase
in vitro, and the two enzymes may form a quinone redox cycle. The biological role of a quinone redox cycle
may be to maintain an intracellular pool of menadione and ubiquinone using a catalytic mechanism that avoids the
formation of a semiquinone intermediate, and to act as a quinone buffer |CITS: [15613473]|.
While menadione appears to specifically induce expression of the FMN-dependent NADH-menadione reductase
activity, 2-methylene-4-buyrolactone (MBL) primarily induces expression of FMN-independent NADPH-menadione
reductase activity |CITS: [8611590]|.
Overexpression of mdaB leads to increased resistance to the tumoricidal agent DMP 840 |CITS: [7568050]|.
A preliminary analysis of the crystal structure of MdaB has been published |CITS: [16511004]|.
mdaB: "modulator of drug activity" |CITS: [7568050]|)""",]},
'B3029' : {'ecocyc-rxns': {"""RXN0-3441""": """menadiol + 2 O2 -> menadione + 2 O2-""",},'ucsd-rxns' : ['QMO2','QMO3',], 'protein-comments' : ["""NIL""","""(YgiN is able to reoxidize menadiol that has been reduced by MdaB quinone reductase in vitro, and the two
enzymes may form a quinone redox cycle. Catalysis by YgiN does not appear to require metal ions or other cofactors.
The reaction is not sensitive to inhibition by heptyl-4-hydroxyquinoline-N-oxide (HOQNO), a typical inhibitor of
single electron reduction reactions, indicating that the reaction proceeds via a two-electron transfer mechanism.
The biological role of a quinone redox cycle may be to maintain an intracellular pool of menadione and ubiquinone
using a catalytic mechanism that avoids the formation of a semiquinone intermediate, and to act as a quinone buffer
|CITS: [15613473]|.
Crystal structures of YgiN alone and in complex with menadione have been solved at 2.2 and 1.7 A resolution,
respectively. The structure is similar to the structure of ActVA-Orf6, a novel monooxygenase from
Streptomyces coelicolor. A co-crystal of YgiN with menadione shows menadione to be located in the active
site |CITS: [15613473]|.
YgiN protein has been detected in E. coli and has orthologs in the genomes of Mycobacterium
tuberculosis, Neisseria gonorrhoea, Bacillus subtilis, Synechocystis sp., and Rhodococcus
erythropolis |CITS: [9868784]|. The ygiN gene may be transcribed in an operon together with mdaB;
the genomic organization of orthologs of both genes is conserved |CITS: [15613473]|.
)""",]},
'B3631' : {'ecocyc-rxns': {"""RXN0-5120""": """heptosyl2-KDO2-lipid A + UDP-D-glucose = glucosyl-heptosyl2-KDO2-lipid A + UDP""",},'ucsd-rxns' : ['GLCTR1',], 'protein-comments' : ["""(The lipopolysaccharide of E. coli K-12 consists of two major components:
the hydrophobic lipid A moiety inserted into the outer membrane and the
phosphorylated core oligosaccharide |CITS:[12045108]|. E. coli K-12
does not produce O antigen to attach to the LPS core due to a defect in the
rfb gene cluster which can be complemented with genes from a second,
independent rfb mutant to produce an O16 type O antigen |CITS:[7517391]|.
E. coli K-12 may have two major pathways for LPS biosynthesis. One
generates LPS cores suitable for O antigen attachment, and a second generates
lipooligosaccharides (LOS) with modifications to the core structure which prevent
O antigen attachment |CITS:[1385388]|.
waaG encodes UDP-glucose:(heptosyl)LPS α-1,3-glucosyltransferase.
WaaG adds the first glucose (GlcI) of the outer core of LPS from UDP-glucose
to the HepII residue of the inner core |CITS:[1348243]|. waaG+
restores flagella and pilli to a waaGPBO deletion mutant |CITS:[1348243]|.
Reviews: |CITS:[12045108],[9791168],[7504166]|
)""",]},
'B4196' : {'ecocyc-rxns': {"""RXN0-705""": """3-keto-L-gulonate 6-phosphate = L-xylulose-5-phosphate + CO2""",},'ucsd-rxns' : ['KG6PDC',], 'protein-comments' : ["""(The crystal structures of the UlaD protein |CITS: [11900527]| and four mutants |CITS: [15157078]| have been
determined. Active site residues and catalytic mechanisms have been studied
|CITS: [11900527][15157077][14567674][15157078]|.
UlaD: "utilization of L-ascorbate" |CITS: [11741871]|.)""",]},
'B0653' : {'ecocyc-rxns': {"""ABC-13-RXN""": """ATP + L-glutamate[periplasmic space] + H2O =ADP + phosphate + L-glutamate[cytosol] """,},'ucsd-rxns' : ['GLUabcpp','ASPabcpp',], 'protein-comments' : ["""NIL""","""(The GltIJKL glutamate transporter is a member of the ATP Binding Cassette (ABC) transporter superfamily
|CITS:[98254124]|. Sequence similarity with known ABC transporter components suggests that GltJK are
integral membrane components and GltL is the ABC protein. GltI (also known as YbeJ) is the presumed
periplasmic binding protein.)""",]},
'B0887' : {'ecocyc-rxns': {"""RXN0-3""": """L-cysteine[cytoplasm] + ATP + H2O =L-cysteine[periplasmic space] + ADP + phosphate ""","""RXN0-21""": """glutathione[cytoplasm] + ATP + H2O =glutathione[periplasmic space] + ADP + phosphate """,},'ucsd-rxns' : ['GTHRDabc2pp','CYSabc2pp',], 'protein-comments' : ["""NIL""","""(The cydDC operon encodes two ATP-binding cassette (ABC) transporter proteins that are most
closely similar to
ABC transporters involved in export |CITS:[98254124]|. Deletion studies have shown that both of these
proteins are essential
for functional cytochrome bd and cytochrome c |CITS:[87194595], [94237457]|. Transport
assays of the heterodimeric CydDC ABC transporter show that it is responsible for transport of glutathione
|CITS:[16040611]| and, to a lesser extent, cysteine from the cytoplasm to the periplasmic space
|CITS:[15470119]|, |CITS:[16040611]|. CydDC is important for maintenance of the optimum redox balance in
the periplasm. Exogenous glutathione or cysteine has been shown to rescue cydC mutants from
temperature-sensitive and survival phenotypes |CITS:[16040611]|. Both CydD and CydC have been
shown experimentally to have six-transmembrane segments, three minor periplasmic loops, and two major
cytoplasmic loops |CITS:[15470119]|.)""",]},
'B0886' : {'ecocyc-rxns': {"""RXN0-3""": """L-cysteine[cytoplasm] + ATP + H2O =L-cysteine[periplasmic space] + ADP + phosphate ""","""RXN0-21""": """glutathione[cytoplasm] + ATP + H2O =glutathione[periplasmic space] + ADP + phosphate """,},'ucsd-rxns' : ['GTHRDabc2pp','CYSabc2pp',], 'protein-comments' : ["""NIL""","""(The cydDC operon encodes two ATP-binding cassette (ABC) transporter proteins that are most
closely similar to
ABC transporters involved in export |CITS:[98254124]|. Deletion studies have shown that both of these
proteins are essential
for functional cytochrome bd and cytochrome c |CITS:[87194595], [94237457]|. Transport
assays of the heterodimeric CydDC ABC transporter show that it is responsible for transport of glutathione
|CITS:[16040611]| and, to a lesser extent, cysteine from the cytoplasm to the periplasmic space
|CITS:[15470119]|, |CITS:[16040611]|. CydDC is important for maintenance of the optimum redox balance in
the periplasm. Exogenous glutathione or cysteine has been shown to rescue cydC mutants from
temperature-sensitive and survival phenotypes |CITS:[16040611]|. Both CydD and CydC have been
shown experimentally to have six-transmembrane segments, three minor periplasmic loops, and two major
cytoplasmic loops |CITS:[15470119]|.)""",]},
'B1612' : {'ecocyc-rxns': {"""FUMHYDR-RXN""": """malate = fumarate + H2O""",},'ucsd-rxns' : ['FUM',], 'protein-comments' : ["""(One of three isozymes in E. coli, fumarase A is a Class I fumarase. The FumA protein is 79% similar to the
FumB protein.)""","""NIL""",]},
'B1232' : {'ecocyc-rxns': {"""FORMYLTHFDEFORMYL-RXN""": """H2O + N10-formyl-THF -> tetrahydrofolate + formate""",},'ucsd-rxns' : ['FTHFD',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B2564' : {'ecocyc-rxns': {"""PDXJ-RXN""": """1-amino-propan-2-one-3-phosphate + 1-deoxy-D-xylulose 5-phosphate = pyridoxine-5'-phosphate + phosphate + 2 H2O""",},'ucsd-rxns' : ['PDX5PS',], 'protein-comments' : ["""(Pyridoxine 5'-phosphate synthase is one of two key enzymes involved in the ring closure of the aromatic pyridoxin
ring in vitamin B12 biosynthesis. The enzyme is mostly present in the gamma subdivision of proteobacteria
|CITS: [11200221]|.
The pdxJ gene is not essential in E. coli |CITS: [1537799]|.)""","""NIL""",]},
'B1492' : {'ecocyc-rxns': {"""TRANS-RXN-261""": """4-aminobutyrate[cytosol] + L-glutamate[periplasmic space] =L-glutamate[cytosol] + 4-aminobutyrate[periplasmic space] """,},'ucsd-rxns' : ['GLUABUTt7pp',], 'protein-comments' : ["""(XasA confers resistance to extreme acid conditions. Insertional inactivation
of the xasA gene results in sensitivity to extreme acid
conditions (pH 2-3) and eliminated glutamic acid enhancement of
acid resistance |CITS: [96272279]|. The xasA gene is located
downstream of the gadB gene encoding glutamic acid decarboxylase
|CITS: [96272279]|. XasA probably mediates export of gamma-aminobutyrate
in exchange for glutamic acid. XasA is a member of the APC superfamily of
amino acid transporters.
YhiE, GadC, Slp-YhiF, HdeA, and HdeD are involved in the resistance to low pH observed upon overexpression of ydeO |CITS: [12694615]|.
Regulation has been described |CITS: [12940989]|.)""",]},
'B3125' : {'ecocyc-rxns': {"""TSA-REDUCT-RXN""": """glycerate + NAD(P)+ = tartronate semialdehyde + NAD(P)H + H+""",},'ucsd-rxns' : ['TRSARr',], 'protein-comments' : ["""(The subunit structure is unknown.)""",]},
'B2210' : {'ecocyc-rxns': {"""MALATE-DEHYDROGENASE-(ACCEPTOR)-RXN""": """an acceptor + malate -> a reduced acceptor + oxaloacetate""",},'ucsd-rxns' : ['MDH3','MDH2',], 'protein-comments' : ["""(The mqo-encoded malate:quinone oxidoreductase (MQO) is membrane-associated and catalyzes the
essentially irreversible oxidation of malate to oxaloacetate |CITS: [10809701]|. Electrons are donated to the electron
transfer chain at the quinone level. The mqo- and mdh-encoded malate dehydrogenases are active at
the same time in the cell, although the mqo dehydrogenase does not seem to play a significant role in malate
oxidation. An mqo deletion strain does not have an obvious growth defect, but mqo can partially
substitute for the function of MDH in an mdh mutant |CITS: [20545431]|.
MQO activity is highest during exponential growth and decreases after the onset of stationary phase
|CITS: [358983][20545431]|. Expression is regulated at the transcriptional level by the ArcA-ArcB two-component
system |CITS: [20545431]|.
mqo: "malate:quinone oxidoreductase")""",]},
'B3127' : {'ecocyc-rxns': {},'ucsd-rxns' : ['GALCTt2rpp','GLCRt2rpp','GLYCAt2rpp',], 'protein-comments' : ["""(YhaU is an uncharacterised member of the major facilitator superfamily (MFS)
of transporters |CITS: [98190790]|.
Based on sequence similarity, YhaU may function as a proton-driven
glucarate uptake system.)""",]},
'B3126' : {'ecocyc-rxns': {"""KDGALDOL-RXN""": """5-keto-4-deoxy-D-glucarate = pyruvate + tartronate semialdehyde""",},'ucsd-rxns' : ['GLCRAL',], 'protein-comments' : ["""(The subunit structure is unknown.)""",]},
'B1238' : {'ecocyc-rxns': {"""THYKI-RXN""": """thymidine + ATP -> dTMP + ADP""","""DURIDKI-RXN""": """deoxyuridine + ATP -> dUMP + ADP""",},'ucsd-rxns' : ['DURIK1','TMDK1',], 'protein-comments' : ["""(Early studies of the enzyme indicated that in the presence
of an activator or an inhibitor deoxynucleotide the enzyme dimerizes.
Dimerization accounts for the regulatory properties of the enzyme,
which has either an active or inactive conformation, depending upon
which effector nucleotide interacts with it. |CITS: [68016086]
[79009996]|)""",]},
'B3433' : {'ecocyc-rxns': {"""ASPARTATE-SEMIALDEHYDE-DEHYDROGENASE-RXN""": """NADP+ + phosphate + L-aspartate-semialdehyde = NADPH + L-aspartyl-4-phosphate""",},'ucsd-rxns' : ['ASAD',], 'protein-comments' : ["""(Each subunit of aspartate semialdehyde dehydrogenase contains three cysteine residues; two are
reactive in the native enzyme, one is partially protected by the substrate |CITS: [80178689]|.
Crystal structures of aspartate semialdehyde dehydrogenase have been solved at high resolution
|CITS: [10369777][11724560][15288787][93078266]|.)""","""NIL""",]},
'B3089' : {'ecocyc-rxns': {"""RXN0-4083""": """Na+[periplasmic space] + L-serine[periplasmic space] =Na+[cytosol] + L-serine[cytosol] """,},'ucsd-rxns' : ['SERt4pp','THRt4pp',], 'protein-comments' : ["""(The YgjU/SstT protein is a member of the DAACS family of sodium ion coupled serine/threonine symporters.
The sstT gene has been cloned and shown to complement a serine transport mutant |CITS:[9852024]|.
The SstT protein has been purified and demonstrated in reconstituted proteoliposomes to mediate the
transport of serine driven by electrochemical sodium ion gradient with a Km and Vmax of 0.82 μM
and 0.37 nmol/min/mg protein respectively. Serine transport was inhibited by L-threonine, but not by
other amino acids |CITS:[12097162]|.
)""",]},
'B1589' : {'ecocyc-rxns': {"""DIMESULFREDUCT-RXN""": """dimethyl sulfoxide + H+ + menaquinol -> dimethylsulfide + H2O + menaquinone-8""",},'ucsd-rxns' : ['TMAOR1','DMSOR1',], 'protein-comments' : ["""(YnfG is highly similar to DmsB, the iron-sulfur cluster-containing subunit of the dimethyl sulfoxide reductase
heterotrimer, and cross-reacts with an anti-DmsB antibody. It contains iron-sulfur clusters which are
indistinguishable from DmsB by EPR spectroscopy. When expressed together with DmsA and YnfH in a plasmid
expression system, YnfG can form a complex with DmsA and YnfH and support growth on DMSO |CITS: [14522592]|.)""","""(A strain carrying a deletion of dmsABC and containing ynfFGH on a multicopy plasmid is able to grow
poorly under anaerobic conditions utilizing dimethyl sulfoxide as a terminal oxidant. The physiological substrate for
this enzyme is unknown |CITS: [14522592]|.)""",]},
'B0118' : {'ecocyc-rxns': {"""4.2.1.99-RXN""": """methylisocitrate = 2-methyl-cis-aconitate + H2O""","""ACONITATEDEHYDR-RXN""": """citrate = cis-aconitate + H2O""","""ACONITATEHYDR-RXN""": """cis-aconitate + H2O = isocitrate""",},'ucsd-rxns' : ['ACONTa','ACONTb','MICITD',], 'protein-comments' : ["""(Purification of the enzyme is described |CITS: [12473114]|. Enzyme activity is sensitive to oxidation, and observations are consistent with dependence of activity on a [4Fe-4S] iron-sulfur cluster |CITS: [12473114]|.
Regulation has been described |CITS: [12473114]|.)""",]},
'B0757' : {'ecocyc-rxns': {"""GALACTOKIN-RXN""": """D-galactose + ATP = α-D-galactose 1-phosphate + ADP""",},'ucsd-rxns' : ['GALKr',], 'protein-comments' : ["""(An amber mutation has been generated |CITS: [12853150]|.)""",]},
'B0115' : {'ecocyc-rxns': {"""PYRUVDEH-RXN""": """pyruvate + coenzyme A + NAD+ -> acetyl-CoA + CO2 + NADH""","""RXN0-1133""": """acetyl-CoA + enzyme N6-(dihydrolipoyl)lysine = coenzyme A + enzyme N6-(S-acetyldihydrolipoyl)lysine""","""DIHYDLIPACETRANS-RXN""": """acetyl-CoA + dihydrolipoamide = coenzyme A + S-acetyldihydrolipoamide""",},'ucsd-rxns' : ['PDH',], 'protein-comments' : ["""(AceF, the "E2" or "core" component of the pyruvate dehydrogenase multienzyme complex, assembles into a 24-subunit |CITS: [386335]| cube |CITS: [3905803], [2266132]|. The E1 dimers of the pyruvate dehydrogenase multienzyme complex catalyze acetylation of the lipoate moieties that are attached to the E2 subunits |CITS: [367364]|. The E2 subunits (AceF) also exhibit transacetylation |CITS: [7032507]|. The structure of the pyruvate dehydrogenase multienzyme complex and the spatial distribution of the E2 lipoyl moieties have been studied by scanning transmission electron microscopy |CITS: [7520749]|.
AceF is a soluble cytoplasmic protein |CITS: [1554745]| that contains an acidic N-terminal lipoyl domain with three roughly 100-residue repeats, each with a lipoyl modification motif and an alanine- and proline-rich segment |CITS: [6430694], [6345153]|. A single lipoyl domain suffices with respect to enzyme activity and protein function |CITS: [3903169]|. The lipoyl domains appear to function independently of each other |CITS: [2509711]|. Lipoyl modification sites (of sequence GDKASME, lipoylated on the lysine) of all three lipoyl domain repeats appear to be fully lipoylated, and all of these lipoyl groups are subject to acetylation by the pyruvate dehydrogenase complex |CITS: [1854331]|. Individual isolated lipoyl domains show differing capacity to bind lipoic acid |CITS: [3117051]|. The enzyme shows a preference for R-lipoic acid, but it can utilize the S-lipoic acid enantiomer |CITS: [8841385]|. A K143Q mutant protein (lacking a functional lipoic acid attachment site in the N-terminal repeat) exhibits some defect inactive site coupling and a two-fold decrease in catalytic activity, compared to wild type |CITS: [2509711]|. Modification of the E2 subunit plays a role in feedback regulation of pyruvate dehydrogenase multienzyme complex activity; reductive acetylation of the E2 lipoyl groups stimulates the kinase activity of the E1 subunit bound to this group, and the kinase activity then inhibits the pyruvate dehydrogenase multienzyme complex |CITS: [8557670]|. Binding to the E1 subunit has been examined; residue D17 of the E1 subunit is essential and E1 residue D24 plays a role in binding |CITS: [12095640]|.
The AceF alanine- and proline-rich region is a flexible linker |CITS: [3280020]| that plays a role in active site coupling and is important for catalytic activity |CITS: [3050122]|. Mutations or moderate deletions within the alanine- and proline-rich linker region, in the context of a mutant protein with only one of the three lipoyl domains, do not compromise the function of the enzyme |CITS: [3297160], [3280020], [3050122]|, whereas deletion to 13 or fewer amino acids causes defects |CITS: [3050122]|.
AceF also contains a C-terminal catalytic and subunit binding domain |CITS: [3530810], [6430694], [6345153]|. The enzyme is sensitive to deletions within this C-terminal domain |CITS: [3903169]|. The residue S550 is important |CITS: [1676519]| and the residue H602 is essential |CITS: [1445221]| for catalysis .
AceF has similar overall domain organization to SucB, the analogous protein in the 2-oxoglutarate dehydrogenase complex; however, the SucB N terminus contains only one lipoyl repeat and the precise location of the alanine- and proline-rich segment differs among the two proteins |CITS: [6376124], [3297046]|.
The human pyruvate dehydrogenase E2 subunit has epitopes that are recognized by autoantibodies associated with primary biliary cirrhosis |CITS: [10807518]| and antibodies associated with some cases of active pulmonary tuberculosis (mycobacterial infection) |CITS: [7683589]|.
Regulation has been described |CITS: [349114], [6455499], [6345153], [3897791], [8262214], [8057842], [9588797], [10197995], [8557670]|.
Review: |CITS: [3332999]|.)""","""NIL""","""NIL""","""NIL""","""(One of the most complicated enzyme systems known. Complex is composed of multiple
copies of three enzymes: E1, E2 and E3, in stoichiometry
of 24:24:12, respectively (12 AceE dimers, a 24-subunit AceF core, and 6 LpdA dimers)
|CITS: [1103138], [3905803], [3925985], [386335]|.
AceF, the "E2" or "core" component of the pyruvate dehydrogenase multienzyme complex, assembles into a 24-subunit |CITS: [386335]| cube |CITS: [3905803], [2266132]|. The E1 dimers of the pyruvate dehydrogenase multienzyme complex catalyze acetylation of the lipoate moieties that are attached to the E2 subunits |CITS: [367364]|. The E2 subunits (AceF) also exhibit transacetylation |CITS: [7032507]|. The structure of the pyruvate dehydrogenase multienzyme complex and the spatial distribution of the E2 lipoyl moieties have been studied by scanning transmission electron microscopy |CITS: [7520749]|.
The E3 component is shared with 2-oxoglutarate dehydrogenase and glycine
cleavage multi-enzyme complexes. E1 and E2 differ slightly between 2-oxoglutarate
and pyruvate complexes, and are designated (o) and (p) to distinguish them. Substrate is
channeled through the catalytic reactions by attachment
in thioester linkage to lipoyl groups via so-called 'swinging arm',
carrying substrate molecules to successive active sites.
|CITS: [89076356]|)""",]},
'B0114' : {'ecocyc-rxns': {"""PYRUVDEH-RXN""": """pyruvate + coenzyme A + NAD+ -> acetyl-CoA + CO2 + NADH""","""RXN0-1134""": """pyruvate + enzyme N6-(lipoyl)lysine = enzyme N6-(S-acetyldihydrolipoyl)lysine + CO2""","""PYRUVATEDECARB-RXN""": """pyruvate + lipoamide = S-acetyldihydrolipoamide + CO2""",},'ucsd-rxns' : ['PDH',], 'protein-comments' : ["""NIL""","""(It is sometimes confusing that this component and the multi-enzyme complex both carry the same name.)""","""(One of the most complicated enzyme systems known. Complex is composed of multiple
copies of three enzymes: E1, E2 and E3, in stoichiometry
of 24:24:12, respectively (12 AceE dimers, a 24-subunit AceF core, and 6 LpdA dimers)
|CITS: [1103138], [3905803], [3925985], [386335]|.
AceF, the "E2" or "core" component of the pyruvate dehydrogenase multienzyme complex, assembles into a 24-subunit |CITS: [386335]| cube |CITS: [3905803], [2266132]|. The E1 dimers of the pyruvate dehydrogenase multienzyme complex catalyze acetylation of the lipoate moieties that are attached to the E2 subunits |CITS: [367364]|. The E2 subunits (AceF) also exhibit transacetylation |CITS: [7032507]|. The structure of the pyruvate dehydrogenase multienzyme complex and the spatial distribution of the E2 lipoyl moieties have been studied by scanning transmission electron microscopy |CITS: [7520749]|.
The E3 component is shared with 2-oxoglutarate dehydrogenase and glycine
cleavage multi-enzyme complexes. E1 and E2 differ slightly between 2-oxoglutarate
and pyruvate complexes, and are designated (o) and (p) to distinguish them. Substrate is
channeled through the catalytic reactions by attachment
in thioester linkage to lipoyl groups via so-called 'swinging arm',
carrying substrate molecules to successive active sites.
|CITS: [89076356]|)""",]},
'B1587' : {'ecocyc-rxns': {"""DIMESULFREDUCT-RXN""": """dimethyl sulfoxide + H+ + menaquinol -> dimethylsulfide + H2O + menaquinone-8""",},'ucsd-rxns' : ['TMAOR1','DMSOR1',], 'protein-comments' : ["""(YnfE is highly similar to DmsA, the catalytic subunit of the dimethyl sulfoxide reductase heterotrimer, and
cross-reacts with an anti-DmsA antibody. The protein is poorly expressed. In a plasmid expression system,
expression of YnfE appears to inhibit expression of YnfFGH |CITS: [14522592]|.
Based on sequence similarity, YnfE was predicted to be a trimethylamine-N-oxide reductase (TMAO reductase II)
|CITS: [12952533]|.)""","""(A strain carrying a deletion of dmsABC and containing ynfFGH on a multicopy plasmid is able to grow
poorly under anaerobic conditions utilizing dimethyl sulfoxide as a terminal oxidant. The physiological substrate for
this enzyme is unknown |CITS: [14522592]|.)""",]},
'B0116' : {'ecocyc-rxns': {"""PYRUVDEH-RXN""": """pyruvate + coenzyme A + NAD+ -> acetyl-CoA + CO2 + NADH""","""GCVMULTI-RXN""": """NAD+ + glycine + tetrahydrofolate = 5,10-methylene-THF + ammonia + CO2 + NADH""","""2OXOGLUTARATEDEH-RXN""": """α-ketoglutarate + coenzyme A + NAD+ = succinyl-CoA + CO2 + NADH""","""RXN0-1142""": """SucB-dihydrolipoate + NAD+ = SucB-lipoate + NADH""","""RXN0-1132""": """enzyme N6-(dihydrolipoyl)lysine + NAD+ = enzyme N6-(lipoyl)lysine + NADH + H+""","""RXN0-1131""": """dihydrolipoate + NAD+ = lipoate + NADH + H+""",},'ucsd-rxns' : ['PDH','AKGDH','GLYCL',], 'protein-comments' : ["""NIL""","""(The same E3 component serves in pyruvate dehydrogenase,
2-oxoglutarate dehydrogenase and glycine cleavage multi-enzyme systems. Another
dihydrolipoate dehydrogenase
activity has been detected in E. coli lpd mutants. There may be an
isozyme. |CIT: [90078101]|)""","""(One of the most complicated enzyme systems known.
A complex composed of multiple copies of 3 enzymes- E1, E2 and E3.
The E3 component is shared with the pyruvate dehydrogenase and glycine cleavage
multi-enzyme complexes. E1
and E2 differ slightly for 2oxoglutarate and pyruvate complexes,
designated (o) and (p) to distinguish them.
Substrate is channeled through the catalytic reactions by attachment
in thioester linkage to lipoyl groups via so-called 'swinging arm',
carrying substrate molecules to successive active sites.)""","""(The glycine cleavage system is a multi-enzyme complex that
catalyzes the reversible oxidation of glycine and generates a C1 moiety. It is the second
major source of C1 units in the cell after serine hydroxymethyl
transferase.
One of the four
subunits, lipoamide dehydrogenase (E3), is shared with pyruvate
dehydrogenase and 2-oxoglutarate dehydrogenase.)""","""(One of the most complicated enzyme systems known. Complex is composed of multiple
copies of three enzymes: E1, E2 and E3, in stoichiometry
of 24:24:12, respectively (12 AceE dimers, a 24-subunit AceF core, and 6 LpdA dimers)
|CITS: [1103138], [3905803], [3925985], [386335]|.
AceF, the "E2" or "core" component of the pyruvate dehydrogenase multienzyme complex, assembles into a 24-subunit |CITS: [386335]| cube |CITS: [3905803], [2266132]|. The E1 dimers of the pyruvate dehydrogenase multienzyme complex catalyze acetylation of the lipoate moieties that are attached to the E2 subunits |CITS: [367364]|. The E2 subunits (AceF) also exhibit transacetylation |CITS: [7032507]|. The structure of the pyruvate dehydrogenase multienzyme complex and the spatial distribution of the E2 lipoyl moieties have been studied by scanning transmission electron microscopy |CITS: [7520749]|.
The E3 component is shared with 2-oxoglutarate dehydrogenase and glycine
cleavage multi-enzyme complexes. E1 and E2 differ slightly between 2-oxoglutarate
and pyruvate complexes, and are designated (o) and (p) to distinguish them. Substrate is
channeled through the catalytic reactions by attachment
in thioester linkage to lipoyl groups via so-called 'swinging arm',
carrying substrate molecules to successive active sites.
|CITS: [89076356]|)""",]},
'B0110' : {'ecocyc-rxns': {"""NACMURLALAAMI-RXN""": """EC# 3.5.1.28""",},'ucsd-rxns' : ['AGM4PA','AM3PA','AGM3PA','AM4PA',], 'protein-comments' : ["""(ampD is a member of the ampDE operon. AmpD is a cytosolic
N-acetylmuramyl-L-alanine amidase responsible for breakdown of anhMurNAc-tri-,
tetra-, and pentapeptides to release the peptides for recycling |CITS:[7958768],[7925310]|.
ampC encodes β-lactamase, though Escherichia coli lacks the
ampR gene encoding the regulator for ampC expression.
In Enterobacter cloacae the signal molecule for AmpR dependent induction
of ampC expression was identified as anhMurNAc-pentapeptide |CITS:[9333034]|.
Deletion from Escherichia coli of ampD resulted in overproduction of
cephalosporinase when ampC and ampR were provided from
Enterobacter cloacae due to the build-up of anhMurNAc-pentapeptide
in the cytoplasm |CITS:[2607970],[9333034]|. Deletion from E. coli of
ampD and ampE resulted in overexpression of AmpC β-lactamase
when ampC and ampR were provided from Citrobacter freundii |CITS:[2691840]|.
In an ampD mutant, N-acetylmuramyl-L-alanyl-D-glutamylmesodiaminopimelic
acid accumulates in the periplasm |CITS: [8878601]|.
Review: |CITS:[8452343]|)""",]},
'B0112' : {'ecocyc-rxns': {"""TRANS-RXN-76""": """L-tryptophan[periplasmic space] + H+[periplasmic space] =L-tryptophan[cytosol] + H+[cytosol] ""","""TRANS-RXN-77""": """H+[periplasmic space] + L-tyrosine[periplasmic space] =H+[cytosol] + L-tyrosine[cytosol] ""","""TRANS-RXN-56""": """H+[periplasmic space] + L-phenylalanine[periplasmic space] =H+[cytosol] + L-phenylalanine[cytosol] """,},'ucsd-rxns' : ['PHEt2rpp','TYRt2rpp','TRPt2rpp','HISt2rpp',], 'protein-comments' : ["""(AroP is an aromatic amino acid permease that is a member of the APC Superfamily of transporters |CITS: [99107637]|.
AroP is referred to as the general aromatic amino acid permease because it is responsible for the transport
of all three aromatic amino acids, phenylalanine, tyrosine, and tryptophan, across the inner membrane
|CITS: [97294474]|. Based on the hydrophobicity profile and distribution of charged amino acid residues,
AroP was shown to have 12 membrane-spanning regions connected by hydrophilic loops
|CITS: [97294474]|. This topographical model is very similar to that reported for the PheP permease,
a phenylalanine-specific transporter, which has 61% amino acid sequence identity with the AroP
permease |CITS: [20200359]|. However, despite their high degree of sequence similarity, their substrate
specificities and affinities differ. A series of AroP-PheP chimeric proteins were made using in vivo
recombination, and their respective substrate profiles and activities were analyzed |CITS: [20200359]|.
The AroP protein was found to transport each of the aromatic amino acids with a Km of
1 μM |CITS: [20200359]|. Wild-type AroP and chimeras that are predominantly AroP exhibited the
ability to transport both phenylalanine and tryptophan to the same steady-state levels, and transport
tyrosine to almost doubling steady-state levels |CITS: [20200359]|. Site directed mutagenisis of the chimera
and AroP has established that a key residue involved in tryptophan transport is tyrosine at position 103 in
AroP |CITS: [20200359]|. Studies with uncouplers of oxidative phosphorylation and with strains deficient in
F0F1-ATPase indicate that transport via the AroP system is driven by the proton
motive force |CITS: [20200359]|. Expression of aroP is subject to regulation involving the TyrR
protein |CITS: [20200359]|.)""",]},
'B0062' : {'ecocyc-rxns': {"""ARABISOM-RXN""": """L-arabinose = L-ribulose""",},'ucsd-rxns' : ['ARAI',], 'protein-comments' : ["""NIL""","""(The subunits are arranged in a stack of two trimers. |CITS:
[78171523]|)""",]},
'B1468' : {'ecocyc-rxns': {"""RXN0-3501""": """menaquinol + NO3- -> menaquinone-8 + nitrite + H2O""",},'ucsd-rxns' : ['NO3R2pp','NO3R1pp',], 'protein-comments' : ["""(The α subunit is the actual site of nitrate reduction and also contains the molybdenum cofactor
|CITS: [92186712]|.
)""","""(E. coli contains three nitrate reductases. Two of them, nitrate reductase A (NRA) and nitrate reductase Z
(NRZ), are membrane bound and biochemically similar. The third nitrate reductase, Nap, is located in the periplasm.
Nitrate reductase A is expressed when levels of nitrate in the environment are high, Nap is expressed when they are
low, while NRZ expression is not dependent on nitrate levels or anaerobiosis. During entry into stationary phase,
transcription of the narZYWV operon is induced, and induction is mainly dependent on the alternative sigma
factor RpoS |CITS: [10564515]|.
By homology whith nitrate reductase A, nitrate reductase Z is a heterotrimer composed of the α-, β- and
γ chains. A fourth polypeptide, encoded by the narW gene, is required for the incorporation of the
molybdenum cofactor into NarZ, the α subunit |CITS: [91042410] [92186712]|.
)""",]},
'B1740' : {'ecocyc-rxns': {"""NAD-SYNTH-GLN-RXN""": """ATP + deamido-NAD + L-glutamine + H2O = AMP + diphosphate + NAD+ + L-glutamate""","""NAD-SYNTH-NH3-RXN""": """ATP + deamido-NAD + ammonia = AMP + diphosphate + NAD+""",},'ucsd-rxns' : ['NADS1',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B1747' : {'ecocyc-rxns': {"""ARGININE-N-SUCCINYLTRANSFERASE-RXN""": """L-arginine + succinyl-CoA = N2-succinyl-L-arginine + coenzyme A""",},'ucsd-rxns' : ['AST',], 'protein-comments' : ["""(The subunit structure has not been determined.)""",]},
'B1746' : {'ecocyc-rxns': {"""SUCCGLUALDDEHYD-RXN""": """N2-succinyl-L-glutamate 5-semialdehyde + NAD+ + H2O = N2-succinylglutamate + NADH""",},'ucsd-rxns' : ['SGSAD',], 'protein-comments' : ["""(A high-throughput screen of purified proteins showed that AstD is an aldehyde dehydrogenase with broad substrate
specificity. The enzyme is active with NAD, but not NADP, as the electron acceptor |CITS: [15808744]|.
Succinylglutamic semialdehyde dehydrogenase catalyzes the fourth reaction in the ammonia-producing arginine
catabolic pathway |CITS: [98361920]|.
The enzymes of the AST pathway (|FRAME: AST-PWY|) are regulated by nitrogen |CITS: [98361920]|.)""",]},
'B1745' : {'ecocyc-rxns': {"""SUCCARGDIHYDRO-RXN""": """N2-succinyl-L-arginine + 2 H2O = N2-succinyl-L-ornithine + 2 ammonia + CO2""",},'ucsd-rxns' : ['SADH',], 'protein-comments' : ["""(The subunit structure has not been determined.)""",]},
'B3432' : {'ecocyc-rxns': {"""GLYCOGEN-BRANCH-RXN""": """a 1,4-α-D-glucan = a glycogen""",},'ucsd-rxns' : ['GLBRAN2',], 'protein-comments' : ["""(Gycogen branching enzyme catalyzes the formation of the branched α-1,6-glucosidic linkages from the
growing polyglucose chain during glycogen biosynthesis.
Biochemical studies of the enzyme have been performed using E. coli B |CITS: [407932]|.
Gycogen branching enzyme has a preference for transferring chains between 5 and 16 glucose units. The minimum
chain length required for branching is 12 |CITS: [9185617]|. Truncation of the amino terminus alters the branching
pattern |CITS: [11795883][13679080]|.
The Glu459 residue is important for specific activity and substrate specificity of the enzyme |CITS: [9636047]|, and the
Tyr300 residue is required for enzymatic activity and thermostability |CITS: [11368019]|.
A crystal structure of the enzyme has been solved at 2.3 Å resolution. The structure of the central domain,
containing the active site, is similar to other amylase family enzymes |CITS: [12196524]|.)""",]},
'B0692' : {'ecocyc-rxns': {"""TRANS-RXN-69""": """H+[periplasmic space] + putrescine[periplasmic space] =H+[cytosol] + putrescine[cytosol] """,},'ucsd-rxns' : ['PTRCt2pp','PTRCORNt7pp',], 'protein-comments' : ["""(PotE is a putrescine transporter that is a member of the Amino Acid-Polyamine-Organocation (APC)
Superfamily of transporters |CITS: [20391827]|. In mutational experiments, where all other spermidine and
putrescine uptake systems (PotABCD and PotFGHI) were lacking, PotE was found to catalyze uptake of
putrescine via a proton symport mechanism with a Km value of 1.8 μM |CITS: [97197801]|.
In experiments examining PotE function and putrescine uptake in inside-out membrane vesicles, PotE was
also found to catalyze putrescine efflux by a putrescine/ornithine antiport system in a 1:1 ratio. The
Km for the antiporter activities of putrescine and ornithine were 73 μM and 108 μM,
respectively |CITS: [97197801]|. Uptake was not disturbed by KCN or CCCP, indicating that the process is not
driven by ATP hydrolysis of the proton motive force |CITS: [92262473]|. There is also evidence of
putrescine/putrescine and ornithine/ornithine antiport. This is supported by experiments where CCCP is used
to disable putrescine uptake and the addition of putrescine or ornithine results in rapid efflux of putrescine
from the cell |CITS: [92262473]|. Hydropathy analysis, PhoA fusions, and B-gal fusions suggest a 12
transmembrane sugment topoloty |CITS: [97197801]|. Site directed mutagenesis has implicated the residue E7,
207 or 433 as important for the uptake of putrescine |CITS: [97197801]|.)""",]},
'B0693' : {'ecocyc-rxns': {"""ORNDECARBOX-RXN""": """L-ornithine = CO2 + putrescine""",},'ucsd-rxns' : ['ORNDC',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B1748' : {'ecocyc-rxns': {"""ACETYLORNTRANSAM-RXN""": """N-acetyl-L-ornithine + α-ketoglutarate = N-acetyl-L-glutamate 5-semialdehyde + L-glutamate""","""SUCCORNTRANSAM-RXN""": """N2-succinyl-L-ornithine + α-ketoglutarate = N2-succinyl-L-glutamate 5-semialdehyde + L-glutamate""",},'ucsd-rxns' : ['SOTA','ACOTA',], 'protein-comments' : ["""(The astC gene product is 60% identical to the argD gene product.
|CITS: [98361920]|)""","""NIL""",]},
'B1466' : {'ecocyc-rxns': {},'ucsd-rxns' : ['NO3R2pp','NO3R1pp',], 'protein-comments' : ["""(The polypeptide encoded by narW, the third gene in the narZYWV operon, is not part of the final
nitrate reductase Z enzyme. By similarity to NarJ, it may act as a private chaperone during the incorporation of the
molybdenum cofactor into NarZ, the α subunit of nitrate reductase Z |CITS: [92186712]|.
)""",]},
'B1467' : {'ecocyc-rxns': {"""RXN0-3501""": """menaquinol + NO3- -> menaquinone-8 + nitrite + H2O""",},'ucsd-rxns' : ['NO3R2pp','NO3R1pp',], 'protein-comments' : ["""(The β subunit is the electron transfer subunit containing the iron-sulfur clusters |CITS: [92186712]|.)""","""(E. coli contains three nitrate reductases. Two of them, nitrate reductase A (NRA) and nitrate reductase Z
(NRZ), are membrane bound and biochemically similar. The third nitrate reductase, Nap, is located in the periplasm.
Nitrate reductase A is expressed when levels of nitrate in the environment are high, Nap is expressed when they are
low, while NRZ expression is not dependent on nitrate levels or anaerobiosis. During entry into stationary phase,
transcription of the narZYWV operon is induced, and induction is mainly dependent on the alternative sigma
factor RpoS |CITS: [10564515]|.
By homology whith nitrate reductase A, nitrate reductase Z is a heterotrimer composed of the α-, β- and
γ chains. A fourth polypeptide, encoded by the narW gene, is required for the incorporation of the
molybdenum cofactor into NarZ, the α subunit |CITS: [91042410] [92186712]|.
)""",]},
'B1465' : {'ecocyc-rxns': {"""RXN0-3501""": """menaquinol + NO3- -> menaquinone-8 + nitrite + H2O""",},'ucsd-rxns' : ['NO3R2pp','NO3R1pp',], 'protein-comments' : ["""(The γ subunit is a membrane-embedded heme-iron subunit resembling cytochrome b, which transfers
electrons from the quinone pool to the β subunit |CITS: [91042410]|.)""","""(E. coli contains three nitrate reductases. Two of them, nitrate reductase A (NRA) and nitrate reductase Z
(NRZ), are membrane bound and biochemically similar. The third nitrate reductase, Nap, is located in the periplasm.
Nitrate reductase A is expressed when levels of nitrate in the environment are high, Nap is expressed when they are
low, while NRZ expression is not dependent on nitrate levels or anaerobiosis. During entry into stationary phase,
transcription of the narZYWV operon is induced, and induction is mainly dependent on the alternative sigma
factor RpoS |CITS: [10564515]|.
By homology whith nitrate reductase A, nitrate reductase Z is a heterotrimer composed of the α-, β- and
γ chains. A fourth polypeptide, encoded by the narW gene, is required for the incorporation of the
molybdenum cofactor into NarZ, the α subunit |CITS: [91042410] [92186712]|.
)""",]},
'B0494' : {'ecocyc-rxns': {"""LYSOPHOSPHOLIPASE-RXN""": """a 2-acyl-sn-glycero-3-phosphocholine + H2O = a carboxylate + L-1-glycero-3-phosphocholine""","""THIOESTER-RXN""": """an acyl-CoA + H2O -> a fatty acid + coenzyme A""",},'ucsd-rxns' : ['LPLIPAL1E161pp','LPLIPAL1E120pp','LPLIPAL1A120pp','LPLIPAL1G161pp','LPLIPAL1A160pp','LPLIPAL1G180pp','LPLIPAL1A161pp','LPLIPAL1G140pp','LPLIPAL1E180pp','LPLIPAL1E140pp','LPLIPAL1G181pp','LPLIPAL1G160pp','LPLIPAL1G141pp','LPLIPAL1E181pp','LPLIPAL1A180pp','LPLIPAL1E141pp','LPLIPAL1G120pp','LPLIPAL1A140pp','LPLIPAL1A141pp','LPLIPAL1E160pp','LPLIPAL1A181pp',], 'protein-comments' : ["""NIL""",]},
'B3519' : {'ecocyc-rxns': {"""TREHALA-RXN""": """trehalose + H2O = 2 β-D-glucose""",},'ucsd-rxns' : ['TREH',], 'protein-comments' : ["""(The subunit structure of the cytoplasmic trehalase has not
been determined.)""",]},
'B0756' : {'ecocyc-rxns': {"""ALDOSE1EPIM-RXN""": """β-D-galactose = α-D-galactose""",},'ucsd-rxns' : ['GALM2pp',], 'protein-comments' : ["""NIL""",]},
'B0185' : {'ecocyc-rxns': {"""ACETYL-COA-CARBOXYLTRANSFER-RXN""": """ATP + acetyl-CoA + HCO3- + H+ = malonyl-CoA + phosphate + ADP""","""RXN0-5055""": """acetyl-CoA + carboxy-biotin-BCCP = malonyl-CoA + a biotin-BCCP (dimer)""",},'ucsd-rxns' : ['ACCOAC',], 'protein-comments' : ["""NIL""","""NIL""","""NIL""","""(The enzyme |FRAME:ACETYL-COA-CARBOXYLMULTI-CPLX| is one of the key enzymes in the
biosynthesis of fatty acids (see |FRAME: FASYN-INITIAL-PWY|).
The enzyme belongs to the family of enzymes that catalyze
the intermolecular transfer of carboxyl groups via the transient formation of a carboxyphosphate
intermediate covalently linked to a biotin prosthetic group |CITS: [15749055]|.
The E. coli enzyme complex is composed of two catalytic units and one carrier protein,
encoded by four different genes.
The catalytic units are |FRAME:BIOTIN-CARBOXYL-CPLX| (BC), a homodimer encoded by the
|FRAME: EG10276| gene, and |FRAME:ACETYL-COA-CARBOXYLMULTI-CPLX| (ACCT), an
α2β2 tetramer, encoded by the |FRAME:EG11647| and
|FRAME: EG10217| genes.
The carrier protein is the |FRAME:BCCP-CPLX| (BCCP), a homodimer encoded by the |FRAME:EG10275| gene.
The BCCP monomer is biotinylated by the enzyme |FRAME:BIOTINLIG-ENZRXN|.
Following dimerization of the biotinylated monomers, |FRAME:BIOTIN-CARBOXYL-CPLX| (BC) catalyzes the addition
of |FRAME: CARBON-DIOXIDE| to the carrier protein dimer, forming |FRAME:Carboxybiotin-BCCP| (carboxy-BCCP).
|FRAME:Carboxybiotin-BCCP|
in turn is the substrate for ACCT, which transfers the carboxy group to |FRAME:ACETYL-COA|,
resulting in the formation of |FRAME:MALONYL-COA| and the regeneration of |FRAME:BCCP-CPLX|.
Both biotinylation and carboxylation of the carrier protein require ATP, while the last step, transfer of the carboxy
group to |FRAME: ACETYL-COA|, does not |CITS: [15749055]|.)""",]},
'B2893' : {'ecocyc-rxns': {"""5.3.4.1-RXN""": """a protein with incorrect disulfide bonds = a protein with correct disulfide bonds""","""DISULFOXRED-RXN""": """a protein with reduced sulfide groups = a protein with oxidized disulfide bonds""",},'ucsd-rxns' : ['TDSR1','DSBCGT',], 'protein-comments' : ["""NIL""","""NIL""","""NIL""",]},
'B2890' : {'ecocyc-rxns': {"""LYSINE--TRNA-LIGASE-RXN""": """L-lysine + tRNAlys + ATP = L-lysyl-tRNAlys + diphosphate + AMP""",},'ucsd-rxns' : ['LYSTRS',], 'protein-comments' : ["""(The lysyl-tRNA synthetase LysS is a member of the family of aminoacyl tRNA synthetases, which interpret the genetic
code by covalently linking amino acids to their specific tRNA molecules. The reaction is driven by ATP hydrolysis.
LysS belongs to the subclass IIb of aminoacyl tRNA synthetases. E. coli contains both a constitutive and an
inducible lysyl tRNA synthetase; lysS encodes the constitutively expressed enzyme.
Key residues for recognition of the cognate amino acid and catalytic activity have been identified |CITS: [15362869]|,
providing insight into differences between the class I and class II tRNA synthetases. A model for the
recognition specificity of the cognate anticodon is presented |CITS: [9614943]|.
Under aerobic conditions and at growth temperatures below 37 degrees C, LysS is required for normal growth
|CITS: [1744045]|; the growth defect can be suppressed by overexpression of lysU, the gene encoding the
inducible lysyl tRNA synthetase |CITS: [1321323]|.
Solution structures |CITS: [7473706]| and a crystal structure |CITS: [11041850]| of LysS are presented, revealing
reorganization of the active site upon lysine binding.
Reviews: |CITS: [7934813][7576245]|)""","""NIL""",]},
'B1768' : {'ecocyc-rxns': {"""PYRAZIN-RXN""": """pyrazinamide + H2O = pyrazinoate + ammonia""","""NICOTINAMID-RXN""": """nicotinamide + H2O = nicotinate + ammonia""",},'ucsd-rxns' : ['NNAM',], 'protein-comments' : ["""(The subunit structure is not known.)""",]},
'B2895' : {'ecocyc-rxns': {},'ucsd-rxns' : ['RNTR3c','RNTR3c','FLDR','RNTR4c','RNTR4c','RNTR1c','RNTR1c','RNTR2c','RNTR2c',], 'protein-comments' : ["""(Flavodoxins are small, acidic electron transfer proteins
which contain FMN as a prosthetic group. They are only able to accept
and donate electrons. Flavodoxin is an important member of the
multi-enzyme complexes that are involved in the activation of
anaerobic nucleoside reductase and pyruvate-formate lyase. Flavodoxins
are functionally interchangeable with ferredoxins but some enzymes are
specific for one or the other. E. coli has at least two flavodoxins.
|CITS: [91154129] [95050480] [93194782]|)""","""NIL""",]},
'B0088' : {'ecocyc-rxns': {"""UDP-NACMURALA-GLU-LIG-RXN""": """D-glutamate + UDP-N-acetylmuramoyl-L-alanine + ATP = UDP-N-acetylmuramoyl-L-alanyl-D-glutamate + phosphate + ADP""",},'ucsd-rxns' : ['UAMAGS',], 'protein-comments' : ["""NIL""",]},
'B3627' : {'ecocyc-rxns': {"""RXN0-5125""": """galactosyl-glucosyl-heptosyl3-KDO2-lipid A-bisphosphate + UDP-D-glucose = galactosyl-glucosyl2-heptosyl3-KDO2-lipid A-bisphosphate + UDP""",},'ucsd-rxns' : ['GLCTR2',], 'protein-comments' : ["""(The lipopolysaccharide of E. coli K-12 consists of two major components:
the hydrophobic lipid A moiety inserted into the outer membrane and the
phosphorylated core oligosaccharide |CITS:[12045108]|. E. coli K-12
does not produce O antigen to attach to the LPS core due to a defect in the
rfb gene cluster which can be complemented with genes from a second,
independent rfb mutant to produce an O16 type O antigen |CITS:[7517391]|.
E. coli K-12 may have two major pathways for LPS biosynthesis. One
generates LPS cores suitable for O antigen attachment, and a second generates
lipooligosaccharides (LOS) with modifications to the core structure which prevent
O antigen attachment |CITS:[1385388]|.
WaaO adds the second glucose (GlcII) to the first glucose (GlcI) of the outer core of LPS |CITS:[1624461]|.
Activity of WaaO requires a functional waaB gene |CITS:[1624461]|.
Reviews: |CITS:[12045108],[9791168],[7504166]|)""",]},
'B2203' : {'ecocyc-rxns': {"""RXN0-2081""": """ubiquinol-10 + NO3- = ubiquinone-10 + nitrite + H2O""","""RXN0-3501""": """menaquinol + NO3- -> menaquinone-8 + nitrite + H2O""",},'ucsd-rxns' : ['NO3R1bpp','NO3R2bpp',], 'protein-comments' : ["""(The napB gene encodes the diheme cytochrome c550 protein which is complexed with NapA in
the periplasm; it receives electrons from the membrane-bound proteins and passes them to NapA.
|CITS: [8039676] [96439840] [96228696] [97078524]|)""","""NIL""","""(E. coli contains three nitrate reductases. Two of them, nitrate reductase A (NRA) and nitrate reductase Z
(NRZ), are membrane bound and biochemically similar. The third nitrate reductase, Nap, is located in the periplasm.
It is induced by anaerobiosis through the mediation of the transcription factor Fnr and low concentrations of nitrate
through the mediation of NarP |CITS: [12029041]|. Nap is not itself a coupling site for generating proton motive force;
acting as a terminal electron acceptor, it does support anaerobic respiration of various carbon sources
|CITS: [11844760]|.
The physiological role of Nap is that of mediating anaerobic respiration at the expense of low concentrations of nitrate.
Owing to the periplasmic location of Nap, the cost of pumping nitrate into the cell is avoided. In addition, Nap has a
significantly higher affinity for nitrate than NRA and is thus able to exploit the low concentrations of nitrate occuring in
the natural environment of E. coli |CITS: [10548536]|. Notably, several pathogenic bacterial species, such as
Haemophilus influenzae, only contain orthologs of the periplasmic nitrate reductase |CITS: [10548536]|. During
glucose fermentation in the absence of menaquinone, a very low level of Nap activity appears to substitute for the
redox-balancing role of fumarate reductase, which is dependent on menaquinone |CITS: [14674886]|.
The nap operon encodes seven proteins. The catalytic portion of the protein, consisting of the periplasmic NapA and
NapB polypeptides, receives electrons via the membrane-bound cytochrome NapC from NapGH or directly from the
quinone pool. The NapD polypeptide is required for enzyme activity and is thought to be involved in the
post-translational assembly of the molybdoprotein NapA. NapF, NapG and NapH are predicted to encode
iron-sulfur proteins and are not required for Nap activity; they do, however, contribute to the maximum rate of nitrate
reduction. NapG and NapH facilitate electron transfer from ubiquinol via NapC to NapAB.
|CITS: [14674886] [11967083] [20018017] [97078524] [96228696] [96439840] [94314186]|)""","""(E. coli contains three nitrate reductases. Two of them, nitrate reductase A (NRA) and nitrate reductase Z
(NRZ), are membrane bound and biochemically similar. The third nitrate reductase, Nap, is located in the periplasm.
It is induced by anaerobiosis through the mediation of the transcription factor Fnr and low concentrations of nitrate
through the mediation of NarP |CITS: [12029041]|. Nap is not itself a coupling site for generating proton motive force;
acting as a terminal electron acceptor, it does support anaerobic respiration of various carbon sources
|CITS: [11844760]|.
The physiological role of Nap is that of mediating anaerobic respiration at the expense of low concentrations of nitrate.
Owing to the periplasmic location of Nap, the cost of pumping nitrate into the cell is avoided. In addition, Nap has a
significantly higher affinity for nitrate than NRA and is thus able to exploit the low concentrations of nitrate occuring in
the natural environment of E. coli |CITS: [10548536]|. Notably, several pathogenic bacterial species, such as
Haemophilus influenzae, only contain orthologs of the periplasmic nitrate reductase |CITS: [10548536]|. During
glucose fermentation in the absence of menaquinone, a very low level of Nap activity appears to substitute for the
redox-balancing role of fumarate reductase, which is dependent on menaquinone |CITS: [14674886]|.
The nap operon encodes seven proteins. The catalytic portion of the protein, consisting of the periplasmic NapA and
NapB polypeptides, receives electrons via the membrane-bound cytochrome NapC from NapGH or directly from the
quinone pool. The NapD polypeptide is required for enzyme activity and is thought to be involved in the
post-translational assembly of the molybdoprotein NapA. NapF, NapG and NapH are predicted to encode
iron-sulfur proteins and are not required for Nap activity; they do, however, contribute to the maximum rate of nitrate
reduction. NapG and NapH facilitate electron transfer from ubiquinol via NapC to NapAB.
|CITS: [14674886] [11967083] [20018017] [97078524] [96228696] [96439840] [94314186]|)""",]},
'B2202' : {'ecocyc-rxns': {"""RXN0-2081""": """ubiquinol-10 + NO3- = ubiquinone-10 + nitrite + H2O""","""RXN0-3501""": """menaquinol + NO3- -> menaquinone-8 + nitrite + H2O""",},'ucsd-rxns' : ['NO3R1bpp','NO3R2bpp',], 'protein-comments' : ["""(The napC gene encodes a membrane-bound tetraheme cytochrome c protein, which passes electrons either
from NapGH or directly from the quinone pool to NapB. |CITS: [8039676] [96439840] [96228696] [97078524]
[14674886]|)""","""(E. coli contains three nitrate reductases. Two of them, nitrate reductase A (NRA) and nitrate reductase Z
(NRZ), are membrane bound and biochemically similar. The third nitrate reductase, Nap, is located in the periplasm.
It is induced by anaerobiosis through the mediation of the transcription factor Fnr and low concentrations of nitrate
through the mediation of NarP |CITS: [12029041]|. Nap is not itself a coupling site for generating proton motive force;
acting as a terminal electron acceptor, it does support anaerobic respiration of various carbon sources
|CITS: [11844760]|.
The physiological role of Nap is that of mediating anaerobic respiration at the expense of low concentrations of nitrate.
Owing to the periplasmic location of Nap, the cost of pumping nitrate into the cell is avoided. In addition, Nap has a
significantly higher affinity for nitrate than NRA and is thus able to exploit the low concentrations of nitrate occuring in
the natural environment of E. coli |CITS: [10548536]|. Notably, several pathogenic bacterial species, such as
Haemophilus influenzae, only contain orthologs of the periplasmic nitrate reductase |CITS: [10548536]|. During
glucose fermentation in the absence of menaquinone, a very low level of Nap activity appears to substitute for the
redox-balancing role of fumarate reductase, which is dependent on menaquinone |CITS: [14674886]|.
The nap operon encodes seven proteins. The catalytic portion of the protein, consisting of the periplasmic NapA and
NapB polypeptides, receives electrons via the membrane-bound cytochrome NapC from NapGH or directly from the
quinone pool. The NapD polypeptide is required for enzyme activity and is thought to be involved in the
post-translational assembly of the molybdoprotein NapA. NapF, NapG and NapH are predicted to encode
iron-sulfur proteins and are not required for Nap activity; they do, however, contribute to the maximum rate of nitrate
reduction. NapG and NapH facilitate electron transfer from ubiquinol via NapC to NapAB.
|CITS: [14674886] [11967083] [20018017] [97078524] [96228696] [96439840] [94314186]|)""","""(E. coli contains three nitrate reductases. Two of them, nitrate reductase A (NRA) and nitrate reductase Z
(NRZ), are membrane bound and biochemically similar. The third nitrate reductase, Nap, is located in the periplasm.
It is induced by anaerobiosis through the mediation of the transcription factor Fnr and low concentrations of nitrate
through the mediation of NarP |CITS: [12029041]|. Nap is not itself a coupling site for generating proton motive force;
acting as a terminal electron acceptor, it does support anaerobic respiration of various carbon sources
|CITS: [11844760]|.
The physiological role of Nap is that of mediating anaerobic respiration at the expense of low concentrations of nitrate.
Owing to the periplasmic location of Nap, the cost of pumping nitrate into the cell is avoided. In addition, Nap has a
significantly higher affinity for nitrate than NRA and is thus able to exploit the low concentrations of nitrate occuring in
the natural environment of E. coli |CITS: [10548536]|. Notably, several pathogenic bacterial species, such as
Haemophilus influenzae, only contain orthologs of the periplasmic nitrate reductase |CITS: [10548536]|. During
glucose fermentation in the absence of menaquinone, a very low level of Nap activity appears to substitute for the
redox-balancing role of fumarate reductase, which is dependent on menaquinone |CITS: [14674886]|.
The nap operon encodes seven proteins. The catalytic portion of the protein, consisting of the periplasmic NapA and
NapB polypeptides, receives electrons via the membrane-bound cytochrome NapC from NapGH or directly from the
quinone pool. The NapD polypeptide is required for enzyme activity and is thought to be involved in the
post-translational assembly of the molybdoprotein NapA. NapF, NapG and NapH are predicted to encode
iron-sulfur proteins and are not required for Nap activity; they do, however, contribute to the maximum rate of nitrate
reduction. NapG and NapH facilitate electron transfer from ubiquinol via NapC to NapAB.
|CITS: [14674886] [11967083] [20018017] [97078524] [96228696] [96439840] [94314186]|)""",]},
'B2201' : {'ecocyc-rxns': {"""TRANS-RXN0-162""": """protoheme IX[cytosol] + ATP + H2O =phosphate + ADP + protoheme IX[periplasmic space] """,},'ucsd-rxns' : ['PHEMEabcpp',], 'protein-comments' : ["""(ccmA is a member of an operon whose gene products (CcmA-H) have been shown to be cytoplasmic membrane proteins required for cytochrome c maturation |CITS:[7635817]|. Sequence similarity and the presence of an ATP-binding motif indicate that CcmA is an ATP-binding member of the ATP-binding cassette (ABC) transporter family |CITS:[10339610]| and is thought to form an ABC transporter CcmAB. The substrate for the putative ABC transporter, CcmAB, is unknown. Heme transport across the cytoplasmic membrane has been shown to occur in the absence of ATP |CITS:[10708391]| and deletion mutation studies suggest that heme transport into the periplasm occurs independently of the putative CcmAB transporter |CITS:[10339610]|.)""","""(The CcmABC (Cytochrome C Maturation proteins) putative transporter is a member of the ATP-Binding
Cassette (ABC) transporter superfamily |CITS: [98254124]|. Sequence analysis suggest that CcmA is the
ATP binding subunit and occurs as a homodimer and CcmB and CcmC are transmembrane domains.
CcmABC has been proposed to function as a heme exporter, which exports heme to the periplasm where it
is incorporated into cytochrome c apoproteins |CITS: [97438699]|. However, CcmC has been shown
to function independently and is essential for heme attachment to CcmE, a periplasmic heme chaperone,
that binds heme covalently in the periplasm and then acts as a heme donor for ligation to apocytochrome
c |CITS:[99272716]|. Analysis of a ccmA deletion mutant has suggested that CcmAB is not
essential for heme export |CITS: [20170685]|.)""","""(Type c cytochrome in Escherichia coli is only synthesized during anaerobic growth conditions |CITS:[8039676]|. CcmA-H in E. coli are cytoplasmic membrane proteins which together make up a type 1 cytochrome c biogenesis system |CITS:[7635817]|. All eight proteins have been shown to be required for cytochrome c maturation |CITS:[8830238]|, |CITS:[7635817]|. In cytochrome c biogenesis, apocytochrome c, is translocated across the cytoplasmic membrane into the periplasm through the sec secretion system |CITS:[9720859]| where it complexes with heme, also transported across the cytoplasmic membrane. While CcmA and CcmB have been shown to constitute an ABC transporter, and are required for proper cytochrome c maturation, they have not been shown to be required for heme transport |CITS:[10708391]|. An intramolecular disulfide bond in the apocyctochrome c must be reduced in order for the covalent attachment of heme cofactor to occur. CcmG and CcmH have been identified as having the characteristic C-X-X-C motif of oxidoreductases and to function in the redox pathway of cytochrome c maturation |CITS:[10841975]|, |CITS:[9914305]|. CcmE acts as a periplasmic heme chaperone, binding heme covalently and transferring it to apocytochrome c |CITS:[10339610]|. Heme binding to CcmE is dependent on the presence of CcmC while the small integral membrane protein CcmD has been shown to play a role in CcmE stabilization |CITS:[10339610]|. Results of mutation deletion studies suggest that a periplasmically-situated hydrophobic surface of CcmC binds heme and presents it to CcmE in the periplasm |CITS:[10998170]|. Studies of ccmD deletion mutants have shown that CcmD affects the level of CcmE in the cytoplasmic membrane and is critical for CcmE function |CITS:[10998170]|. Deletion mutation and immunoprecipitation studies suggest that CcmE shuttles between CcmC and CcmF for heme transfer to apocytochrome c |CITS:[14532274]|.)""",]},
'B0978' : {'ecocyc-rxns': {"""CYT-UBIQUINOL-OXID-RXN""": """ubiquinol-8 + O2 = ubiquinone-8 + 2 H2O""",},'ucsd-rxns' : ['CYTBDpp','CYTBD2pp',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B1124' : {'ecocyc-rxns': {"""ABC-25-RXN""": """ATP + putrescine[periplasmic space] + H2O =ADP + phosphate + putrescine[cytosol] ""","""ABC-24-RXN""": """ATP + spermidine[periplasmic space] + H2O =ADP + phosphate + spermidine[cytosol] """,},'ucsd-rxns' : ['PTRCabcpp','SPMDabcpp',], 'protein-comments' : ["""NIL""","""(PotABCD is an ATP-dependent polyamine transporter that is a member of the ATP-Binding
Cassette (ABC) Superfamily of transporters |CITS: [20053876]|. The transporter consists of a membrane
associated ATPase (PotA), two transmembrane proteins (PotB and PotC), and a periplasmic
substrate-binding protein (PotD) |CITS: [20053876]|. Knockout mutants in each of the four genes indicated
that they are all required for polyamine transport |CITS: [93374918] [20053876]|. PotA has been purified to homogeneity
and was shown to have magnesium and spermidine-dependent ATPase activity, with a Km
of 385 μM for ATP |CITS: [96029616] [20053876]|. Based on hydropathy analysis and sequence similarity, PotB and
PotC are the membrane components of the ABC transporter |CITS: [20053876]|. PotD is the periplasmic
substrate-binding protein that acts to recognize and facilitate the transport of the polyamines
|CITS: [20053876] [99315781]|. PotD preferentially binds spermidine, but will also bind putrescine with a lower affinity
(Km values of 0.1 μM and 1.5 μM for spermidine and putrescine, respectively |CITS: [20053876]|).
The dissociation constant for the binding of spermidine by PotD was found to be 3.2 μM
with an optimal spermidine concentration of 5-10 μM |CITS: [93374918]|. X-ray crystallography of
PotD showed that it has two domains with β-α -β topology, with four
acidic residues, used to recognize the positively charged nitrogen atoms of the spermidine
substrate, located in the central cleft between the two domains |CITS: [20053876] [99318982]|.
)""",]},
'B2206' : {'ecocyc-rxns': {"""RXN0-2081""": """ubiquinol-10 + NO3- = ubiquinone-10 + nitrite + H2O""","""RXN0-3501""": """menaquinol + NO3- -> menaquinone-8 + nitrite + H2O""",},'ucsd-rxns' : ['NO3R1bpp','NO3R2bpp',], 'protein-comments' : ["""(The napA gene encodes the periplasmic nitrate reductase molybdoprotein with an
Fe-S center. |CITS: [96228696] [97078524]|)""","""NIL""","""(E. coli contains three nitrate reductases. Two of them, nitrate reductase A (NRA) and nitrate reductase Z
(NRZ), are membrane bound and biochemically similar. The third nitrate reductase, Nap, is located in the periplasm.
It is induced by anaerobiosis through the mediation of the transcription factor Fnr and low concentrations of nitrate
through the mediation of NarP |CITS: [12029041]|. Nap is not itself a coupling site for generating proton motive force;
acting as a terminal electron acceptor, it does support anaerobic respiration of various carbon sources
|CITS: [11844760]|.
The physiological role of Nap is that of mediating anaerobic respiration at the expense of low concentrations of nitrate.
Owing to the periplasmic location of Nap, the cost of pumping nitrate into the cell is avoided. In addition, Nap has a
significantly higher affinity for nitrate than NRA and is thus able to exploit the low concentrations of nitrate occuring in
the natural environment of E. coli |CITS: [10548536]|. Notably, several pathogenic bacterial species, such as
Haemophilus influenzae, only contain orthologs of the periplasmic nitrate reductase |CITS: [10548536]|. During
glucose fermentation in the absence of menaquinone, a very low level of Nap activity appears to substitute for the
redox-balancing role of fumarate reductase, which is dependent on menaquinone |CITS: [14674886]|.
The nap operon encodes seven proteins. The catalytic portion of the protein, consisting of the periplasmic NapA and
NapB polypeptides, receives electrons via the membrane-bound cytochrome NapC from NapGH or directly from the
quinone pool. The NapD polypeptide is required for enzyme activity and is thought to be involved in the
post-translational assembly of the molybdoprotein NapA. NapF, NapG and NapH are predicted to encode
iron-sulfur proteins and are not required for Nap activity; they do, however, contribute to the maximum rate of nitrate
reduction. NapG and NapH facilitate electron transfer from ubiquinol via NapC to NapAB.
|CITS: [14674886] [11967083] [20018017] [97078524] [96228696] [96439840] [94314186]|)""","""(E. coli contains three nitrate reductases. Two of them, nitrate reductase A (NRA) and nitrate reductase Z
(NRZ), are membrane bound and biochemically similar. The third nitrate reductase, Nap, is located in the periplasm.
It is induced by anaerobiosis through the mediation of the transcription factor Fnr and low concentrations of nitrate
through the mediation of NarP |CITS: [12029041]|. Nap is not itself a coupling site for generating proton motive force;
acting as a terminal electron acceptor, it does support anaerobic respiration of various carbon sources
|CITS: [11844760]|.
The physiological role of Nap is that of mediating anaerobic respiration at the expense of low concentrations of nitrate.
Owing to the periplasmic location of Nap, the cost of pumping nitrate into the cell is avoided. In addition, Nap has a
significantly higher affinity for nitrate than NRA and is thus able to exploit the low concentrations of nitrate occuring in
the natural environment of E. coli |CITS: [10548536]|. Notably, several pathogenic bacterial species, such as
Haemophilus influenzae, only contain orthologs of the periplasmic nitrate reductase |CITS: [10548536]|. During
glucose fermentation in the absence of menaquinone, a very low level of Nap activity appears to substitute for the
redox-balancing role of fumarate reductase, which is dependent on menaquinone |CITS: [14674886]|.
The nap operon encodes seven proteins. The catalytic portion of the protein, consisting of the periplasmic NapA and
NapB polypeptides, receives electrons via the membrane-bound cytochrome NapC from NapGH or directly from the
quinone pool. The NapD polypeptide is required for enzyme activity and is thought to be involved in the
post-translational assembly of the molybdoprotein NapA. NapF, NapG and NapH are predicted to encode
iron-sulfur proteins and are not required for Nap activity; they do, however, contribute to the maximum rate of nitrate
reduction. NapG and NapH facilitate electron transfer from ubiquinol via NapC to NapAB.
|CITS: [14674886] [11967083] [20018017] [97078524] [96228696] [96439840] [94314186]|)""",]},
'B2205' : {'ecocyc-rxns': {"""RXN0-2081""": """ubiquinol-10 + NO3- = ubiquinone-10 + nitrite + H2O""",},'ucsd-rxns' : ['NO3R1bpp',], 'protein-comments' : ["""(The napG gene encodes a non-haem iron-sulfur protein. |CITS: [96439840] [96228696] [97078524]|
NapG together with NapH is required for electron transfer from ubiquinol, but not menaquinol, via NapC to the NapAB
complex |CITS: [11967083][14674886]|. NapG contains a twin-arginine sequence which is essential for its function,
and some evidence for periplasmic localization of the protein has been obtained |CITS: [14674886]|.)""","""(Both NapG and NapH are required for efficient electron transfer from ubiquinol, but not menaquinol, via NapC to the
NapAB complex. NapGH acts as an alternative quinol dehydrogenase to NapC, which can utilize menaquinol directly
|CITS: [11967083][14674886]|.
No direct evidence for the formation of a NapGH complex has been obtained yet, but the available experimental data
is consistent with its existence |CITS: [14674886]|.)""","""(E. coli contains three nitrate reductases. Two of them, nitrate reductase A (NRA) and nitrate reductase Z
(NRZ), are membrane bound and biochemically similar. The third nitrate reductase, Nap, is located in the periplasm.
It is induced by anaerobiosis through the mediation of the transcription factor Fnr and low concentrations of nitrate
through the mediation of NarP |CITS: [12029041]|. Nap is not itself a coupling site for generating proton motive force;
acting as a terminal electron acceptor, it does support anaerobic respiration of various carbon sources
|CITS: [11844760]|.
The physiological role of Nap is that of mediating anaerobic respiration at the expense of low concentrations of nitrate.
Owing to the periplasmic location of Nap, the cost of pumping nitrate into the cell is avoided. In addition, Nap has a
significantly higher affinity for nitrate than NRA and is thus able to exploit the low concentrations of nitrate occuring in
the natural environment of E. coli |CITS: [10548536]|. Notably, several pathogenic bacterial species, such as
Haemophilus influenzae, only contain orthologs of the periplasmic nitrate reductase |CITS: [10548536]|. During
glucose fermentation in the absence of menaquinone, a very low level of Nap activity appears to substitute for the
redox-balancing role of fumarate reductase, which is dependent on menaquinone |CITS: [14674886]|.
The nap operon encodes seven proteins. The catalytic portion of the protein, consisting of the periplasmic NapA and
NapB polypeptides, receives electrons via the membrane-bound cytochrome NapC from NapGH or directly from the
quinone pool. The NapD polypeptide is required for enzyme activity and is thought to be involved in the
post-translational assembly of the molybdoprotein NapA. NapF, NapG and NapH are predicted to encode
iron-sulfur proteins and are not required for Nap activity; they do, however, contribute to the maximum rate of nitrate
reduction. NapG and NapH facilitate electron transfer from ubiquinol via NapC to NapAB.
|CITS: [14674886] [11967083] [20018017] [97078524] [96228696] [96439840] [94314186]|)""",]},
'B0945' : {'ecocyc-rxns': {"""DIHYDROOROTOX-RXN""": """O2 + dihydroorotate = H2O2 + orotate""",},'ucsd-rxns' : ['DHORD2','DHORD5',], 'protein-comments' : ["""NIL""","""(The enzyme is a membrane-bound flavoprotein.)""",]},
'B0340' : {'ecocyc-rxns': {"""4.3.99.1-RXN""": """HCO3- + cyanate = carbamate + CO2""",},'ucsd-rxns' : ['CYNTAH',], 'protein-comments' : ["""NIL""","""(The native enzyme has a molecular weight of ca. 150 kDa as estimated by sucrose density gradient centrifugation
and gel-filtration chromatography on Bio-Gel P-300. The enzyme is an oligomer composed of apparently identical
subunits which each have a molecular weight of ca. 15 kDa as estimated by SDS-Page |CITS: [6994799]| .)""",]},
'B0341' : {'ecocyc-rxns': {"""TRANS-RXN-14""": """H+[periplasmic space] + cyanate[periplasmic space] =H+[cytosol] + cyanate[cytosol] """,},'ucsd-rxns' : ['CYNTt2pp',], 'protein-comments' : ["""(CynX is a putative cyanate transporter. CynX is a member of the major facilitator
superfamily (MFS) of transporters |CITS: [98190790]|, and the cynX gene
has been shown to be part of a cyanate-induced operon with cynS and cynT,
encoding cyanase and carbonic anhydrase, respectively |CITS: [93186712] [89008347]|.
However, no phenotype has been observed for a knockout mutation in cynX
|CITS: [93186712]|.)""",]},
'B2803' : {'ecocyc-rxns': {"""DARABKIN-RXN""": """D-ribulose + ATP -> D-ribulose-1-phosphate + ADP""","""FUCULOKIN-RXN""": """L-fuculose + ATP -> fuculose-1-phosphate + ADP""",},'ucsd-rxns' : ['FCLK',], 'protein-comments' : ["""NIL""",]},
'B0343' : {'ecocyc-rxns': {"""TRANS-RXN-24""": """H+[periplasmic space] + lactose[periplasmic space] =H+[cytosol] + lactose[cytosol] """,},'ucsd-rxns' : ['LCTStpp',], 'protein-comments' : ["""(The lactose permease LacY is a lactose/proton symporter, responsible
for the uptake of lactose and other galactosides. LacY is probably the
best characterised secondary transporter. The lacY gene was the
first transporter gene to be cloned and sequenced |CITS: [78135240] [80120651]|.
The lactose permease has been solubilised, purified, reconstituted into
liposomes, and shown to mediate lactose/proton symport with a 1:1
stoichiometry |CITS: [81046907] [82053021] [82053021] [86230079]|. LacY
transports lactose and melibiose with similar affinities (Km = 0.1-1 mM)
|CITS: [78043231]|.
LacY is a member of the major facilitator superfamily (MFS) of
transporters |CITS: [93174460]|.
Purified LacY functions as a monomer |CITS: [94261597]| and consists of
12 transmembrane segments based on topological studies |CITS: [90311318]|.
LacY has been extensively mutagenised, a functional Cys-less transporter
was generated and Cys-scanning mutagenesis has altered every residue
in this transporter to a cysteine. Only six residues (Glu-126, Arg-144,
Glu-269, Arg-302, His-322 and Glu-325) are absolutely essential for lactose
transport |CITS: [98437318]|. A structural model for LacY has been developed,
without crystallographic data, using techniques such as second-site suppressor
analysis, excimer fluorescence, engineered divalent metal binding sites,
chemical cleavage, electron paramagnetic resonance and thiol crosslinking
|CITS: [97303165]|. The crystal structure of LacY has also been determined at 3.5 A
resolution |CITS: [22262313]|. The lacY gene forms part of the well known lactose-inducible lac
operon with the lacZ gene encoding β-galactosidase, the lacA
gene encoding thio-β-galactoside transacetylase and the lacI gene
encoding the lactose repressor.
A LacY Cys-154-Gly mutant is able to bind substrate but has no transport activity due to decreased
conformational flexibility and a more compact structure |CITS:[12627968]|. The crystal structure of a
Cys-154-Gly mutant locked in the inward facing conformation with bound substrate has been determined
to a resolution of 3.5 angstroms. LacY has two six-helix domains with the same topology and approximate
two-fold symmetry between them. The inward and outward facing conformations of LacY are likely the
result of rotation in the flexible loop connecting the two domains. Residues in the N-terminal portion of the
substrate binding site are involved in substrate specificity, while those in the C-terminal portion are
involved in substrate affinity |CITS:[12893935]|. The face of helix IX containing Arg-302 is involved in
ligand-induced conformational changes and forms part of the proton translocation pathway
|CITS:[12718531]|. Glu-325 and Arg-302 are involved in proton translocation, while His-322 and
Glu-269 couple substrate binding with proton translocation |CITS:[12893935]|. Second site suppressor
analysis shows that Glu-126 and Arg-144 are not required for sugar binding, though they do play a role
in maintenance of secondary structure |CITS:[12549931]|. There is a salt bridge between Glu-126 and
Arg-144, which is broken upon substrate binding |CITS:[15272008]|. Trp-151 is an important part of the
binding site |CITS:[12578349]|. Luminescence spectroscopy experiments show that the galactopyranosyl
ring of the substrate has a direct stacking interaction with the indole ring of Trp-151 |CITS:[14566061]|.
Glu-269 is predicted to participate in substrate recognition by hydrogen bonding to the C-3 OH group of
the galactopyranosyl ring |CITS:[12660154]|. The formation of the substrate binding site of the inward
facing conformation of LacY is optimized by a hydrogen bond between Glu-269 and the indole N of
Trp-151 |CITS:[15364943]|.
)""",]},
'B0344' : {'ecocyc-rxns': {"""BETAGALACTOSID-RXN""": """H2O + lactose = β-D-galactose + β-D-glucose""",},'ucsd-rxns' : ['LACZ',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B3942' : {'ecocyc-rxns': {"""CATAL-RXN""": """2 H2O2 = 2 H2O + O2""","""PEROXID-RXN""": """a reduced acceptor + H2O2 = an acceptor + 2 H2O""",},'ucsd-rxns' : ['CAT',], 'protein-comments' : ["""(The KatG enzyme is a bifunctional hydroperoxidase I, having both catalase and peroxidase activity.
Monofunctional and bifunctional peroxidases share highly similar active sites. A 35 amino acid structure connecting
the F and G helices in KatG is unique to the bifunctional enzyme; deletion of this loop causes loss of 99.8% of
catalase activity, while the mutant enzyme retains 50% of its peroxidase activity |CITS: [15147967]|.
Regulation is reviewed in |CITS: [7557318]|)""","""NIL""",]},
'B2418' : {'ecocyc-rxns': {"""PYRAMKIN-RXN""": """ATP + pyridoxamine = ADP + pyridoxamine 5'-phosphate""","""OHMETPYRKIN-RXN""": """ATP + hydroxymethylpyrimidine = ADP + hydroxymethylpyrimidine phosphate""","""PNKIN-RXN""": """ATP + pyridoxine -> ADP + pyridoxine-5'-phosphate""","""PYRIDOXKIN-RXN""": """ATP + pyridoxal -> ADP + pyridoxal 5'-phosphate""",},'ucsd-rxns' : ['HMPK1','PYDXK','PYDAMK','PYDXNK',], 'protein-comments' : ["""(The subunit structure is unknown.)""","""NIL""",]},
'B0347' : {'ecocyc-rxns': {"""MHPHYDROXY-RXN""": """3-(3-hydroxyphenyl)propionate + NADH + O2 = H2O + 3-(2,3-dihydroxyphenyl)propionate + NAD+""",},'ucsd-rxns' : ['3HCINNMH','3HPPPNH',], 'protein-comments' : ["""NIL""",]},
'B2416' : {'ecocyc-rxns': {"""TRANS-RXN-153""": """phosphoenolpyruvate + arbutin[periplasmic space] =arbutin-6-phosphate[cytosol] + pyruvate ""","""TRANS-RXN-153A""": """phosphoenolpyruvate + salicin[periplasmic space] =salicin-6-phosphate[cytosol] + pyruvate ""","""TRANS-RXN-155B""": """phosphoenolpyruvate + chitobiose[periplasmic space] =pyruvate + diacetylchitobiose-6-phosphate[cytosol] ""","""TRANS-RXN-155""": """phosphoenolpyruvate + cellobiose[periplasmic space] =cellobiose-6-phosphate[cytosol] + pyruvate ""","""TRANS-RXN-158""": """phosphoenolpyruvate + fructose[periplasmic space] =fructose-1-phosphate[cytosol] + pyruvate ""","""TRANS-RXN-161""": """phosphoenolpyruvate + galactitol[periplasmic space] =galactitol-1-phosphate[cytosol] + pyruvate ""","""RXN0-2522""": """phosphoenolpyruvate + 2-O-α-mannosyl-D-glycerate[periplasmic space] =2-(α-D-mannosyl)-3-phosphoglycerate[cytosol] + pyruvate ""","""TRANS-RXN-167A""": """phosphoenolpyruvate + glucosamine[periplasmic space] =D-glucosamine-6-phosphate[cytosol] + pyruvate ""","""TRANS-RXN-157""": """phosphoenolpyruvate + β-D-glucose[periplasmic space] =β-D-glucose-6-phosphate[cytosol] + pyruvate ""","""TRANS-RXN-165""": """phosphoenolpyruvate + mannose[periplasmic space] =mannose-6-phosphate[cytosol] + pyruvate ""","""TRANS-RXN-158A""": """phosphoenolpyruvate + fructose[periplasmic space] =D-fructose-6-phosphate[cytosol] + pyruvate ""","""TRANS-RXN-156""": """phosphoenolpyruvate + mannitol[periplasmic space] =mannitol-1-phosphate[cytosol] + pyruvate ""","""TRANS-RXN-167""": """phosphoenolpyruvate + N-acetyl-D-glucosamine[periplasmic space] =N-acetyl-D-glucosamine-6-phosphate[cytosol] + pyruvate ""","""TRANS-RXN-168""": """phosphoenolpyruvate + trehalose[periplasmic space] =trehalose 6-phosphate[cytosol] + pyruvate ""","""RXN0-2461""": """phosphoenolpyruvate + L-ascorbate[periplasmic space] =L-ascorbate-6-phosphate[cytosol] + pyruvate ""","""RXN0-17""": """N-acetylmuramate[periplasmic space] + phosphoenolpyruvate =MurNAc-6-P[cytoplasm] + pyruvate ""","""TRANS-RXN-169""": """phosphoenolpyruvate + D-sorbitol[periplasmic space] =D-sorbitol-6-phosphate[cytosol] + pyruvate """,},'ucsd-rxns' : ['GAMptspp','MANptspp','GALTptspp','ACGAptspp','ACGAptspp','ACMUMptspp','SUCptspp','SBTptspp','TREptspp','ASCBptspp','FRUpts2pp','MNLptspp','MANGLYCptspp','GLCptspp','GLCptspp','GLCptspp','FRUptspp','ACMANAptspp','MALTptspp','DHAPT',], 'protein-comments' : ["""(Enzyme I and HPr are the two sugar-non-specific protein constituents of the
PTS. They initiate phosphoryl transfer to sugar in a reaction that also
requires the sugar-specific Enzyme II |CITS: [94066914]|. Enzyme I uses
phosphoenolpyruvate (PEP) as the phosphoryl donor, autophosphorylates on
the N3 position of a histidyl residue and transfers the phosphate to the
small heat stable PTS protein HPr.
Enzyme I is homologous to PEP synthases and pyruvate:phosphate dikinases.
These three homologous enzymes all catalyze PEP-dependent
autophosphorylation reactions employing the same mechanism. They are all
homodimeric enzymes with a requirement for a divalent metal ion. This
requirement is provided by Mg2+ under normal physiological conditions.)""","""(GutABE, the glucitol PTS permease, belongs to the functional superfamily
of the phosphoenolpyruvate (PEP)-dependent, sugar transporting
phosphotransferase system (PTS). The PTS transports and simultaneously
phosphorylates its sugar substrates in a process called group
translocation. GutAB takes up exogenous glucitol, releasing the
phosphate ester into the cell cytoplasm in preparation for oxidation
to fructose-6-P and subsequent metabolism, primarily via glycolysis
|CITS: [94066914]|.
GutABE comprises the Enzyme IIGut complex. The
enzyme possesses a split IIC domain unlike all other characterized Enzyme
II complexes of the PTS |CITS: [94066914]|. GutA is a (putative) 4 TMS integral
membrane protein of 187 amino acyl residues. GutE is a larger protein of
319 residues that includes the hydrophilic IIB domain fused to a
hydrophobic (putative) 4 TMS domain |CITS: [97035393]|. GutB is the hydrophilic IIA
domain. Thus, the integral membrane IIC constituent of the glucitol
permease is split in half and encoded by two distinct genes, gutA and gutE.
gutB and gutE, respectively, encode the IIA and IIB constituents.
The IIB domain of GutE and the IIA (GutB) protein are localized to the
cytoplasmic side of the membrane. The overall PTS-mediated phosphoryl
transfer reaction, requiring the two general energy coupling proteins of
the PTS, Enzyme I and HPr, as well as the three domains of the Enzyme II
complex is:
PEP --> Enzyme I(his~~P)
--> HPr(his~~P)
--> IIA(his~~P) -->
IIB(cys~~P) -(IIC)-> glucitol-6-P.
GutABE transports glucitol with low micromolar affinities.
The gut operon is inducible in wild type E. coli K12
by the presence of exogenous glucitol. The gut operon
(gutABDMRQ) contains the gutA, gutB and gutE genes,
encoding the Enzyme IIGut complex, and the
gutD gene encoding glucitol-6-P dehydrogenase that oxidizes
glucitol-6-P to fructose-6-P. GutM and GutR are positive and
negative transcriptional regulators of gut operon expression,
respectively |CITS: [89094828]|. The function of GutQ is not known |CITS: [89094828]|. gut
operon expression is under the control of the cyclic AMP-cyclic
AMP receptor protein (CRP) complex.
)""","""(MurP, the N-acetymuramic acid PTS permease, belongs to the functional superfamily of the
phosphoenolpyruvate (PEP)-dependent, sugar transporting phosphotransferase system (PTS). The PTS
transports and simultaneously phosphorylates its sugar substrates in a process called group translocation.
murP encodes the PTS EIIB and -C sugar-specific domains. The PTS EIIAGlc domain
is also required for transport. MurP functions in the uptake of exogenous N-acetylmuramic acid (MurNAc),
releasing the phosphate ester into the cell cytoplasm in preparation for metabolism. MurP and
EIIAGlc are required for growth on MurNAc as the sole carbon and energy source
|CITS:[15060041]|.
The overall PTS-mediated phosphoryl transfer reaction, requiring the two general energy coupling proteins
of the PTS, Enzyme I and HPr, as well as the three domains of the Enzyme II complex is:
PEP--> Enzyme I(his~~P) --> HPr(his~~P) --> IIA(his~~P) --> IIB(cys~~P) -(IIC)-> N-acetylmuramic acid-6-P.
)""","""(SgcABC, a putative PTS permease, belongs to the functional superfamily
of the phosphoenolpyruvate (PEP)-dependent, sugar transporting
phosphotransferase system (PTS). The PTS transports and simultaneously
phosphorylates its sugar substrates in a process called group
translocation. SgcABC presumably takes up an exogenous sugar,
releasing the phosphate ester into the cell cytoplasm in preparation
for metabolism |CITS: [8246840]| . The overall PTS-mediated phosphoryl transfer
reaction, requiring the two general energy coupling proteins of
the PTS, Enzyme I and HPr, as well as the three domains of the
Enzyme II complex is:
PEP --> Enzyme I(his~~P)
--> HPr(his~~P)
--> IIA(his~~P) -->
IIB(cys~~P) -(IIC)-> sugar-P.
SgcA (Enzyme IIASgc) is homologous to the
IIA domains of the fructose- and mannitol-specific PTS permeases.
SgcB (Enzyme IIBSgc) is homologous to the
IIB domain of the galactitol-specific PTS permease, and SgcC (Enzyme
IICSgc) is homologous to the IIC domain of
the galactitol PTS permease |CITS: [8019415]| . The function of these proteins
is not known, but they may function in the transport and phosphorylation
of 5-carbon sugars |CITS: [9274005]| . Expression of the sgc operon in
which the encoding genes are found has not been studied.
)""","""(SgaTBA, a putative PTS permease, belongs to the functional superfamily
of the phosphoenolpyruvate (PEP)-dependent, sugar transporting
phosphotransferase system (PTS). The PTS transports and simultaneously
phosphorylates its sugar substrates in a process called group
translocation. SgaTBA presumably takes up an exogenous sugar,
releasing the phosphate ester into the cell cytoplasm in preparation
for metabolism |CITS: [8246840]| . The overall PTS-mediated phosphoryl transfer
reaction, requiring the two general energy coupling proteins of
the PTS, Enzyme I and HPr, as well as the three domains of the
Enzyme II complex is:
PEP --> Enzyme I(his~~P)
--> HPr(his~~P)
--> IIA(his~~P) -->
IIB(cys~~P) -(IIC)-> sugar-P.
The sga operon encodes SgaT, an integral membrane putative
transporter protein with 12 putative transmembrane α-helical
spanners that might function as a PTS Enzyme IIC; SgaB, the putative
Enzyme IIBSga, and SgaA, the putative Enzyme
IIASga |CITS: [REIZERGENOMESCITECH153]|. SgaB is homologous to the IIB
domains of the lactose-cellobiose PTS permease family. SgaA is
homologous to the IIA domains/proteins of the fructose-mannitol
PTS permease family. Little is known regarding the function of
these enzymes or expression of the sga operon in which
the encoding genes are found. However, the sga genes may
allow metabolism and interconversion of pentose and hexose phosphate
esters |CITS: [9274005]| .
Deletion mutation studies |CITS:[12644495]| indicate that all three components
are necessary for the uptake and utiliztion of L-ascorbate in vivo as well as for the
phosphorylation of L-ascorbate in vitro.)""","""(AgaBCDVWX, the putative N-acetylgalactosamine PTS permease, belongs
to the functional superfamily of the phosphoenolpyruvate (PEP)-dependent,
sugar transporting phosphotransferase system (PTS). The PTS transports
and simultaneously phosphorylates its sugar substrates in a process
called group translocation. AgaBCDVWX may take up exogenous N-acetylgalactosamine,
releasing the phosphate ester into the cell cytoplasm in preparation
for metabolism |CITS: [8246840]| .
AgaB and AgaV are Enzymes IIB; AgaC and AgaW are an Enzyme IIC
and a truncated Enzyme IIC, respectively; AgaD is an Enzyme
IID, and AgaX, which is encoded by a gene outside of the aga
operon, is an Enzyme IIA. All of these proteins are homologous
to the mannose Enzyme II complex proteins (the splinter group
enzymes) |CITS: [8932697]| . The overall PTS-mediated phosphoryl transfer reaction,
requiring the two general energy coupling proteins of the PTS,
Enzyme I and HPr, as well as the four domains of the Enzyme II
complex is proposed to be:
PEP -->
Enzyme I(his~~P) -->
HPr(his~~P)
-->
IIA(his~~P) -->
IIB(his~~P) -(IICD)-> N-acetylgalactosamine-6-P.
The aga operon (agaZVWASYBCDI) also encodes putative
enzymes that may be a kinase (AgaZ), a deacetylase (AgaA), a synthase
(AgaS), an aldolase (AgaY) and an isomerase (AgaI), all sugar
metabolic enzymes. The agaR gene, encoding a putative
transcriptional regulatory protein, precedes and is divergently
transcribed from the aga operon. Nothing is known concerning
expression of the aga operon. It may be cryptic in wild
type E. coli K12.)""","""(TreB, the trehalose PTS permease, belongs to the functional superfamily
of the phosphoenolpyruvate (PEP)-dependent, sugar transporting
phosphotransferase system (PTS). The PTS transports and simultaneously
phosphorylates its sugar substrates in a process called group
translocation. TreB together with IIAGlc
takes up exogenous trehalose, releasing the phosphate ester into
the cell cytoplasm in preparation for hydrolysis via phosphotrehalase
(TreA). Subsequent metabolism occurs primarily via glycolysis
|CITS: [8246840]| .
TreB, the Enzyme IITre complex, possesses
two domains in a single polypeptide chain with the domain order
IIB-IIC |CITS: [7608078]| . The IIB and IIC domains are homologous to the IIB
and IIC domains of PtsG, the glucose-specific PTS Enzyme II.
PtsG has been reported to possess 8 transmembrane α-helical
segments in its IIC domain. The IIB domain is localized to the
cytoplasmic side of the membrane, and it uses the glucose Enzyme
IIA to phosphorylate IIBTre. The overall
PTS-mediated phosphoryl transfer reaction, requiring the two general
energy coupling proteins of the PTS, Enzyme I and HPr, as well
as the three domains of the Enzyme II complex is:
PEP --> Enzyme I(his~~P)
--> HPr(his~~P)
--> IIA(his~~P) -->
IIB(cys~~P) -(IIC)-> trehalose-6-P.
TreB transports trehalose with micromolar affinity.
The tre operon is inducible in wild type E. coli K12
by the presence of low concentrations of trehalose. The treBC
operon contains the treB gene encoding the Enzyme IITre
and the treC gene encoding a phospho-trehalase that hydrolyzes
the α,α-glycosidic
bond in trehalose-6-phosphate |CITS: [8083158]| . The monocistronic treR
operon, encoding the repressor of the treBC operon is upstream
of the treBC operon and is transcribed in the same direction.
tre operon expression is under the control of the cyclic
AMP-cyclic AMP receptor protein (CRP) complex as well as that
of TreR. Metabolism of trehalose can occur either by a PTS-dependent
(low trehalose concentrations) or a PTS-independent (high trehalose
concentrations) mechanism. The latter process involves periplasmic
hydrolysis of trehalose to glucose.
)""","""(NagE, the N-acetylglucosamine PTS permease, belongs to the functional
superfamily of the phosphoenolpyruvate (PEP)-dependent, sugar
transporting phosphotransferase system (PTS). The PTS transports
and simultaneously phosphorylates its sugar substrates in a process
called group translocation. NagE takes up exogenous N-acetylglucosamine,
releasing the phosphate ester into the cell cytoplasm in preparation
for metabolism, primarily via glycolysis |CITS: [94066914]|.
NagE, the Enzyme IINag complex, possesses
three domains in a single polypeptide chain with the domain order
IIC-IIB-IIA |CITS: [89050950]|. It is homologous to PtsG/Crr (the glucose-specific
PTS Enzyme II) which has been reported to possess 8 transmembrane
α-helical segments in its IIC domain.
The IIB and IIA domains are localized to the cytoplasmic side
of the membrane. The overall PTS-mediated phosphoryl transfer
reaction, requiring the two general energy coupling proteins of
the PTS, Enzyme I and HPr, as well as the three domains of the
Enzyme II complex is:
PEP--> Enzyme
I(his~~P) --> HPr(his~~P)
--> IIA(his~~P)
--> IIB(cys~~P)
-(IIC)-> N-acetylglucosamine-6-P.
NagE transports N-acetylglucosamine with low micromolar affinity.
It can also transport antibiotics such as streptozotocin.
The monocistronic nagE operon and the nagBACD operon
comprise part of the nag regulon and are transcribed from
divergent promoters. The nagBACD operon encodes (a) glucosamine-P
deaminase (NagB), (b) N-acetylglucosamine-6-P deacetylase (NagA),
(c) the nag regulon transcriptional regulator (NagC) and
(d) a gene of unknown function which is, however, homologous to
functionally characterized phosphatases (NagD) |CITS: [89343637]|. NagC together
with the cyclic AMP-cyclic AMP receptor protein (CRP) complex
controls expression of the nag regulon |CITS: [92114782] [95311313]|.)""","""(MtlA, the mannitol PTS permease, belongs to the functional superfamily
of the phosphoenolpyruvate (PEP)-dependent, sugar transporting
phosphotransferase system (PTS). The PTS transports and simultaneously
phosphorylates its sugar substrates in a process called group
translocation. MtlA takes up exogenous mannitol, releasing the
phosphate ester, mannitol-1-P, into the cell cytoplasm in preparation
for oxidation to fructose-6-P by the NAD-dependent mannitol-P
dehydrogenase (MtlD). Subsequent metabolism is primarily via
glycolysis |CITS: [94066914]|.
MtlA, the Enzyme IIMtl complex, possesses
three domains in a single polypeptide chain with the domain order
IIC-IIB-IIA |CITS: [83291014]|. It is homologous to FruAB, the fructose-specific
PTS Enzyme II. The secondary structure of IIAMtl
has been solved by NMR |CITS: [94004470]|. MtlA has been reported to possess
6 transmembrane α-helical segments
in its IIC domain |CITS: [92052139]|. The IIB and IIA domains are localized
to the cytoplasmic side of the membrane. The overall PTS-mediated
phosphoryl transfer reaction, requiring the two general energy
coupling proteins of the PTS, Enzyme I and HPr, as well as the
three domains of the Enzyme II complex is:
PEP --> Enzyme I(his~~P)
--> HPr(his~~P)
--> IIA(his~~P) -->
IIB(cys~~P) -(IIC)-> mannitol-1-P.
MtlA transports mannitol with low micromolar affinity.
The mtl operon (mtlADR) is inducible (~~20x) by
growth of wild type E. coli K12 in the presence of mannitol.
The MtlR protein is a negative transcriptional regulator of the
operon |CITS: [94131964]|. The operon is also positively controlled by the cyclic
AMP-cyclic AMP receptor protein (CRP) complex and negatively by
the catabolite repressor/activator (Cra) protein.
)""","""(ManXYZ, the mannose PTS permease, belongs to the functional superfamily
of the phosphoenolpyruvate (PEP)-dependent, sugar transporting
phosphotransferase system (PTS). The PTS transports and simultaneously
phosphorylates its sugar substrates in a process called group
translocation. ManXYZ takes up exogenous hexoses (mannose, glucose,
glucosamine, fructose, 2-deoxyglucose, mannosamine, N-acetylglucosamine,
etc.), releasing the phosphate esters into the cell cytoplasm
in preparation for metabolism, primarily via glycolysis |CITS: [8246840]|.
ManXYZ, the Enzyme IIMan complex, possesses
four domains in three polypeptide chains, ManX=IIABMan,
ManY=IICMan and ManZ=IIDMan.
They are members of the mannose PTS permease family, the "splinter
group", which is not homologous to most other PTS permeases.
The IIB and IIA domains (ManX) form a homodimer that is localized
to the cytoplasmic side of the membrane |CITS: [94086520]|. ManXYZ was shown to exist in two forms. It is
oligomeric within the membrane and monomeric in its soluble form in the cytoplasm. Both forms exhibit
PEP-dependent sugar phosphorylation and sugar phosphate-dependent transphosphorylation activities,
though the kinetic properties of these reactions differ between the two forms of the protein
|CITS:[15576795]|. IIC and IID are integral membrane proteins with six and one transmembrane
α-helical spanner(s), respectively |CITS: [8774730]|. The 3-dimensional structure of
IIAMan and the secondary structure of IIBMan
have been determined |CITS: [8676384] [9030753]|. The overall PTS-mediated phosphoryl
transfer reaction, requiring the two general energy coupling proteins
of the PTS, Enzyme I and HPr, as well as the three domains of
the Enzyme II complex is:
PEP --> Enzyme I(his~~P)
--> HPr(his~~P)
--> IIA(his~~P) -->
IIB(his~~P)-(IICD)-> hexose-6-P.
ManXYZ transports mannose with micromolar affinity.
The manXYZ operon is either constitutively expressed or
inducibly expressed in response to extracellular sugar substrates
depending on the E. coli strain examined. The Mlc protein
plays a role in transcriptional regulation of this operon |CITS: [98143423]|.
The manXYZ operon is also subject to positive control
by the cyclic AMP-cyclic AMP receptor protein (CRP) complex.
)""","""(MalX, the maltose-glucose PTS permease, belongs to the functional
superfamily of the phosphoenolpyruvate (PEP)-dependent, sugar
transporting phosphotransferase system (PTS). The PTS transports
and simultaneously phosphorylates its sugar substrates in a process
called group translocation. MalX presumably takes up exogenous
sugar, releasing the phosphate ester into the cell cytoplasm in
preparation for metabolism |CITS: [8246840]|. The overall PTS-mediated phosphoryl
transfer reaction, requiring the two general energy coupling proteins
of the PTS, Enzyme I and HPr, as well as the three domains of
the Enzyme II complex is:
PEP --> Enzyme I(his~~P)
--> HPr(his~~P)
--> IIA(his~~P) -->
IIB(cys~~P) -(IIC)-> sugar-P.
The MalX (Enzyme IICBMal) can use glucose
and maltose as substrates. It may catalyze facilitated diffusion
as well as group translocation |CITS: [1856179]| . The protein presumably functions
with the glucose Enzyme IIA and is homologous to the glucose-
and N-acetylglucosamine-specific Enzyme IICBs. The physiological
function of MalX is not known |CITS: [1856179]|.
)""","""(Frx (HrsA), a putative PTS permease, belongs to the functional
superfamily of the phosphoenolpyruvate (PEP)-dependent, sugar
transporting phosphotransferase system (PTS). The PTS transports
and simultaneously phosphorylates its sugar substrates in a process
called group translocation. Frx presumably takes up an exogenous
sugar, releasing the phosphate ester into the cell cytoplasm in
preparation for metabolism (1).
Frx is a fructose-like PTS permease with the domain order IIA-IIB-IIC
(2, 3). Nothing is known about its sugar specificity, its function
or regulation of its synthesis. The overall PTS-mediated phosphoryl
transfer reaction, requiring the two general energy coupling proteins
of the PTS, Enzyme I and HPr, as well as the three domains of
the Enzyme II complex is:
PEP --> Enzyme I(his~~P)
--> HPr(his~~P)
--> IIA(his~~P) -->
IIB(cys~~P) -(IIC)-> β-glucoside-6-P.)""","""(GlvCB, a PTS permease of unknown specificity |CITS: [8019415]| belongs to the
functional superfamily of the phosphoenolpyruvate (PEP)-dependent,
sugar transporting phosphotransferase system (PTS). The PTS transports
and simultaneously phosphorylates its sugar substrates in a process
called group translocation. GlvCB presumably functions in the
uptake of exogenous sugar(s) in conjunction with a IIA protein
such as IIAGlc, releasing the phosphate esters
into the cell cytoplasm in preparation for metabolism via glycolysis
|CITS: [8246840]|.
GlvC, the Enzyme IICGlv and GlvB, the Enzyme
IIBGlv are homologous to the C and B domains
in PtsG (the glucose-specific PTS Enzyme II) which has been reported
to possess 8 transmembrane α-helical
segments in its IIC domain. The IIB domain is presumably localized
to the cytoplasmic side of the membrane and may function with
the glucose IIA protein. The overall PTS-mediated phosphoryl
transfer reaction, requiring the two general energy coupling proteins
of the PTS, Enzyme I and HPr, as well as the three domains of
the Enzyme II complex is:
PEP --> Enzyme I(his~~P)
--> HPr(his~~P)
--> IIA(his~~P) -->
IIB(cys~~P) -(IIC)-> sugar-P.
The glv operon (glvCBG) may be cryptic in wild
type E. coli K12. GlvG probably encodes an α-
or β-phosphoglucosidase as it is homologous
to such enzymes. Nothing is known about the expression or regulation
of the operon |CITS: [8019415]|.)""","""(GatABC, the galactitol PTS permease, belongs to the functional
superfamily of the phosphoenolpyruvate (PEP)-dependent, sugar
transporting phosphotransferase system (PTS). The PTS transports
and simultaneously phosphorylates its sugar substrates in a process
called group translocation. GatABC takes up exogenous galactitol,
releasing the phosphate ester into the cell cytoplasm in preparation
for oxidation and further metabolism, primarily via a modified
glycolytic pathway, the tagatose-6-P glycolytic pathway |CITS: [94066914] [97290497] [97114348]|.
GatABC, the Enzyme IIGat complex, possesses
three polypeptide chains, GatA (IIAGat), GatB
(IIBGat) and GatC (IICGat).
GatB is homologous to IIBSga and IIBSgc
and shows limited sequence similarity to the IIB proteins of the
lactose and cellobiose permeases (IIBLac and
IIBCel) |CITS:[reizergenomescitech153] [97419490]|. GatC is homologous to the
SgcC (IICSgc) protein |CITS:[reizergenomescitech153]| and shows limited
sequence similarity to IICFru. The latter
domain has been reported to possess 6 transmembrane α-helical
segments. The IIB and IIA proteins are localized to the cytoplasmic
side of the membrane. The overall PTS-mediated phosphoryl transfer
reaction, requiring the two general energy coupling proteins of
the PTS, Enzyme I and HPr, as well as the three domains of the
Enzyme II complex is:
PEP --> Enzyme I(his~~P)
--> HPr(his~~P)
--> IIA(his~~P) -->
IIB(cys~~P) -(IIC)-> galactitol-1-P.
GatABC transports galactitol with micromolar affinity.
The gat operon (gatYZABCDR) contains the gatY
gene encoding tagatose 1,6-bis-P aldolase and the gatZ
gene encoding tagatose 6-P kinase as well as gatD, the
NAD-dependent galactitol 1-P dehydrogenase |CITS: [95290497] [97113438]|. gatR
encodes the repressor of the gat operon. The gat
operon is either constitutively expressed or galactitol inducible
in wild type E. coli strains. In E. coli strains
which express the gat operon constitutively, the gatR
gene is truncated. The gat operon is subject to positive
control by the cyclic AMP-cyclic AMP receptor protein (CRP) complex.)""","""(FrwCBD PtsA, a putative PTS permease, belongs to the functional
superfamily of the phosphoenolpyruvate (PEP)-dependent, sugar
transporting phosphotransferase system (PTS). The PTS transports
and simultaneously phosphorylates its sugar substrates in a process
called group translocation. FrwCBD PtsA presumably takes up unknown
exogenous sugars, releasing the phosphate esters into the cell
cytoplasm in preparation for metabolism |CITS: [8246840]| .
FrwC (Enzyme IICFrw), FrwB (Enzyme IIBFrw),
FrwD (Enzyme IIBFrw') and PtsA
(an Enzyme I-Enzyme IIAFrw hybrid protein)
are all encoded within the frw gene cluster. The Frw proteins
and protein domains are homologous to constituents of the fructose
Enzyme II complexes. The frw gene cluster also encodes
several enzymes concerned with anaerobic carbon metabolism. At
least two operons are present in the frw gene cluster,
but the operon structures are not clearly defined. The overall
PTS-mediated phosphoryl transfer reaction, requiring the two general
energy coupling proteins of the PTS, Enzyme I and HPr, as well
as the three domains of the Enzyme II complex is:
PEP --> Enzyme I(his~~P)
--> HPr(his~~P)
--> IIA(his~~P) -->
IIB(cys~~P) -(IIC)-> sugar-P.
Nothing is known regarding the expression of the frw gene
cluster or its regulation.)""","""(FrvAB, a PTS permease of unknown specificity, belongs to the
functional superfamily of the phosphoenolpyruvate (PEP)-dependent,
sugar transporting phosphotransferase system (PTS). The PTS transports
and simultaneously phosphorylates its sugar substrates in a process
called group translocation. FrvAB presumably takes up an exogenous
PTS sugar, releasing the phosphate ester into the cell cytoplasm
in preparation for metabolism |CITS: [8246840] [8019415]|.
FrvAB, the Enzyme IIFrv complex, possesses
two domains in a single polypeptide chain (FrvB) with the domain
order IIB-IIC and one domain in FrvA which corresponds to a IIA
protein. It is homologous to the fructose- and mannitol-specific
PTS Enzymes II. The latter has been reported to possess 6 transmembrane
α-helical segments in its IIC domain.
The IIB and IIA domains are localized to the cytoplasmic side
of the membrane. The overall PTS-mediated phosphoryl transfer
reaction, requiring the two general energy coupling proteins of
the PTS, Enzyme I and HPr, as well as the three domains of the
Enzyme II complex is presumably:
PEP --> Enzyme I(his~~P)
--> HPr(his~~P)
--> IIA(his~~P) -->
IIB(cys~~P) -(IIC)-> sugar-P.
The frv operon (frvABXR) encodes, in addition to
FrvAB, a probable hydrolase (FrvX) and a transcriptional regulatory
protein (FrvR). It is presumably cryptic, but nothing is known
regarding its expression.
)""","""(FruAB, the fructose PTS permease, belongs to the functional superfamily
of the phosphoenolpyruvate (PEP)-dependent, sugar transporting
phosphotransferase system (PTS). The PTS transports and simultaneously
phosphorylates its sugar substrates in a process called group
translocation. FruAB takes up exogenous fructose, releasing the
1-phosphate ester into the cell cytoplasm in preparation for metabolism,
primarily via glycolysis |CITS: [8246840]|.
FruAB, the Enzyme IIFru complex, possesses
three domains in the FruA protein with the domain order IIB'-IIB-IIC
|CITS: [89341690]| and three domains in its FruB protein, also named diphosphoryl
transfer protein (DTP), with the domain order IIA-M-H where IIA
is the first phosphorylation site domain, M is a central domain
of unknown function, and H is an HPr-like domain called FPr (fructose-inducible
HPr) |CITS: [2546043]|. FruAB is homologous to MtlA (the mannitol-specific
PTS Enzyme II) which has been reported to possess 6 transmembrane
α-helical segments in its IIC domain.
The IIA, IIB and IIB' domains are localized to the cytoplasmic
side of the membrane. IIB' is required for high affinity binding
of FruB to FruA but does not participate in phosphoryl transfer
|CITS: [8626640]|. The overall PTS-mediated phosphoryl transfer reaction, requiring
the two general energy coupling proteins of the PTS, Enzyme I
and HPr, as well as the three domains of the Enzyme II complex
is:
PEP --> Enzyme I(his~~P)
--> HPr(his~~P)
--> IIA(his~~P) -->
IIB(cys~~P) -(IIC)-> fructose-1-P.
FruAB transports fructose with low micromolar affinity.
The fru operon is inducible in wild type E. coli K12
due to the presence of the fructose repressor, FruR, also known
as the catabolite repressor/activator (Cra) protein. Cra is a
member of the LacI-GalR family |CITS: [2203752] [8230205]|. The fru operon
is also subject to positive control by the cyclic AMP-cyclic AMP
receptor protein (CRP) complex. The fru operon contains
the fruB gene, the fruK gene (encoding fructose-1-P
kinase) and the fruA gene in that order. The fruR gene
does not map near the fru operon. FruK is a homologue
of phosphofructokinase.)""","""(PtsG/Crr, the glucose-specific PTS permease, belongs to the functional
superfamily of the phosphoenolpyruvate (PEP)-dependent, sugar
transporting phosphotransferase system (PTS). The PTS transports
and simultaneously phosphorylates its sugar substrates in a process
called group translocation. PtsG/Crr takes up exogenous glucose,
releasing the phosphate ester into the cell cytoplasm in preparation
for metabolism, primarily via glycolysis|CITS: [8246840]|. It can also transport
the nonmetabolizable glucoside, methyl α-glucoside
with 10-fold lower affinity.
The Enzyme IIGlc complex possesses two domains
in a single polypeptide chain with the domain order IIC-IIB (PtsG),
and it functions with an additional polypeptide chain, the Crr
or IIAGlc protein. The IIC domain of PtsG
has been reported to possess 8 transmembrane α-helical
segments |CITS: [8505291]|. The IIB domain of PtsG and IIAGlc
are localized to the cytoplasmic side of the membrane. The overall
PTS-mediated phosphoryl transfer reaction, requiring the two general
energy coupling proteins of the PTS, Enzyme I and HPr, as well
as the three domains of the Enzyme II complex is:
PEP --> Enzyme I(his~~P)
--> HPr(his~~P)
--> IIA(his~~P) -->
IIB(cys~~P) -(IIC)-> glucose-6-P.
PtsG transports glucose with low micromolar affinity.
The ptsG operon in wild type E. coli K12 is 5-10x
inducible by growth in the presence of glucose, but some E.
coli strains synthesize PtsG constitutively. IIAGlc
is synthesized constitutively from its own promoter, but it is
also slightly inducible as a result of read through from the weaker
ptsH promoter of the pts operon. ptsG but
not crr is subject to positive control by the cyclic AMP-cyclic
AMP receptor protein (CRP) complex. The ptsG operon contains
only the ptsG gene encoding the Enzyme IICBGlc.
Both the IIAGlc protein and the IIBGlc
domain of the PtsG protein have been solved in 3-dimensions by
X-ray crystallography and NMR spectroscopy, and the 3-dimensional
structure of the complex of IIAGlc with HPr
has also been solved |CITS: [1911744],[8418852],[8784182]|. PtsG was shown to exist in two forms. It is
oligomeric within the membrane and monomeric in its soluble form in the cytoplasm. Both forms exhibit
PEP-dependent sugar phosphorylation and sugar phosphate-dependent transphosphorylation activities,
though the kinetic properties of these reactions differ between the two forms of the protein
|CITS:[15576795]|.)""","""(CmtAB, the "cryptic mannitol" PTS permease, belongs
to the functional superfamily of the phosphoenolpyruvate (PEP)-dependent,
sugar transporting phosphotransferase system (PTS). The PTS transports
and simultaneously phosphorylates its sugar substrates in a process
called group translocation. CmtAB presumably takes up an exogenous
sugar, releasing the phosphate ester into the cell cytoplasm in
preparation for metabolism |CITS: [94066914]| . The overall PTS-mediated phosphoryl
transfer reaction, requiring the two general energy coupling proteins
of the PTS, Enzyme I and HPr, as well as the three domains of
the Enzyme II complex is:
PEP --> Enzyme I(his~~P)
--> HPr(his~~P)
--> IIA(his~~P) -->
IIB(cys~~P) -(IIC)-> sugar-P.
CmtA (Enzyme IIBCCmt) and CmtB (Enzyme IIACmt)
encode a mannitol-like PTS permease. The two genes complemented
a mannitol-negative E. coli mutant when expressed using
a heterologous promoter |CITS: [93357262]| . The cmt genes are therefore
believed to be cryptic in wild-type E.coli. The
natural substrate(s) of the "cryptic mannitol" permease
are not known.
)""","""(ChbA-ChbB-ChbC, the N,N'-diacetylchitobiose PTS permease (previously
designated CelABC, the Cellobiose/Arbutin/Salicin PTS permease), belongs to
the functional superfamily of the phosphoenolpyruvate (PEP)-dependent,
sugar transporting phosphotransferase system (PTS). The PTS transports and
simultaneously phosphorylates its sugar substrates in a process called
group translocation. The ChbABC complex takes up exogenous
N,N'-diacetylchitobiose, releasing the phosphate ester into the cell
cytoplasm in preparation for hydrolysis and metabolism, primarily via
glycolysis |CITS: [84246840]|. Only this disaccharide is an inducer of the system, but
other beta-glucosides are substrates |CITS: [98070757]|.
The Enzyme IIChb complex, possesses three
polypeptide chains, ChbA, ChbB and ChbC |CITS: [90185128] [91227627]|. It is homologous
to the well-characterized lactose-specific PTS Enzyme II of Gram-positive
bacteria. IIC (ChbC) is an integral membrane transport protein
while IIA (ChbA) and IIB (ChbB) are localized to the cytoplasmic
side of the membrane. The overall PTS-mediated phosphoryl transfer
reaction, requiring the two general energy coupling proteins of
the PTS, Enzyme I and HPr, as well as the three proteins of the
Enzyme II complex is:
PEP --> Enzyme I(his~~P)
--> HPr(his~~P)
--> IIA(his~~P) -->
IIB(cys~~P) -(IIC)-> diacetylchitobiose-6-P.
IIChb transports its substrates with micromolar affinity.
As noted above, the chb operon is inducible in wild type E. coli
K12, but it has been reported to be activated for β-glucoside uptake by the
insertion of an IS1 insertion sequence elements upstream of the coding
region of the chb operon in some E. coli isolates |CITS: [90185128]|. The chb operon
contains in addition to chbA, chbB and chbC, which encode the Enzyme IIChb,
the chbR gene, which encodes a negative regulatory protein, and the chbF
gene encoding an enzyme that can function as either a
phospho-β-N,N'-diacetylchitobiase or a phospho-β-glucosidase. The operon
also includes the chbG gene of unknown function. The operon gene order is
chbBCARFG. ChbR and ChbF are paralogues of MelR, the repressor of the E.
coli melibiose operon, and melA, the α-galactosidase of the melibiose
operon, respectively |CITS: [90185127]|. The solution structure of the trimeric IIAChb has
been determined by NMR spectroscopy |CITS:[15654077]|. The 3-dimensional
structure of IIBChb has been determined |CITS: [97184687]|. The chb operon is subject to positive control by the
cyclic AMP-cyclic AMP receptor protein complex.)""","""(BglF, the aromatic β-glucoside (Arbutin/Salicin)
PTS permease, belongs to the functional superfamily of the phosphoenolpyruvate
(PEP)-dependent, sugar transporting phosphotransferase system
(PTS). The PTS transports and simultaneously phosphorylates its
sugar substrates in a process called group translocation. BglF
takes up exogenous β-glucosides, releasing
the phosphate esters into the cell cytoplasm in preparation for
hydrolysis and metabolism, primarily via glycolysis |CITS: [94066914]|.
BglF, the Enzyme IIBgl complex, possesses
three domains in a single polypeptide chain with the domain order
IIB-IIC-IIA. It is homologous to PtsG (the glucose-specific PTS
Enzyme II) which has been reported to possess 8 transmembrane
α-helical segments in its IIC domain.
The IIB and IIA domains are localized to the cytoplasmic side
of the membrane. The overall PTS-mediated phosphoryl transfer
reaction, requiring the two general energy coupling proteins of
the PTS, Enzyme I and HPr, as well as the three domains of the
Enzyme II complex is:
PEP --> Enzyme I(his~~P)
--> HPr(his~~P)
--> IIA(his~~P) -->
IIB(cys~~P) -(IIC)-> β-glucoside-6-P
.
BglF transports its β-glucoside substrates
with micromolar affinities.
The bgl operon is cryptic in wild type E. coli K12.
It has been reported to be activated by the insertion of an IS
element into the region upstream of the operon in some E. coli
isolates |CITS: [92159025]|. Crypticity of this and other E. coli β-glucoside
metabolic operons presumably serves as a protective device against
toxic β-glucosides found in nature.
The bgl operon contains the bglG gene encoding
a bgl operon-specific antiterminator, the blgF gene
encoding the Enzyme IIBgl and the bglB
gene encoding a phospho-β-glucosidase
that hydrolyzes the aglycone from the glycoside phosphate ester
|CITS: [87222180]|. Insertion of an IS element upstream of the operon activates
a promoter, and the operon is then subject to β-glucoside
induction by a mechanism in which BglF-mediated phosphorylation
of BglG controls its transcriptional antitermination activity
|CITS: [89376535]|. The operon is subject to positive control by cyclic AMP
and the cyclic AMP receptor protein (CRP).
)""","""(AscF, the Arbutin/Salicin/Cellobiose PTS permease, belongs to
the functional superfamily of the phosphoenolpyruvate (PEP)-dependent,
sugar transporting phosphotransferase system (PTS). The PTS transports
and simultaneously phosphorylates its sugar substrates in a process
called group translocation. AscF takes up exogenous β-glucosides,
releasing the phosphate esters into the cell cytoplasm in preparation
for hydrolysis and metabolism, primarily via glycolysis |CITS:[94066914]|.
AscF, the Enzyme IIAsc complex, possesses
three domains in a single polypeptide chain with the domain order
IIB-IIC-IIA. It is homologous to PtsG (the glucose-specific PTS
Enzyme II) which has been reported to possess 8 transmembrane
α-helical segments in its IIC domain.
The IIB and IIA domains are localized to the cytoplasmic side
of the membrane. The overall PTS-mediated phosphoryl transfer
reaction, requiring the two general energy coupling proteins of
the PTS, Enzyme I and HPr, as well as the three domains of the
Enzyme II complex is:
PEP --> Enzyme I(his~~P)
--> HPr(his~~P)
--> IIA(his~~P) -->
IIB(cys~~P) -(IIC)-> β-glucoside-6-P.
AscF transports its β-glucoside substrates
with micromolar affinities.
The asc operon is cryptic in wild type E. coli K12.
It has been reported to be activated by the insertion of IS186
into the ascG (repressor) gene in some E. coli isolates
|CITS: [92334140]|. Crypticity of this and other E. coli β-glucoside
metabolic operons presumably serves as a protective device against
toxic β-glucosides found in nature.
The asc operon contains the ascF gene encoding
the Enzyme IIAsc and the ascB gene
encoding a phospho-β-glucosidase that
hydrolyzes the aglycone from the glycoside phosphate ester. The
monocistronic ascG gene, encoding the repressor of the
ascFB operon, and the ascFB operon are transcribed
from divergent promoters. AscF and AscB are paralogues of BglF
and BglA, respectively. AscG is paralogous to GalR. The bgl
and asc operons are estimated to have arisen by operon
duplication about 3x108 years ago.
)""",]},
'B2417' : {'ecocyc-rxns': {"""TRANS-RXN-157""": """phosphoenolpyruvate + β-D-glucose[periplasmic space] =β-D-glucose-6-phosphate[cytosol] + pyruvate ""","""TRANS-RXN-168""": """phosphoenolpyruvate + trehalose[periplasmic space] =trehalose 6-phosphate[cytosol] + pyruvate ""","""RXN0-17""": """N-acetylmuramate[periplasmic space] + phosphoenolpyruvate =MurNAc-6-P[cytoplasm] + pyruvate """,},'ucsd-rxns' : ['ACGAptspp','ACMUMptspp','SUCptspp','TREptspp','GLCptspp','GLCptspp','MALTptspp',], 'protein-comments' : ["""(contains a PTS Enzyme IIA domain)""","""(MurP, the N-acetymuramic acid PTS permease, belongs to the functional superfamily of the
phosphoenolpyruvate (PEP)-dependent, sugar transporting phosphotransferase system (PTS). The PTS
transports and simultaneously phosphorylates its sugar substrates in a process called group translocation.
murP encodes the PTS EIIB and -C sugar-specific domains. The PTS EIIAGlc domain
is also required for transport. MurP functions in the uptake of exogenous N-acetylmuramic acid (MurNAc),
releasing the phosphate ester into the cell cytoplasm in preparation for metabolism. MurP and
EIIAGlc are required for growth on MurNAc as the sole carbon and energy source
|CITS:[15060041]|.
The overall PTS-mediated phosphoryl transfer reaction, requiring the two general energy coupling proteins
of the PTS, Enzyme I and HPr, as well as the three domains of the Enzyme II complex is:
PEP--> Enzyme I(his~~P) --> HPr(his~~P) --> IIA(his~~P) --> IIB(cys~~P) -(IIC)-> N-acetylmuramic acid-6-P.
)""","""(MalX, the maltose-glucose PTS permease, belongs to the functional
superfamily of the phosphoenolpyruvate (PEP)-dependent, sugar
transporting phosphotransferase system (PTS). The PTS transports
and simultaneously phosphorylates its sugar substrates in a process
called group translocation. MalX presumably takes up exogenous
sugar, releasing the phosphate ester into the cell cytoplasm in
preparation for metabolism |CITS: [8246840]|. The overall PTS-mediated phosphoryl
transfer reaction, requiring the two general energy coupling proteins
of the PTS, Enzyme I and HPr, as well as the three domains of
the Enzyme II complex is:
PEP --> Enzyme I(his~~P)
--> HPr(his~~P)
--> IIA(his~~P) -->
IIB(cys~~P) -(IIC)-> sugar-P.
The MalX (Enzyme IICBMal) can use glucose
and maltose as substrates. It may catalyze facilitated diffusion
as well as group translocation |CITS: [1856179]| . The protein presumably functions
with the glucose Enzyme IIA and is homologous to the glucose-
and N-acetylglucosamine-specific Enzyme IICBs. The physiological
function of MalX is not known |CITS: [1856179]|.
)""","""(TreB, the trehalose PTS permease, belongs to the functional superfamily
of the phosphoenolpyruvate (PEP)-dependent, sugar transporting
phosphotransferase system (PTS). The PTS transports and simultaneously
phosphorylates its sugar substrates in a process called group
translocation. TreB together with IIAGlc
takes up exogenous trehalose, releasing the phosphate ester into
the cell cytoplasm in preparation for hydrolysis via phosphotrehalase
(TreA). Subsequent metabolism occurs primarily via glycolysis
|CITS: [8246840]| .
TreB, the Enzyme IITre complex, possesses
two domains in a single polypeptide chain with the domain order
IIB-IIC |CITS: [7608078]| . The IIB and IIC domains are homologous to the IIB
and IIC domains of PtsG, the glucose-specific PTS Enzyme II.
PtsG has been reported to possess 8 transmembrane α-helical
segments in its IIC domain. The IIB domain is localized to the
cytoplasmic side of the membrane, and it uses the glucose Enzyme
IIA to phosphorylate IIBTre. The overall
PTS-mediated phosphoryl transfer reaction, requiring the two general
energy coupling proteins of the PTS, Enzyme I and HPr, as well
as the three domains of the Enzyme II complex is:
PEP --> Enzyme I(his~~P)
--> HPr(his~~P)
--> IIA(his~~P) -->
IIB(cys~~P) -(IIC)-> trehalose-6-P.
TreB transports trehalose with micromolar affinity.
The tre operon is inducible in wild type E. coli K12
by the presence of low concentrations of trehalose. The treBC
operon contains the treB gene encoding the Enzyme IITre
and the treC gene encoding a phospho-trehalase that hydrolyzes
the α,α-glycosidic
bond in trehalose-6-phosphate |CITS: [8083158]| . The monocistronic treR
operon, encoding the repressor of the treBC operon is upstream
of the treBC operon and is transcribed in the same direction.
tre operon expression is under the control of the cyclic
AMP-cyclic AMP receptor protein (CRP) complex as well as that
of TreR. Metabolism of trehalose can occur either by a PTS-dependent
(low trehalose concentrations) or a PTS-independent (high trehalose
concentrations) mechanism. The latter process involves periplasmic
hydrolysis of trehalose to glucose.
)""","""(PtsG/Crr, the glucose-specific PTS permease, belongs to the functional
superfamily of the phosphoenolpyruvate (PEP)-dependent, sugar
transporting phosphotransferase system (PTS). The PTS transports
and simultaneously phosphorylates its sugar substrates in a process
called group translocation. PtsG/Crr takes up exogenous glucose,
releasing the phosphate ester into the cell cytoplasm in preparation
for metabolism, primarily via glycolysis|CITS: [8246840]|. It can also transport
the nonmetabolizable glucoside, methyl α-glucoside
with 10-fold lower affinity.
The Enzyme IIGlc complex possesses two domains
in a single polypeptide chain with the domain order IIC-IIB (PtsG),
and it functions with an additional polypeptide chain, the Crr
or IIAGlc protein. The IIC domain of PtsG
has been reported to possess 8 transmembrane α-helical
segments |CITS: [8505291]|. The IIB domain of PtsG and IIAGlc
are localized to the cytoplasmic side of the membrane. The overall
PTS-mediated phosphoryl transfer reaction, requiring the two general
energy coupling proteins of the PTS, Enzyme I and HPr, as well
as the three domains of the Enzyme II complex is:
PEP --> Enzyme I(his~~P)
--> HPr(his~~P)
--> IIA(his~~P) -->
IIB(cys~~P) -(IIC)-> glucose-6-P.
PtsG transports glucose with low micromolar affinity.
The ptsG operon in wild type E. coli K12 is 5-10x
inducible by growth in the presence of glucose, but some E.
coli strains synthesize PtsG constitutively. IIAGlc
is synthesized constitutively from its own promoter, but it is
also slightly inducible as a result of read through from the weaker
ptsH promoter of the pts operon. ptsG but
not crr is subject to positive control by the cyclic AMP-cyclic
AMP receptor protein (CRP) complex. The ptsG operon contains
only the ptsG gene encoding the Enzyme IICBGlc.
Both the IIAGlc protein and the IIBGlc
domain of the PtsG protein have been solved in 3-dimensions by
X-ray crystallography and NMR spectroscopy, and the 3-dimensional
structure of the complex of IIAGlc with HPr
has also been solved |CITS: [1911744],[8418852],[8784182]|. PtsG was shown to exist in two forms. It is
oligomeric within the membrane and monomeric in its soluble form in the cytoplasm. Both forms exhibit
PEP-dependent sugar phosphorylation and sugar phosphate-dependent transphosphorylation activities,
though the kinetic properties of these reactions differ between the two forms of the protein
|CITS:[15576795]|.)""",]},
'B2414' : {'ecocyc-rxns': {"""CYSSYNMULTI-RXN""": """L-serine + acetyl-CoA + hydrogen sulfide = L-cysteine + coenzyme A + acetate""","""ACSERLY-RXN""": """O-acetyl-L-serine + hydrogen sulfide = L-cysteine + acetate""",},'ucsd-rxns' : ['CYSS',], 'protein-comments' : ["""(Ssi5: "sulfate starvation-induced" |CITS: [8774726]|.
Regulation has been described |CITS: [8774726]|. Protein abundance is increased by sulfate starvation |CITS: [8774726]|.)""","""NIL""","""(Serine O-acetyl transferase is associated in a bifunctional complex with O-acetyl serine (thiol) lyase A
(O-acetylserine sulfhydrolase A) |CITS: [88009872] [91099514]|. The complex dissociates in the presence of
O-acetylserine, the product of the serine-O-acetyltransferase-catalyzed reaction |CITS: [ColiSalII] [91099514]
[88009872]|.
)""",]},
'B2415' : {'ecocyc-rxns': {"""RXN0-2461""": """phosphoenolpyruvate + L-ascorbate[periplasmic space] =L-ascorbate-6-phosphate[cytosol] + pyruvate ""","""TRANS-RXN-168""": """phosphoenolpyruvate + trehalose[periplasmic space] =trehalose 6-phosphate[cytosol] + pyruvate ""","""TRANS-RXN-167A""": """phosphoenolpyruvate + glucosamine[periplasmic space] =D-glucosamine-6-phosphate[cytosol] + pyruvate ""","""TRANS-RXN-167""": """phosphoenolpyruvate + N-acetyl-D-glucosamine[periplasmic space] =N-acetyl-D-glucosamine-6-phosphate[cytosol] + pyruvate ""","""TRANS-RXN-165""": """phosphoenolpyruvate + mannose[periplasmic space] =mannose-6-phosphate[cytosol] + pyruvate ""","""TRANS-RXN-158A""": """phosphoenolpyruvate + fructose[periplasmic space] =D-fructose-6-phosphate[cytosol] + pyruvate ""","""RXN0-2522""": """phosphoenolpyruvate + 2-O-α-mannosyl-D-glycerate[periplasmic space] =2-(α-D-mannosyl)-3-phosphoglycerate[cytosol] + pyruvate ""","""TRANS-RXN-161""": """phosphoenolpyruvate + galactitol[periplasmic space] =galactitol-1-phosphate[cytosol] + pyruvate ""","""TRANS-RXN-158""": """phosphoenolpyruvate + fructose[periplasmic space] =fructose-1-phosphate[cytosol] + pyruvate ""","""TRANS-RXN-157""": """phosphoenolpyruvate + β-D-glucose[periplasmic space] =β-D-glucose-6-phosphate[cytosol] + pyruvate ""","""TRANS-RXN-156""": """phosphoenolpyruvate + mannitol[periplasmic space] =mannitol-1-phosphate[cytosol] + pyruvate ""","""TRANS-RXN-155B""": """phosphoenolpyruvate + chitobiose[periplasmic space] =pyruvate + diacetylchitobiose-6-phosphate[cytosol] ""","""TRANS-RXN-155""": """phosphoenolpyruvate + cellobiose[periplasmic space] =cellobiose-6-phosphate[cytosol] + pyruvate ""","""TRANS-RXN-153A""": """phosphoenolpyruvate + salicin[periplasmic space] =salicin-6-phosphate[cytosol] + pyruvate ""","""TRANS-RXN-153""": """phosphoenolpyruvate + arbutin[periplasmic space] =arbutin-6-phosphate[cytosol] + pyruvate ""","""RXN0-17""": """N-acetylmuramate[periplasmic space] + phosphoenolpyruvate =MurNAc-6-P[cytoplasm] + pyruvate ""","""TRANS-RXN-169""": """phosphoenolpyruvate + D-sorbitol[periplasmic space] =D-sorbitol-6-phosphate[cytosol] + pyruvate """,},'ucsd-rxns' : ['GAMptspp','MANptspp','GALTptspp','ACGAptspp','ACGAptspp','ACMUMptspp','SUCptspp','SBTptspp','TREptspp','ASCBptspp','FRUpts2pp','MNLptspp','MANGLYCptspp','GLCptspp','GLCptspp','GLCptspp','FRUptspp','ACMANAptspp','MALTptspp','DHAPT',], 'protein-comments' : ["""(HPr (heat stable, histidyl phosphorylatable protein) is the second of two
sugar-non-specific protein constituents of the PTS |CITS: [94066914]|. It accepts a
phosphoryl group from Enzyme I-P, becomes phosphorylated on a histidyl
residue (histidine 15, phosphorylated on position N1), and transfers the
phosphate to a histidyl residue (N3) in any one of the many sugar-specific
Enzyme IIA proteins/domains. HPr is a small monomeric,
single domain, protein that is relatively heat stable. It serves as an
intermediary phosphoryl transfer protein between Enzyme I and the various
sugar-specific Enzyme II complexes of the PTS.
)""","""(GutABE, the glucitol PTS permease, belongs to the functional superfamily
of the phosphoenolpyruvate (PEP)-dependent, sugar transporting
phosphotransferase system (PTS). The PTS transports and simultaneously
phosphorylates its sugar substrates in a process called group
translocation. GutAB takes up exogenous glucitol, releasing the
phosphate ester into the cell cytoplasm in preparation for oxidation
to fructose-6-P and subsequent metabolism, primarily via glycolysis
|CITS: [94066914]|.
GutABE comprises the Enzyme IIGut complex. The
enzyme possesses a split IIC domain unlike all other characterized Enzyme
II complexes of the PTS |CITS: [94066914]|. GutA is a (putative) 4 TMS integral
membrane protein of 187 amino acyl residues. GutE is a larger protein of
319 residues that includes the hydrophilic IIB domain fused to a
hydrophobic (putative) 4 TMS domain |CITS: [97035393]|. GutB is the hydrophilic IIA
domain. Thus, the integral membrane IIC constituent of the glucitol
permease is split in half and encoded by two distinct genes, gutA and gutE.
gutB and gutE, respectively, encode the IIA and IIB constituents.
The IIB domain of GutE and the IIA (GutB) protein are localized to the
cytoplasmic side of the membrane. The overall PTS-mediated phosphoryl
transfer reaction, requiring the two general energy coupling proteins of
the PTS, Enzyme I and HPr, as well as the three domains of the Enzyme II
complex is:
PEP --> Enzyme I(his~~P)
--> HPr(his~~P)
--> IIA(his~~P) -->
IIB(cys~~P) -(IIC)-> glucitol-6-P.
GutABE transports glucitol with low micromolar affinities.
The gut operon is inducible in wild type E. coli K12
by the presence of exogenous glucitol. The gut operon
(gutABDMRQ) contains the gutA, gutB and gutE genes,
encoding the Enzyme IIGut complex, and the
gutD gene encoding glucitol-6-P dehydrogenase that oxidizes
glucitol-6-P to fructose-6-P. GutM and GutR are positive and
negative transcriptional regulators of gut operon expression,
respectively |CITS: [89094828]|. The function of GutQ is not known |CITS: [89094828]|. gut
operon expression is under the control of the cyclic AMP-cyclic
AMP receptor protein (CRP) complex.
)""","""(MurP, the N-acetymuramic acid PTS permease, belongs to the functional superfamily of the
phosphoenolpyruvate (PEP)-dependent, sugar transporting phosphotransferase system (PTS). The PTS
transports and simultaneously phosphorylates its sugar substrates in a process called group translocation.
murP encodes the PTS EIIB and -C sugar-specific domains. The PTS EIIAGlc domain
is also required for transport. MurP functions in the uptake of exogenous N-acetylmuramic acid (MurNAc),
releasing the phosphate ester into the cell cytoplasm in preparation for metabolism. MurP and
EIIAGlc are required for growth on MurNAc as the sole carbon and energy source
|CITS:[15060041]|.
The overall PTS-mediated phosphoryl transfer reaction, requiring the two general energy coupling proteins
of the PTS, Enzyme I and HPr, as well as the three domains of the Enzyme II complex is:
PEP--> Enzyme I(his~~P) --> HPr(his~~P) --> IIA(his~~P) --> IIB(cys~~P) -(IIC)-> N-acetylmuramic acid-6-P.
)""","""(AscF, the Arbutin/Salicin/Cellobiose PTS permease, belongs to
the functional superfamily of the phosphoenolpyruvate (PEP)-dependent,
sugar transporting phosphotransferase system (PTS). The PTS transports
and simultaneously phosphorylates its sugar substrates in a process
called group translocation. AscF takes up exogenous β-glucosides,
releasing the phosphate esters into the cell cytoplasm in preparation
for hydrolysis and metabolism, primarily via glycolysis |CITS:[94066914]|.
AscF, the Enzyme IIAsc complex, possesses
three domains in a single polypeptide chain with the domain order
IIB-IIC-IIA. It is homologous to PtsG (the glucose-specific PTS
Enzyme II) which has been reported to possess 8 transmembrane
α-helical segments in its IIC domain.
The IIB and IIA domains are localized to the cytoplasmic side
of the membrane. The overall PTS-mediated phosphoryl transfer
reaction, requiring the two general energy coupling proteins of
the PTS, Enzyme I and HPr, as well as the three domains of the
Enzyme II complex is:
PEP --> Enzyme I(his~~P)
--> HPr(his~~P)
--> IIA(his~~P) -->
IIB(cys~~P) -(IIC)-> β-glucoside-6-P.
AscF transports its β-glucoside substrates
with micromolar affinities.
The asc operon is cryptic in wild type E. coli K12.
It has been reported to be activated by the insertion of IS186
into the ascG (repressor) gene in some E. coli isolates
|CITS: [92334140]|. Crypticity of this and other E. coli β-glucoside
metabolic operons presumably serves as a protective device against
toxic β-glucosides found in nature.
The asc operon contains the ascF gene encoding
the Enzyme IIAsc and the ascB gene
encoding a phospho-β-glucosidase that
hydrolyzes the aglycone from the glycoside phosphate ester. The
monocistronic ascG gene, encoding the repressor of the
ascFB operon, and the ascFB operon are transcribed
from divergent promoters. AscF and AscB are paralogues of BglF
and BglA, respectively. AscG is paralogous to GalR. The bgl
and asc operons are estimated to have arisen by operon
duplication about 3x108 years ago.
)""","""(BglF, the aromatic β-glucoside (Arbutin/Salicin)
PTS permease, belongs to the functional superfamily of the phosphoenolpyruvate
(PEP)-dependent, sugar transporting phosphotransferase system
(PTS). The PTS transports and simultaneously phosphorylates its
sugar substrates in a process called group translocation. BglF
takes up exogenous β-glucosides, releasing
the phosphate esters into the cell cytoplasm in preparation for
hydrolysis and metabolism, primarily via glycolysis |CITS: [94066914]|.
BglF, the Enzyme IIBgl complex, possesses
three domains in a single polypeptide chain with the domain order
IIB-IIC-IIA. It is homologous to PtsG (the glucose-specific PTS
Enzyme II) which has been reported to possess 8 transmembrane
α-helical segments in its IIC domain.
The IIB and IIA domains are localized to the cytoplasmic side
of the membrane. The overall PTS-mediated phosphoryl transfer
reaction, requiring the two general energy coupling proteins of
the PTS, Enzyme I and HPr, as well as the three domains of the
Enzyme II complex is:
PEP --> Enzyme I(his~~P)
--> HPr(his~~P)
--> IIA(his~~P) -->
IIB(cys~~P) -(IIC)-> β-glucoside-6-P
.
BglF transports its β-glucoside substrates
with micromolar affinities.
The bgl operon is cryptic in wild type E. coli K12.
It has been reported to be activated by the insertion of an IS
element into the region upstream of the operon in some E. coli
isolates |CITS: [92159025]|. Crypticity of this and other E. coli β-glucoside
metabolic operons presumably serves as a protective device against
toxic β-glucosides found in nature.
The bgl operon contains the bglG gene encoding
a bgl operon-specific antiterminator, the blgF gene
encoding the Enzyme IIBgl and the bglB
gene encoding a phospho-β-glucosidase
that hydrolyzes the aglycone from the glycoside phosphate ester
|CITS: [87222180]|. Insertion of an IS element upstream of the operon activates
a promoter, and the operon is then subject to β-glucoside
induction by a mechanism in which BglF-mediated phosphorylation
of BglG controls its transcriptional antitermination activity
|CITS: [89376535]|. The operon is subject to positive control by cyclic AMP
and the cyclic AMP receptor protein (CRP).
)""","""(ChbA-ChbB-ChbC, the N,N'-diacetylchitobiose PTS permease (previously
designated CelABC, the Cellobiose/Arbutin/Salicin PTS permease), belongs to
the functional superfamily of the phosphoenolpyruvate (PEP)-dependent,
sugar transporting phosphotransferase system (PTS). The PTS transports and
simultaneously phosphorylates its sugar substrates in a process called
group translocation. The ChbABC complex takes up exogenous
N,N'-diacetylchitobiose, releasing the phosphate ester into the cell
cytoplasm in preparation for hydrolysis and metabolism, primarily via
glycolysis |CITS: [84246840]|. Only this disaccharide is an inducer of the system, but
other beta-glucosides are substrates |CITS: [98070757]|.
The Enzyme IIChb complex, possesses three
polypeptide chains, ChbA, ChbB and ChbC |CITS: [90185128] [91227627]|. It is homologous
to the well-characterized lactose-specific PTS Enzyme II of Gram-positive
bacteria. IIC (ChbC) is an integral membrane transport protein
while IIA (ChbA) and IIB (ChbB) are localized to the cytoplasmic
side of the membrane. The overall PTS-mediated phosphoryl transfer
reaction, requiring the two general energy coupling proteins of
the PTS, Enzyme I and HPr, as well as the three proteins of the
Enzyme II complex is:
PEP --> Enzyme I(his~~P)
--> HPr(his~~P)
--> IIA(his~~P) -->
IIB(cys~~P) -(IIC)-> diacetylchitobiose-6-P.
IIChb transports its substrates with micromolar affinity.
As noted above, the chb operon is inducible in wild type E. coli
K12, but it has been reported to be activated for β-glucoside uptake by the
insertion of an IS1 insertion sequence elements upstream of the coding
region of the chb operon in some E. coli isolates |CITS: [90185128]|. The chb operon
contains in addition to chbA, chbB and chbC, which encode the Enzyme IIChb,
the chbR gene, which encodes a negative regulatory protein, and the chbF
gene encoding an enzyme that can function as either a
phospho-β-N,N'-diacetylchitobiase or a phospho-β-glucosidase. The operon
also includes the chbG gene of unknown function. The operon gene order is
chbBCARFG. ChbR and ChbF are paralogues of MelR, the repressor of the E.
coli melibiose operon, and melA, the α-galactosidase of the melibiose
operon, respectively |CITS: [90185127]|. The solution structure of the trimeric IIAChb has
been determined by NMR spectroscopy |CITS:[15654077]|. The 3-dimensional
structure of IIBChb has been determined |CITS: [97184687]|. The chb operon is subject to positive control by the
cyclic AMP-cyclic AMP receptor protein complex.)""","""(CmtAB, the "cryptic mannitol" PTS permease, belongs
to the functional superfamily of the phosphoenolpyruvate (PEP)-dependent,
sugar transporting phosphotransferase system (PTS). The PTS transports
and simultaneously phosphorylates its sugar substrates in a process
called group translocation. CmtAB presumably takes up an exogenous
sugar, releasing the phosphate ester into the cell cytoplasm in
preparation for metabolism |CITS: [94066914]| . The overall PTS-mediated phosphoryl
transfer reaction, requiring the two general energy coupling proteins
of the PTS, Enzyme I and HPr, as well as the three domains of
the Enzyme II complex is:
PEP --> Enzyme I(his~~P)
--> HPr(his~~P)
--> IIA(his~~P) -->
IIB(cys~~P) -(IIC)-> sugar-P.
CmtA (Enzyme IIBCCmt) and CmtB (Enzyme IIACmt)
encode a mannitol-like PTS permease. The two genes complemented
a mannitol-negative E. coli mutant when expressed using
a heterologous promoter |CITS: [93357262]| . The cmt genes are therefore
believed to be cryptic in wild-type E.coli. The
natural substrate(s) of the "cryptic mannitol" permease
are not known.
)""","""(PtsG/Crr, the glucose-specific PTS permease, belongs to the functional
superfamily of the phosphoenolpyruvate (PEP)-dependent, sugar
transporting phosphotransferase system (PTS). The PTS transports
and simultaneously phosphorylates its sugar substrates in a process
called group translocation. PtsG/Crr takes up exogenous glucose,
releasing the phosphate ester into the cell cytoplasm in preparation
for metabolism, primarily via glycolysis|CITS: [8246840]|. It can also transport
the nonmetabolizable glucoside, methyl α-glucoside
with 10-fold lower affinity.
The Enzyme IIGlc complex possesses two domains
in a single polypeptide chain with the domain order IIC-IIB (PtsG),
and it functions with an additional polypeptide chain, the Crr
or IIAGlc protein. The IIC domain of PtsG
has been reported to possess 8 transmembrane α-helical
segments |CITS: [8505291]|. The IIB domain of PtsG and IIAGlc
are localized to the cytoplasmic side of the membrane. The overall
PTS-mediated phosphoryl transfer reaction, requiring the two general
energy coupling proteins of the PTS, Enzyme I and HPr, as well
as the three domains of the Enzyme II complex is:
PEP --> Enzyme I(his~~P)
--> HPr(his~~P)
--> IIA(his~~P) -->
IIB(cys~~P) -(IIC)-> glucose-6-P.
PtsG transports glucose with low micromolar affinity.
The ptsG operon in wild type E. coli K12 is 5-10x
inducible by growth in the presence of glucose, but some E.
coli strains synthesize PtsG constitutively. IIAGlc
is synthesized constitutively from its own promoter, but it is
also slightly inducible as a result of read through from the weaker
ptsH promoter of the pts operon. ptsG but
not crr is subject to positive control by the cyclic AMP-cyclic
AMP receptor protein (CRP) complex. The ptsG operon contains
only the ptsG gene encoding the Enzyme IICBGlc.
Both the IIAGlc protein and the IIBGlc
domain of the PtsG protein have been solved in 3-dimensions by
X-ray crystallography and NMR spectroscopy, and the 3-dimensional
structure of the complex of IIAGlc with HPr
has also been solved |CITS: [1911744],[8418852],[8784182]|. PtsG was shown to exist in two forms. It is
oligomeric within the membrane and monomeric in its soluble form in the cytoplasm. Both forms exhibit
PEP-dependent sugar phosphorylation and sugar phosphate-dependent transphosphorylation activities,
though the kinetic properties of these reactions differ between the two forms of the protein
|CITS:[15576795]|.)""","""(FruAB, the fructose PTS permease, belongs to the functional superfamily
of the phosphoenolpyruvate (PEP)-dependent, sugar transporting
phosphotransferase system (PTS). The PTS transports and simultaneously
phosphorylates its sugar substrates in a process called group
translocation. FruAB takes up exogenous fructose, releasing the
1-phosphate ester into the cell cytoplasm in preparation for metabolism,
primarily via glycolysis |CITS: [8246840]|.
FruAB, the Enzyme IIFru complex, possesses
three domains in the FruA protein with the domain order IIB'-IIB-IIC
|CITS: [89341690]| and three domains in its FruB protein, also named diphosphoryl
transfer protein (DTP), with the domain order IIA-M-H where IIA
is the first phosphorylation site domain, M is a central domain
of unknown function, and H is an HPr-like domain called FPr (fructose-inducible
HPr) |CITS: [2546043]|. FruAB is homologous to MtlA (the mannitol-specific
PTS Enzyme II) which has been reported to possess 6 transmembrane
α-helical segments in its IIC domain.
The IIA, IIB and IIB' domains are localized to the cytoplasmic
side of the membrane. IIB' is required for high affinity binding
of FruB to FruA but does not participate in phosphoryl transfer
|CITS: [8626640]|. The overall PTS-mediated phosphoryl transfer reaction, requiring
the two general energy coupling proteins of the PTS, Enzyme I
and HPr, as well as the three domains of the Enzyme II complex
is:
PEP --> Enzyme I(his~~P)
--> HPr(his~~P)
--> IIA(his~~P) -->
IIB(cys~~P) -(IIC)-> fructose-1-P.
FruAB transports fructose with low micromolar affinity.
The fru operon is inducible in wild type E. coli K12
due to the presence of the fructose repressor, FruR, also known
as the catabolite repressor/activator (Cra) protein. Cra is a
member of the LacI-GalR family |CITS: [2203752] [8230205]|. The fru operon
is also subject to positive control by the cyclic AMP-cyclic AMP
receptor protein (CRP) complex. The fru operon contains
the fruB gene, the fruK gene (encoding fructose-1-P
kinase) and the fruA gene in that order. The fruR gene
does not map near the fru operon. FruK is a homologue
of phosphofructokinase.)""","""(FrvAB, a PTS permease of unknown specificity, belongs to the
functional superfamily of the phosphoenolpyruvate (PEP)-dependent,
sugar transporting phosphotransferase system (PTS). The PTS transports
and simultaneously phosphorylates its sugar substrates in a process
called group translocation. FrvAB presumably takes up an exogenous
PTS sugar, releasing the phosphate ester into the cell cytoplasm
in preparation for metabolism |CITS: [8246840] [8019415]|.
FrvAB, the Enzyme IIFrv complex, possesses
two domains in a single polypeptide chain (FrvB) with the domain
order IIB-IIC and one domain in FrvA which corresponds to a IIA
protein. It is homologous to the fructose- and mannitol-specific
PTS Enzymes II. The latter has been reported to possess 6 transmembrane
α-helical segments in its IIC domain.
The IIB and IIA domains are localized to the cytoplasmic side
of the membrane. The overall PTS-mediated phosphoryl transfer
reaction, requiring the two general energy coupling proteins of
the PTS, Enzyme I and HPr, as well as the three domains of the
Enzyme II complex is presumably:
PEP --> Enzyme I(his~~P)
--> HPr(his~~P)
--> IIA(his~~P) -->
IIB(cys~~P) -(IIC)-> sugar-P.
The frv operon (frvABXR) encodes, in addition to
FrvAB, a probable hydrolase (FrvX) and a transcriptional regulatory
protein (FrvR). It is presumably cryptic, but nothing is known
regarding its expression.
)""","""(GatABC, the galactitol PTS permease, belongs to the functional
superfamily of the phosphoenolpyruvate (PEP)-dependent, sugar
transporting phosphotransferase system (PTS). The PTS transports
and simultaneously phosphorylates its sugar substrates in a process
called group translocation. GatABC takes up exogenous galactitol,
releasing the phosphate ester into the cell cytoplasm in preparation
for oxidation and further metabolism, primarily via a modified
glycolytic pathway, the tagatose-6-P glycolytic pathway |CITS: [94066914] [97290497] [97114348]|.
GatABC, the Enzyme IIGat complex, possesses
three polypeptide chains, GatA (IIAGat), GatB
(IIBGat) and GatC (IICGat).
GatB is homologous to IIBSga and IIBSgc
and shows limited sequence similarity to the IIB proteins of the
lactose and cellobiose permeases (IIBLac and
IIBCel) |CITS:[reizergenomescitech153] [97419490]|. GatC is homologous to the
SgcC (IICSgc) protein |CITS:[reizergenomescitech153]| and shows limited
sequence similarity to IICFru. The latter
domain has been reported to possess 6 transmembrane α-helical
segments. The IIB and IIA proteins are localized to the cytoplasmic
side of the membrane. The overall PTS-mediated phosphoryl transfer
reaction, requiring the two general energy coupling proteins of
the PTS, Enzyme I and HPr, as well as the three domains of the
Enzyme II complex is:
PEP --> Enzyme I(his~~P)
--> HPr(his~~P)
--> IIA(his~~P) -->
IIB(cys~~P) -(IIC)-> galactitol-1-P.
GatABC transports galactitol with micromolar affinity.
The gat operon (gatYZABCDR) contains the gatY
gene encoding tagatose 1,6-bis-P aldolase and the gatZ
gene encoding tagatose 6-P kinase as well as gatD, the
NAD-dependent galactitol 1-P dehydrogenase |CITS: [95290497] [97113438]|. gatR
encodes the repressor of the gat operon. The gat
operon is either constitutively expressed or galactitol inducible
in wild type E. coli strains. In E. coli strains
which express the gat operon constitutively, the gatR
gene is truncated. The gat operon is subject to positive
control by the cyclic AMP-cyclic AMP receptor protein (CRP) complex.)""","""(GlvCB, a PTS permease of unknown specificity |CITS: [8019415]| belongs to the
functional superfamily of the phosphoenolpyruvate (PEP)-dependent,
sugar transporting phosphotransferase system (PTS). The PTS transports
and simultaneously phosphorylates its sugar substrates in a process
called group translocation. GlvCB presumably functions in the
uptake of exogenous sugar(s) in conjunction with a IIA protein
such as IIAGlc, releasing the phosphate esters
into the cell cytoplasm in preparation for metabolism via glycolysis
|CITS: [8246840]|.
GlvC, the Enzyme IICGlv and GlvB, the Enzyme
IIBGlv are homologous to the C and B domains
in PtsG (the glucose-specific PTS Enzyme II) which has been reported
to possess 8 transmembrane α-helical
segments in its IIC domain. The IIB domain is presumably localized
to the cytoplasmic side of the membrane and may function with
the glucose IIA protein. The overall PTS-mediated phosphoryl
transfer reaction, requiring the two general energy coupling proteins
of the PTS, Enzyme I and HPr, as well as the three domains of
the Enzyme II complex is:
PEP --> Enzyme I(his~~P)
--> HPr(his~~P)
--> IIA(his~~P) -->
IIB(cys~~P) -(IIC)-> sugar-P.
The glv operon (glvCBG) may be cryptic in wild
type E. coli K12. GlvG probably encodes an α-
or β-phosphoglucosidase as it is homologous
to such enzymes. Nothing is known about the expression or regulation
of the operon |CITS: [8019415]|.)""","""(Frx (HrsA), a putative PTS permease, belongs to the functional
superfamily of the phosphoenolpyruvate (PEP)-dependent, sugar
transporting phosphotransferase system (PTS). The PTS transports
and simultaneously phosphorylates its sugar substrates in a process
called group translocation. Frx presumably takes up an exogenous
sugar, releasing the phosphate ester into the cell cytoplasm in
preparation for metabolism (1).
Frx is a fructose-like PTS permease with the domain order IIA-IIB-IIC
(2, 3). Nothing is known about its sugar specificity, its function
or regulation of its synthesis. The overall PTS-mediated phosphoryl
transfer reaction, requiring the two general energy coupling proteins
of the PTS, Enzyme I and HPr, as well as the three domains of
the Enzyme II complex is:
PEP --> Enzyme I(his~~P)
--> HPr(his~~P)
--> IIA(his~~P) -->
IIB(cys~~P) -(IIC)-> β-glucoside-6-P.)""","""(MalX, the maltose-glucose PTS permease, belongs to the functional
superfamily of the phosphoenolpyruvate (PEP)-dependent, sugar
transporting phosphotransferase system (PTS). The PTS transports
and simultaneously phosphorylates its sugar substrates in a process
called group translocation. MalX presumably takes up exogenous
sugar, releasing the phosphate ester into the cell cytoplasm in
preparation for metabolism |CITS: [8246840]|. The overall PTS-mediated phosphoryl
transfer reaction, requiring the two general energy coupling proteins
of the PTS, Enzyme I and HPr, as well as the three domains of
the Enzyme II complex is:
PEP --> Enzyme I(his~~P)
--> HPr(his~~P)
--> IIA(his~~P) -->
IIB(cys~~P) -(IIC)-> sugar-P.
The MalX (Enzyme IICBMal) can use glucose
and maltose as substrates. It may catalyze facilitated diffusion
as well as group translocation |CITS: [1856179]| . The protein presumably functions
with the glucose Enzyme IIA and is homologous to the glucose-
and N-acetylglucosamine-specific Enzyme IICBs. The physiological
function of MalX is not known |CITS: [1856179]|.
)""","""(ManXYZ, the mannose PTS permease, belongs to the functional superfamily
of the phosphoenolpyruvate (PEP)-dependent, sugar transporting
phosphotransferase system (PTS). The PTS transports and simultaneously
phosphorylates its sugar substrates in a process called group
translocation. ManXYZ takes up exogenous hexoses (mannose, glucose,
glucosamine, fructose, 2-deoxyglucose, mannosamine, N-acetylglucosamine,
etc.), releasing the phosphate esters into the cell cytoplasm
in preparation for metabolism, primarily via glycolysis |CITS: [8246840]|.
ManXYZ, the Enzyme IIMan complex, possesses
four domains in three polypeptide chains, ManX=IIABMan,
ManY=IICMan and ManZ=IIDMan.
They are members of the mannose PTS permease family, the "splinter
group", which is not homologous to most other PTS permeases.
The IIB and IIA domains (ManX) form a homodimer that is localized
to the cytoplasmic side of the membrane |CITS: [94086520]|. ManXYZ was shown to exist in two forms. It is
oligomeric within the membrane and monomeric in its soluble form in the cytoplasm. Both forms exhibit
PEP-dependent sugar phosphorylation and sugar phosphate-dependent transphosphorylation activities,
though the kinetic properties of these reactions differ between the two forms of the protein
|CITS:[15576795]|. IIC and IID are integral membrane proteins with six and one transmembrane
α-helical spanner(s), respectively |CITS: [8774730]|. The 3-dimensional structure of
IIAMan and the secondary structure of IIBMan
have been determined |CITS: [8676384] [9030753]|. The overall PTS-mediated phosphoryl
transfer reaction, requiring the two general energy coupling proteins
of the PTS, Enzyme I and HPr, as well as the three domains of
the Enzyme II complex is:
PEP --> Enzyme I(his~~P)
--> HPr(his~~P)
--> IIA(his~~P) -->
IIB(his~~P)-(IICD)-> hexose-6-P.
ManXYZ transports mannose with micromolar affinity.
The manXYZ operon is either constitutively expressed or
inducibly expressed in response to extracellular sugar substrates
depending on the E. coli strain examined. The Mlc protein
plays a role in transcriptional regulation of this operon |CITS: [98143423]|.
The manXYZ operon is also subject to positive control
by the cyclic AMP-cyclic AMP receptor protein (CRP) complex.
)""","""(MtlA, the mannitol PTS permease, belongs to the functional superfamily
of the phosphoenolpyruvate (PEP)-dependent, sugar transporting
phosphotransferase system (PTS). The PTS transports and simultaneously
phosphorylates its sugar substrates in a process called group
translocation. MtlA takes up exogenous mannitol, releasing the
phosphate ester, mannitol-1-P, into the cell cytoplasm in preparation
for oxidation to fructose-6-P by the NAD-dependent mannitol-P
dehydrogenase (MtlD). Subsequent metabolism is primarily via
glycolysis |CITS: [94066914]|.
MtlA, the Enzyme IIMtl complex, possesses
three domains in a single polypeptide chain with the domain order
IIC-IIB-IIA |CITS: [83291014]|. It is homologous to FruAB, the fructose-specific
PTS Enzyme II. The secondary structure of IIAMtl
has been solved by NMR |CITS: [94004470]|. MtlA has been reported to possess
6 transmembrane α-helical segments
in its IIC domain |CITS: [92052139]|. The IIB and IIA domains are localized
to the cytoplasmic side of the membrane. The overall PTS-mediated
phosphoryl transfer reaction, requiring the two general energy
coupling proteins of the PTS, Enzyme I and HPr, as well as the
three domains of the Enzyme II complex is:
PEP --> Enzyme I(his~~P)
--> HPr(his~~P)
--> IIA(his~~P) -->
IIB(cys~~P) -(IIC)-> mannitol-1-P.
MtlA transports mannitol with low micromolar affinity.
The mtl operon (mtlADR) is inducible (~~20x) by
growth of wild type E. coli K12 in the presence of mannitol.
The MtlR protein is a negative transcriptional regulator of the
operon |CITS: [94131964]|. The operon is also positively controlled by the cyclic
AMP-cyclic AMP receptor protein (CRP) complex and negatively by
the catabolite repressor/activator (Cra) protein.
)""","""(NagE, the N-acetylglucosamine PTS permease, belongs to the functional
superfamily of the phosphoenolpyruvate (PEP)-dependent, sugar
transporting phosphotransferase system (PTS). The PTS transports
and simultaneously phosphorylates its sugar substrates in a process
called group translocation. NagE takes up exogenous N-acetylglucosamine,
releasing the phosphate ester into the cell cytoplasm in preparation
for metabolism, primarily via glycolysis |CITS: [94066914]|.
NagE, the Enzyme IINag complex, possesses
three domains in a single polypeptide chain with the domain order
IIC-IIB-IIA |CITS: [89050950]|. It is homologous to PtsG/Crr (the glucose-specific
PTS Enzyme II) which has been reported to possess 8 transmembrane
α-helical segments in its IIC domain.
The IIB and IIA domains are localized to the cytoplasmic side
of the membrane. The overall PTS-mediated phosphoryl transfer
reaction, requiring the two general energy coupling proteins of
the PTS, Enzyme I and HPr, as well as the three domains of the
Enzyme II complex is:
PEP--> Enzyme
I(his~~P) --> HPr(his~~P)
--> IIA(his~~P)
--> IIB(cys~~P)
-(IIC)-> N-acetylglucosamine-6-P.
NagE transports N-acetylglucosamine with low micromolar affinity.
It can also transport antibiotics such as streptozotocin.
The monocistronic nagE operon and the nagBACD operon
comprise part of the nag regulon and are transcribed from
divergent promoters. The nagBACD operon encodes (a) glucosamine-P
deaminase (NagB), (b) N-acetylglucosamine-6-P deacetylase (NagA),
(c) the nag regulon transcriptional regulator (NagC) and
(d) a gene of unknown function which is, however, homologous to
functionally characterized phosphatases (NagD) |CITS: [89343637]|. NagC together
with the cyclic AMP-cyclic AMP receptor protein (CRP) complex
controls expression of the nag regulon |CITS: [92114782] [95311313]|.)""","""(TreB, the trehalose PTS permease, belongs to the functional superfamily
of the phosphoenolpyruvate (PEP)-dependent, sugar transporting
phosphotransferase system (PTS). The PTS transports and simultaneously
phosphorylates its sugar substrates in a process called group
translocation. TreB together with IIAGlc
takes up exogenous trehalose, releasing the phosphate ester into
the cell cytoplasm in preparation for hydrolysis via phosphotrehalase
(TreA). Subsequent metabolism occurs primarily via glycolysis
|CITS: [8246840]| .
TreB, the Enzyme IITre complex, possesses
two domains in a single polypeptide chain with the domain order
IIB-IIC |CITS: [7608078]| . The IIB and IIC domains are homologous to the IIB
and IIC domains of PtsG, the glucose-specific PTS Enzyme II.
PtsG has been reported to possess 8 transmembrane α-helical
segments in its IIC domain. The IIB domain is localized to the
cytoplasmic side of the membrane, and it uses the glucose Enzyme
IIA to phosphorylate IIBTre. The overall
PTS-mediated phosphoryl transfer reaction, requiring the two general
energy coupling proteins of the PTS, Enzyme I and HPr, as well
as the three domains of the Enzyme II complex is:
PEP --> Enzyme I(his~~P)
--> HPr(his~~P)
--> IIA(his~~P) -->
IIB(cys~~P) -(IIC)-> trehalose-6-P.
TreB transports trehalose with micromolar affinity.
The tre operon is inducible in wild type E. coli K12
by the presence of low concentrations of trehalose. The treBC
operon contains the treB gene encoding the Enzyme IITre
and the treC gene encoding a phospho-trehalase that hydrolyzes
the α,α-glycosidic
bond in trehalose-6-phosphate |CITS: [8083158]| . The monocistronic treR
operon, encoding the repressor of the treBC operon is upstream
of the treBC operon and is transcribed in the same direction.
tre operon expression is under the control of the cyclic
AMP-cyclic AMP receptor protein (CRP) complex as well as that
of TreR. Metabolism of trehalose can occur either by a PTS-dependent
(low trehalose concentrations) or a PTS-independent (high trehalose
concentrations) mechanism. The latter process involves periplasmic
hydrolysis of trehalose to glucose.
)""","""(AgaBCDVWX, the putative N-acetylgalactosamine PTS permease, belongs
to the functional superfamily of the phosphoenolpyruvate (PEP)-dependent,
sugar transporting phosphotransferase system (PTS). The PTS transports
and simultaneously phosphorylates its sugar substrates in a process
called group translocation. AgaBCDVWX may take up exogenous N-acetylgalactosamine,
releasing the phosphate ester into the cell cytoplasm in preparation
for metabolism |CITS: [8246840]| .
AgaB and AgaV are Enzymes IIB; AgaC and AgaW are an Enzyme IIC
and a truncated Enzyme IIC, respectively; AgaD is an Enzyme
IID, and AgaX, which is encoded by a gene outside of the aga
operon, is an Enzyme IIA. All of these proteins are homologous
to the mannose Enzyme II complex proteins (the splinter group
enzymes) |CITS: [8932697]| . The overall PTS-mediated phosphoryl transfer reaction,
requiring the two general energy coupling proteins of the PTS,
Enzyme I and HPr, as well as the four domains of the Enzyme II
complex is proposed to be:
PEP -->
Enzyme I(his~~P) -->
HPr(his~~P)
-->
IIA(his~~P) -->
IIB(his~~P) -(IICD)-> N-acetylgalactosamine-6-P.
The aga operon (agaZVWASYBCDI) also encodes putative
enzymes that may be a kinase (AgaZ), a deacetylase (AgaA), a synthase
(AgaS), an aldolase (AgaY) and an isomerase (AgaI), all sugar
metabolic enzymes. The agaR gene, encoding a putative
transcriptional regulatory protein, precedes and is divergently
transcribed from the aga operon. Nothing is known concerning
expression of the aga operon. It may be cryptic in wild
type E. coli K12.)""","""(SgaTBA, a putative PTS permease, belongs to the functional superfamily
of the phosphoenolpyruvate (PEP)-dependent, sugar transporting
phosphotransferase system (PTS). The PTS transports and simultaneously
phosphorylates its sugar substrates in a process called group
translocation. SgaTBA presumably takes up an exogenous sugar,
releasing the phosphate ester into the cell cytoplasm in preparation
for metabolism |CITS: [8246840]| . The overall PTS-mediated phosphoryl transfer
reaction, requiring the two general energy coupling proteins of
the PTS, Enzyme I and HPr, as well as the three domains of the
Enzyme II complex is:
PEP --> Enzyme I(his~~P)
--> HPr(his~~P)
--> IIA(his~~P) -->
IIB(cys~~P) -(IIC)-> sugar-P.
The sga operon encodes SgaT, an integral membrane putative
transporter protein with 12 putative transmembrane α-helical
spanners that might function as a PTS Enzyme IIC; SgaB, the putative
Enzyme IIBSga, and SgaA, the putative Enzyme
IIASga |CITS: [REIZERGENOMESCITECH153]|. SgaB is homologous to the IIB
domains of the lactose-cellobiose PTS permease family. SgaA is
homologous to the IIA domains/proteins of the fructose-mannitol
PTS permease family. Little is known regarding the function of
these enzymes or expression of the sga operon in which
the encoding genes are found. However, the sga genes may
allow metabolism and interconversion of pentose and hexose phosphate
esters |CITS: [9274005]| .
Deletion mutation studies |CITS:[12644495]| indicate that all three components
are necessary for the uptake and utiliztion of L-ascorbate in vivo as well as for the
phosphorylation of L-ascorbate in vitro.)""","""(FrwCBD PtsA, a putative PTS permease, belongs to the functional
superfamily of the phosphoenolpyruvate (PEP)-dependent, sugar
transporting phosphotransferase system (PTS). The PTS transports
and simultaneously phosphorylates its sugar substrates in a process
called group translocation. FrwCBD PtsA presumably takes up unknown
exogenous sugars, releasing the phosphate esters into the cell
cytoplasm in preparation for metabolism |CITS: [8246840]| .
FrwC (Enzyme IICFrw), FrwB (Enzyme IIBFrw),
FrwD (Enzyme IIBFrw') and PtsA
(an Enzyme I-Enzyme IIAFrw hybrid protein)
are all encoded within the frw gene cluster. The Frw proteins
and protein domains are homologous to constituents of the fructose
Enzyme II complexes. The frw gene cluster also encodes
several enzymes concerned with anaerobic carbon metabolism. At
least two operons are present in the frw gene cluster,
but the operon structures are not clearly defined. The overall
PTS-mediated phosphoryl transfer reaction, requiring the two general
energy coupling proteins of the PTS, Enzyme I and HPr, as well
as the three domains of the Enzyme II complex is:
PEP --> Enzyme I(his~~P)
--> HPr(his~~P)
--> IIA(his~~P) -->
IIB(cys~~P) -(IIC)-> sugar-P.
Nothing is known regarding the expression of the frw gene
cluster or its regulation.)""","""(SgcABC, a putative PTS permease, belongs to the functional superfamily
of the phosphoenolpyruvate (PEP)-dependent, sugar transporting
phosphotransferase system (PTS). The PTS transports and simultaneously
phosphorylates its sugar substrates in a process called group
translocation. SgcABC presumably takes up an exogenous sugar,
releasing the phosphate ester into the cell cytoplasm in preparation
for metabolism |CITS: [8246840]| . The overall PTS-mediated phosphoryl transfer
reaction, requiring the two general energy coupling proteins of
the PTS, Enzyme I and HPr, as well as the three domains of the
Enzyme II complex is:
PEP --> Enzyme I(his~~P)
--> HPr(his~~P)
--> IIA(his~~P) -->
IIB(cys~~P) -(IIC)-> sugar-P.
SgcA (Enzyme IIASgc) is homologous to the
IIA domains of the fructose- and mannitol-specific PTS permeases.
SgcB (Enzyme IIBSgc) is homologous to the
IIB domain of the galactitol-specific PTS permease, and SgcC (Enzyme
IICSgc) is homologous to the IIC domain of
the galactitol PTS permease |CITS: [8019415]| . The function of these proteins
is not known, but they may function in the transport and phosphorylation
of 5-carbon sugars |CITS: [9274005]| . Expression of the sgc operon in
which the encoding genes are found has not been studied.
)""",]},
'B2413' : {'ecocyc-rxns': {},'ucsd-rxns' : ['SULabcpp',], 'protein-comments' : ["""(A cysZ mutant is deficient in sulfate assimilation |CITS: [6302202]|.)""",]},
'B2411' : {'ecocyc-rxns': {"""DNA-LIGASE-(NAD(+))-RXN""": """(deoxynucleotides)n + (deoxynucleotides)(m) + NAD+ -> (deoxynucleotides)(n+m) + nicotinamide mononucleotide + AMP""",},'ucsd-rxns' : ['NADDP',], 'protein-comments' : ["""(LigA is one of two known NAD(+)-dependent DNA ligases, catalyzing the
formation of phosphodiester bonds in duplex DNA.
LigA ligates duplex DNA in an NAD(+)-dependent fashion |CITS: [5341238][5341057][4291949]|.
Kinetic evaluations have yielded differing kM values for NAD(+) ranging
from 0.7 to 7 μM, a kM for strand breaks of 0.03-0.06 μM and
a turnover number of 25 ligations per minute |CITS: [4295585][4355585]|.
LigA functions as a monomer |CITS: [4355584]|.
The LigA amino-terminal Ia domain is required for reactivity
with NAD(+) and may contain an NAD(+)-binding site, though
NAD(+) binding may instead occur in the middle of the protein |CITS: [11781321][15671015]|.
The BRCT domain binds DNA and contributes to
but is not essential for DNA joining activity |CITS: [15848142]|.
LigA is required for most illegitimate recombination |CITS: [11333216]|.
However, a deficiency in LigA function yields enhanced mutation |CITS: [1105587]|.)""",]},
'B0029' : {'ecocyc-rxns': {"""ISPH2-RXN""": """1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate + NAD(P)H + H+ = Δ3-isopentenyl-PP + NAD(P)+ + H2O""","""RXN0-884""": """1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate + NAD(P)H + H+ = dimethylallyl-pyrophosphate + NAD(P)+ + H2O""",},'ucsd-rxns' : ['DMPPS','IPDPS',], 'protein-comments' : ["""(IspH acts in the mevalonate-independent pathway of isopentenyl diphosphate biosynthesis |CITS: [11818558], [12198182], [12571359]|. IspH is reported to be involved in control of guanosine 3',5'-bispyrophosphate synthetase I (RelA) |CITS: [9537400]|, regulation of the stringent response |CITS: [8432714], [1464070]|, and in resistance to penicillin |CITS: [8432714], [1464070]|.
IspH is essential |CITS: [11717301], [11418107]|. Supplementation of a mutant with downstream pathway intermediates rescues the viability |CITS: [11717301], [11418107]|. Reduction of protein abundance results in cell lysis |CITS: [11717301]|.
A mutant exhibits accumulation of a phosphate-containing antigen that activates human Vgamma9/Vdelta2 T lymphocytes |CITS: [12047749]|. This antigen is identified as (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate (HMB-PP) |CITS: [11741609]|.
IspH is predicted to be a globular protein |CITS: [11717301]|.
IspH has 34% identity to Campylobacter jejuni LytB |CITS: [9418246]| and has similarity to a Listeria monocytogenes protein involved in bile resistance |CITS: [12450822]|, to Acinetobacter sp. BD413 LytB |CITS: [10763755]|, and to hypothetical protein sequences from a number of gram-negative bacteria |CITS: [9537400]|. Functional complementation of the viability of a mutant is observed upon expression of related genes from Enterobacter aerogenes and Pseudomonas fluorescens |CITS: [9537400]|
)""",]},
'B3784' : {'ecocyc-rxns': {"""GLCNACPTRANS-RXN""": """UDP-N-acetyl-D-glucosamine + undecaprenyl phosphate = UMP + undecaprenyl-N-acetyl-α-D-glucosaminyl-pyrophosphate""",},'ucsd-rxns' : ['ACGAMT',], 'protein-comments' : ["""NIL""",]},
'B4034' : {'ecocyc-rxns': {"""RXN0-2543""": """maltose[extracellular space] =maltose[cytosol] ""","""ABC-16-RXN""": """ATP + maltose[periplasmic space] + H2O =ADP + phosphate + maltose[cytosol] """,},'ucsd-rxns' : ['MALTTTRabcpp','MALTTRabcpp','MALTPTabcpp','MALTHXabcpp','MALTabcpp','14GLUCANabcpp',], 'protein-comments' : ["""(Regulation has been described |CITS: [11350954]|. Transcription is regulated by the CreBC two-component system |CITS: [11350954]|.
Targeting of MalE to the Sec-translocase for transport across the inner membrane is
SecB-dependent |CITS:[16352602]|.)""","""(MalKFGE is a maltose transport system that is a member of the ATP-Binding Cassette (ABC) Superfamily
of transporters |CITS: [96381453]|. Based on sequence similarity, MalE is the periplasmic maltose-binding
protein, MalF and MalG are the integral membrane components, and MalK is the ATP-binding component
of the ABC transporter. A 10-fold increase in the level of maltose transport activity was observed in
membrane vesicles when the membrane associated components of the transport system (MalF, MalG, and
MalK) were overproduced |CITS: [90170921]|. Maltose transport activity abolished in proteoliposomes
prepared from a strain with a deletion of the mal genes |CITS: [90170921]|. The purified MalKFGE
complex exhibits transport-associated ATPase activity, and mutations in the malK gene resulted in
loss of transport activity without affecting protein stability |CITS: [94043174]|.)""","""NIL""",]},
'B4035' : {'ecocyc-rxns': {"""RXN0-2543""": """maltose[extracellular space] =maltose[cytosol] ""","""ABC-16-RXN""": """ATP + maltose[periplasmic space] + H2O =ADP + phosphate + maltose[cytosol] """,},'ucsd-rxns' : ['MALTTTRabcpp','MALTTRabcpp','MALTPTabcpp','MALTHXabcpp','MALTabcpp','14GLUCANabcpp',], 'protein-comments' : ["""(MalK inhibits the activation of MalT by competing with the binding of the inducer maltotriose to MalT
|CITS: [15180985]|.)""","""(MalKFGE is a maltose transport system that is a member of the ATP-Binding Cassette (ABC) Superfamily
of transporters |CITS: [96381453]|. Based on sequence similarity, MalE is the periplasmic maltose-binding
protein, MalF and MalG are the integral membrane components, and MalK is the ATP-binding component
of the ABC transporter. A 10-fold increase in the level of maltose transport activity was observed in
membrane vesicles when the membrane associated components of the transport system (MalF, MalG, and
MalK) were overproduced |CITS: [90170921]|. Maltose transport activity abolished in proteoliposomes
prepared from a strain with a deletion of the mal genes |CITS: [90170921]|. The purified MalKFGE
complex exhibits transport-associated ATPase activity, and mutations in the malK gene resulted in
loss of transport activity without affecting protein stability |CITS: [94043174]|.)""","""NIL""",]},
'B4032' : {'ecocyc-rxns': {"""RXN0-2543""": """maltose[extracellular space] =maltose[cytosol] ""","""ABC-16-RXN""": """ATP + maltose[periplasmic space] + H2O =ADP + phosphate + maltose[cytosol] """,},'ucsd-rxns' : ['MALTTTRabcpp','MALTTRabcpp','MALTPTabcpp','MALTHXabcpp','MALTabcpp','14GLUCANabcpp',], 'protein-comments' : ["""NIL""","""(MalKFGE is a maltose transport system that is a member of the ATP-Binding Cassette (ABC) Superfamily
of transporters |CITS: [96381453]|. Based on sequence similarity, MalE is the periplasmic maltose-binding
protein, MalF and MalG are the integral membrane components, and MalK is the ATP-binding component
of the ABC transporter. A 10-fold increase in the level of maltose transport activity was observed in
membrane vesicles when the membrane associated components of the transport system (MalF, MalG, and
MalK) were overproduced |CITS: [90170921]|. Maltose transport activity abolished in proteoliposomes
prepared from a strain with a deletion of the mal genes |CITS: [90170921]|. The purified MalKFGE
complex exhibits transport-associated ATPase activity, and mutations in the malK gene resulted in
loss of transport activity without affecting protein stability |CITS: [94043174]|.)""","""NIL""",]},
'B4033' : {'ecocyc-rxns': {"""RXN0-2543""": """maltose[extracellular space] =maltose[cytosol] ""","""ABC-16-RXN""": """ATP + maltose[periplasmic space] + H2O =ADP + phosphate + maltose[cytosol] """,},'ucsd-rxns' : ['MALTTTRabcpp','MALTTRabcpp','MALTPTabcpp','MALTHXabcpp','MALTabcpp','14GLUCANabcpp',], 'protein-comments' : ["""NIL""","""(MalKFGE is a maltose transport system that is a member of the ATP-Binding Cassette (ABC) Superfamily
of transporters |CITS: [96381453]|. Based on sequence similarity, MalE is the periplasmic maltose-binding
protein, MalF and MalG are the integral membrane components, and MalK is the ATP-binding component
of the ABC transporter. A 10-fold increase in the level of maltose transport activity was observed in
membrane vesicles when the membrane associated components of the transport system (MalF, MalG, and
MalK) were overproduced |CITS: [90170921]|. Maltose transport activity abolished in proteoliposomes
prepared from a strain with a deletion of the mal genes |CITS: [90170921]|. The purified MalKFGE
complex exhibits transport-associated ATPase activity, and mutations in the malK gene resulted in
loss of transport activity without affecting protein stability |CITS: [94043174]|.)""","""NIL""",]},
'B0180' : {'ecocyc-rxns': {"""RXN0-2144""": """β-hydroxy-cis-Δ5-dodecenoyl-ACP = H2O + trans-Δ3-cis-Δ5-dodecenoyl-ACP""","""3-HYDROXYDECANOYL-ACP-DEHYDR-RXN""": """a D-3-hydroxy-acyl-ACP = a trans-Δ2-enoyl-acyl-ACP + H2O""",},'ucsd-rxns' : ['3HAD160','3HAD161','3HAD100','3HAD80','3HAD120','3HAD121','3HAD60','3HAD180','3HAD181','3HAD40','3HAD141','3HAD140',], 'protein-comments' : ["""NIL""","""(Certain mutations in fabZ have been found as suppressor mutations; its sabA1 allele changes the
suppression of the OmpF315 phenotype by asmB1, and increased fabZ expression suppresses
OmpF315 itself |CITS: [9535089]|. The sfhC21 allele of fabZ allows survival of ftsH null mutants
|CITS: [10048027]|.
It appears that the FabZ protein undergoes oligomerization. The precise subunit structure has not been determined
|CITS: [95105173]|.)""",]},
'B3564' : {'ecocyc-rxns': {"""RXN0-382""": """ATP + 1-deoxy-D-xylulose = 1-deoxy-D-xylulose 5-phosphate + ADP""","""XYLULOKIN-RXN""": """xylulose + ATP = D-xylulose-5-phosphate + ADP""",},'ucsd-rxns' : ['XYLK','DXYLK',], 'protein-comments' : ["""NIL""",]},
'B2964' : {'ecocyc-rxns': {"""TRANS-RXN-108""": """H+[periplasmic space] + a nucleoside[periplasmic space] =H+[cytosol] + a nucleoside[cytosol] """,},'ucsd-rxns' : ['ADNt2pp','THMDt2pp','DADNt2pp','GSNt2pp','URIt2pp','CYTDt2pp','DCYTt2pp','DINSt2pp','INSt2pp','DURIt2pp','DGSNt2pp',], 'protein-comments' : ["""(NupG is one of two high-affinity nucleoside transporters in E. coli.
Studies of chromosomal mutants using membrane vesicles have shown that
NupG differs from NupC by mediating transport of all nucleosides whereas
NupC does not transport guanosine or deoxyguanosine |CITS: [73250126]
[79173073]|. The cloned nupG gene has been demonstrated to
complement nupG chromosomal mutations |CITS: [88029453]|.
NupG is a member of the major facilitator superfamily (MFS) of transporters
|CITS: [98190790]| and presumably functions as a nucleoside/proton
symporter.
Analysis of nupG-lacZ fusions has shown that expression of
nupG is regulated by the CytR and DeoR transcriptional regulators.
Imported nucleosides serve as precursors of DNA and RNA, as well as
of histidine and various co-factors.
Purification studies showed that recombinant NupG transported purine
(adenosine) and pyrimidine (uridine) nucleosides with apparent K(m)
values of approximately 20-30 uM Transport was energized primarily
by the proton motive force (pmf) across the cell membrane |CITS:[15513740]|.)""",]},
'B3867' : {'ecocyc-rxns': {"""HEMN-RXN""": """coproporphyrinogen III + 2 S-adenosyl-L-methionine = protoporphyrinogen IX + 2 CO2 + 2 L-methionine + 2 5'-deoxyadenosine""",},'ucsd-rxns' : ['CPPPGO2',], 'protein-comments' : ["""(E. coli contains two coproporphyrinogen III oxidases, one that is active under aerobic conditions, the
hemF gene product, and one that is active under anaerobic conditions, the hemN gene product
|CITS: [7768836][9325429]|.
HemN is monomeric when overproduced and purified under anaerobic conditions and might be
membrane-associated in vivo. The enzyme contains and oxygen-sensitive [4Fe-4S] iron-sulfur cluster;
mutations in specific residues important for iron-sulfur cluster coordination and catalysis have been analyzed and a
catalytic mechanism has been proposed |CITS: [12114526]|. HemN has been classified as a "Radical SAM enzyme"
|CITS: [11222759]|. S-adenosylmethionine (SAM) is consumed during catalysis, and the role of a second SAM
binding site in HemN has been investigated by site-directed mutagenesis |CITS: [15967800]|.
A crystal structure of HemN has been solved at 2.07 A resolution; the 4Fe-4S cluster is coordinated by three
conserved cysteine residues, and two molecules of SAM are present |CITS: [14633981]|.
Expression of hemN is increased under anaerobic growth conditions |CITS: [7768836]|.)""",]},
'B0025' : {'ecocyc-rxns': {"""RIBOFLAVINKIN-RXN""": """riboflavin + ATP = FMN + ADP""","""FADSYN-RXN""": """FMN + ATP = FAD + diphosphate""",},'ucsd-rxns' : ['RBFK','FMNAT',], 'protein-comments' : ["""(It is thought that ribF encodes a bifunctional protein with riboflavin kinase and FMN adenylyltransferase
activities. These enzymes transform riboflavin into the coenzyme forms of FMN and FAD, respectively
|CITS: [ColiSalII]|. ribF can complement the lethal defect of a ribC mutant in Bacillus subtilis
|CITS: [9473052]|.
Genetic footprinting indicated that ribF is essential for growth in E. coli |CITS: [12142426]|.)""",]},
'B2963' : {'ecocyc-rxns': {},'ucsd-rxns' : ['MLTGY3pp','MLTGY4pp','MLTGY1pp','MLTGY2pp',], 'protein-comments' : ["""(E. coli contains a large number of murein hydrolase enzymes. MltC belongs to the family of lytic
transglycosylases which degrade GlcNAcMurNAc glycan strands, resulting in the formation of a
1,6-anhydro-MurNAc residue at the released product. These enzymes are involved in the cleavage of the septum
during cell division.
Peptidoglycan hydrolase activity of MltC was demonstrated |CITS: [9158737]|.
A mutant containing deletions in mltC, mltD, and mltE has a defect in cell separation, growing as
short chains of cells |CITS: [12399477]|. These chain-forming mutants have a defect in the barrier function of the
outer membrane. A mutant strain lacking all six known lytic transglycosylases (mltA mltB mltC mltD mltE slt) is
unable to induce β-lactamase and is more susceptible to certain high-molecular weight antibiotics which are
normally inactive against Gram-negative bacteria, such as bacitracin, gallidermin and vancomycin |CITS: [15793119]|.
Expression of mltC is induced by oxidative stress via SoxS |CITS: [14594836]|.
Review: |CITS: [7487333]|)""",]},
'B1519' : {'ecocyc-rxns': {"""RXN0-2441""": """trans-aconitate + S-adenosyl-L-methionine -> (E)-3-(methoxycarbonyl)pent-2-enedioate + S-adenosyl-L-homocysteine""",},'ucsd-rxns' : ['ACONMT',], 'protein-comments' : ["""(The tam gene encodes a trans-aconitate methyltransferase |CITS: [10224113]|. This enzyme may serve to eliminate the inhibitory compound trans-aconitate, which forms spontaneously from cis-aconitate and which may have detrimental effects on normal cellular metabolism |CITS: [10224113]|.
The enzyme is cytosolic |CITS: [10224113]|. The enzyme is monomeric |CITS: [10224113]|. The reaction generates monomethyl esters of trans-aconitate, and di- or tri-methyl esters are not observed |CITS: [10224113]|.
A tam mutant does not exhibit obvious defects in growth or stationary phase viability |CITS: [10224113]|.
Regulation has been described |CITS: [10224113]|. Expression is RpoS-regulated, and transient induction is observed upon entry into stationary phase |CITS: [10224113]|.)""",]},
'B0591' : {'ecocyc-rxns': {"""RXN0-8""": """enterobactin[cytoplasm] + H+[extracellular space] =enterobactin[extracellular space] + H+[cytoplasm] """,},'ucsd-rxns' : ['FEENTERtpp',], 'protein-comments' : ["""NIL""","""(The EntS protein is a member of the major facilitator superfamily (MFS) of transporters |CITS: [98190790]|.
Based on sequence similarity, it functions as a proton-driven efflux system.
Siderophore nutrition assays have shown that an entS mutant is unable to export enterobactin
efficiently to alleviate iron deprivation |CITS:[12068807]|, though some export does still occur through
another mechanism. Deletion of tolC abolishes enterobactin export completely. Enterobactin
appears to have more than one mechanism for export to the periplasm, one involving EntS, but TolC is the
only outer membrane channel that can export enterobactin from the periplasm |CITS:[16166532]|.
)""",]},
'B0765' : {'ecocyc-rxns': {"""ABC-19-RXN""": """ATP + MoO42-[periplasmic space] + H2O =ADP + phosphate + MoO42-[cytosol] """,},'ucsd-rxns' : ['TUNGSabcpp','MOBDabcpp',], 'protein-comments' : ["""NIL""","""(ModCBA is a high-affinity molybdate transporter that is a member of the ATP-Binding Cassette (ABC)
Superfamily of transporters |CITS: [96381453]|. Based on sequence similarity, modA encodes the
periplasmic binding component, modB encodes the integral membrane component, and modC
encodes the ATP-binding component of the ABC transporter. Complementation of a mod mutant with
the cloned mod genes restored molybdate uptake activities |CITS: [96151473]|. In a mod
mutant, molybdate is not transported by the ModCBA system but by the sulfate transport system or by a
nonspecific anion transporter |CITS: [98004559]|. Transcription of mod genes is regulated by
molybdate and a repressor protein, ModE |CITS: [98004559]|.)""",]},
'B4477' : {'ecocyc-rxns': {"""DEHYDDEOXPHOSGALACT-ALDOL-RXN""": """2-dehydro-3-deoxy-D-galactonate-6-phosphate = D-glyceraldehyde-3-phosphate + pyruvate""",},'ucsd-rxns' : ['DDPGALA',], 'protein-comments' : ["""(The subunit structure is unknown.)""",]},
'B1329' : {'ecocyc-rxns': {},'ucsd-rxns' : ['3PEPTabcpp',], 'protein-comments' : ["""(Periplasmic binding component of Murein Tripeptide ABC Transporter |CITS:[9495761]|.)""","""(OppABCDF is an ATP-dependent oligopeptide transporter that is a
member of the ATP-Binding Cassette (ABC) Superfamily of transporters |CITS:[1738314]|.
OppABCDF has not been investigated in detail in E. coli,
but the orthologous system in Salmonella typhimurium has been
extensively characterized. Binding affinity and competition assays have
shown that OppABCDF will transport oligopeptides up to five amino acids
in length, but has no affinity for free amino acids |CITS:[3536860],[8801122]|.
The system has been observed to function in oligopeptide uptake, as
well as recycling of cell wall peptides |CITS:[2821267]|. Based on
sequence similarity, OppB and OppC are the membrane components
of the ABC transporter, and OppD and OppF are the ATP-binding
components of the ABC transporter |CITS:[8801122],[1738314]|.
OppA is the periplasmic substrate-binding component, however MppA
can replace OppA as a periplasmic-binding component of the transporter
when it binds murein tripeptides |CITS:[9495761]|. MppA was shown to be
required for murein tripeptide transport in a diaminoimelic acid-requiring
strain |CITS:[9495761]|. Insertion mutation of the oppF gene has
shown that OppF is required for Opp transporter function |CITS:[2821267]|.
In addition, Insertional mutants of each of the opp genes were
constructed, and the opp-minus strains were unable to utilize the
peptide Pro-Gly-Gly, normally transported by the wild-type transporter |CITS:[2821267]|.
Expression of oppABCD increased after long-term adaptation
to growth in complex medium with acetate or propionate |CITS:[12620868]|.
Expression of mppA decreased after long-term adaptation to growth
in complex medium with acetate or propionate |CITS:[12620868]|.
Expression of mppA was shown to be activated by cyclic AMP
receptor protein |CITS:[15520470]|.
)""",]},
'B2366' : {'ecocyc-rxns': {"""DSERDEAM-RXN""": """D-serine = pyruvate + ammonia""",},'ucsd-rxns' : ['SERD_D',], 'protein-comments' : ["""NIL""",]},
'B0763' : {'ecocyc-rxns': {"""ABC-19-RXN""": """ATP + MoO42-[periplasmic space] + H2O =ADP + phosphate + MoO42-[cytosol] """,},'ucsd-rxns' : ['TUNGSabcpp','MOBDabcpp',], 'protein-comments' : ["""NIL""","""(ModCBA is a high-affinity molybdate transporter that is a member of the ATP-Binding Cassette (ABC)
Superfamily of transporters |CITS: [96381453]|. Based on sequence similarity, modA encodes the
periplasmic binding component, modB encodes the integral membrane component, and modC
encodes the ATP-binding component of the ABC transporter. Complementation of a mod mutant with
the cloned mod genes restored molybdate uptake activities |CITS: [96151473]|. In a mod
mutant, molybdate is not transported by the ModCBA system but by the sulfate transport system or by a
nonspecific anion transporter |CITS: [98004559]|. Transcription of mod genes is regulated by
molybdate and a repressor protein, ModE |CITS: [98004559]|.)""",]},
'B4474' : {'ecocyc-rxns': {"""RXN0-4841""": """psicoselysine = fructoselysine""",},'ucsd-rxns' : ['FRULYSE',], 'protein-comments' : ["""(Fructoselysine 3-epimerase catalyzes the interconversion of fructoselysine and psicoselysine |CITS: [14641112]|.
Fructoselysine 3-epimerase activity is undetectable when cells are grown on glucose; stationary phase
extract of cells grown on fructoselysine or psicoselysine have an epimerase activity of 2 nmol/min per mg of protein
|CITS: [14641112]|.
FrlC: "fructoselysine" |CITS: [12147680]|.)""","""NIL""",]},
'B2114' : {'ecocyc-rxns': {"""METHIONINE--TRNA-LIGASE-RXN""": """tRNAmet + L-methionine + ATP = L-methionyl-tRNAmet + diphosphate + AMP""",},'ucsd-rxns' : ['METTRS',], 'protein-comments' : ["""(MetG is a member of the family of aminoacyl tRNA synthetases, which interpret the genetic code by covalently linking amino acids to their specific tRNA molecules. The reaction is driven by ATP hydrolysis.
MetG belongs to the Class I aminoacyl tRNA synthetases; apart from sequence motifs whithin the active site, the different enzymes show little similarity in their primary amino acid sequences.
The metG gene has been cloned by complementation of the metG83 mutation |CITS: [6094501]|. Mutagenesis of the metG gene has been used to study the domain structure of the enzyme |CITS: [2477552]|.
Several X-ray crystal structures have been determined |CITS: [7042987][2254937][10600385][11243794]|. Methionine and methionyl adenylate analogues have been used to study conformational changes during catalysis |CITS: [12946347]|.)""","""NIL""",]},
'B0760' : {'ecocyc-rxns': {},'ucsd-rxns' : ['TUNGSabcpp','MOBDabcpp',], 'protein-comments' : ["""(ModF is an uncharacterized member of the
ABC superfamily of transporters |CITS: [99091701]|.
It is the putative ATP-binding component of a
transport system whose other members are as yet
unidentified. Based on sequence similarity, this
system may function in the ATP-dependent uptake of
molybdenum.)""",]},
'B1767' : {'ecocyc-rxns': {"""ASPARAGHYD-RXN""": """L-asparagine + H2O = L-aspartate + ammonia""",},'ucsd-rxns' : ['ASNN',], 'protein-comments' : ["""NIL""","""(Coli synthesizes two L-asparaginases, I and II, which are
distinct in a number of ways. First, asparaginase I is located in the
cytoplasm, whereas asparaginase II is secreted. Asparaginase II in
contrast to asparaginase I is dramatically regulated by oxygen; under
anaerobic conditions the levels of asparaginase II are considerably
higher than in aerated cultures. Finally, whereas asparaginase I has a
relativly low affinity for its substrate, asparaginase II has a much
higher affinity, and has found widespread use in the treatment of
childhood acute lymphocytic leukemia. |CITS:[86168005]|)""",]},
'B1719' : {'ecocyc-rxns': {"""THREONINE--TRNA-LIGASE-RXN""": """tRNAthr + L-threonine + ATP -> L-threonyl-tRNAthr + diphosphate + AMP""",},'ucsd-rxns' : ['THRTRS',], 'protein-comments' : ["""(Threonyl-tRNA synthetase (ThrRS) is a member of the family of aminoacyl-tRNA synthetases, which interpret the
genetic code by covalently linking amino acids to their specific tRNA molecules. The reaction is driven by ATP
hydrolysis. ThrRS belongs to the Class II aminoacyl tRNA synthetases, which share three regions of homology
|CITS: [2203971][1852601]|.
Specificity determinants within tRNAThr that are important for recognition by ThrRS have been
identified |CITS: [2457500][2109304][1567450]|. Specificity determinants within ThrRS have been investigated and
support an induced fit model for the adenylation reaction |CITS: [14690420]|. A zinc ion at the active site is used to
discriminate against valine at the activation step |CITS: [10881191]|, while the N-terminal domain contains an editing
function that is able to deacylate mischarged Ser-tRNAThr |CITS: [11136973][15525511]|.
Threonyl-tRNA synthetase represses its own expression at the translational level
|CITS: [6325425][3930755][3510186]|. Mutations that affect autoregulation map to a region between the transcription
start site and the start of the thrS open reading frame; the site has sequence and structural similarity to parts of
tRNAThr |CITS: [3086882][3054873][3072027]|. ThrRS interacts with both an anticodon- and an
acceptor-like structure in the mRNA leader region |CITS: [1701663][1383551][8199252][7683056]|.
Defects in the regulatory and aminoacylation functions in ThrRS are correlated, suggesting that the enzyme
recognizes its mRNA and tRNA ligands in analogous ways |CITS: [2676521]|; however, one ThrRS dimer binds only
one operator region, but each of the two ThrRS subunits binds one tRNAThr |CITS: [8918475]|. A
change in the leader region according to tRNA identity rules to resemble the tRNAMet anticodon leads
to translational regulation of ThrRS by tRNAMet |CITS: [1372129]|. tRNAThr acts as an
antirepressor |CITS: [2254931]|, and the operator site of the mRNA acts as a competitive inhibitor of
tRNAThr aminoacylation |CITS: [1280807]|.
Binding of ThrRS to its mRNA target sites prevents the ribosome from binding and initiating translation
|CITS: [2207165]|. Competition between ThrRS and the ribosome for binding to the mRNA can be explained by steric
hindrance |CITS: [9767575]|. The catalytic C-terminal domain of ThrRS is responsible for operator binding, while the
N-terminal domain of ThrRS is responsible for competition with the ribosome |CITS: [12581352]|.
ThrRS is a dimer in solution |CITS: [330505]|. Crystal structures of ThrRS in various conformations have been
determined, elucidating the role of the zinc ion in the active site, the nature of the editing domain, and the structural
basis for translational control |CITS: [10319817][10881191][11953757][15525511]|.
ThrRS is under growth rate-dependent control which acts at the level of translation and requires feedback regulation
by ThrRS |CITS: [8757280]|.
Reviews: |CITS: [10966471][8419283][10881182][12615010][12787346]|
)""","""NIL""",]},
'B0734' : {'ecocyc-rxns': {"""CYT-UBIQUINOL-OXID-RXN""": """ubiquinol-8 + O2 = ubiquinone-8 + 2 H2O""",},'ucsd-rxns' : ['CYTBDpp',], 'protein-comments' : ["""(CydB is required for binding the heme b595 component and one heme d (iron-chlorin) component of cytochrome
bd-I |CITS: [1851043]|.
A cydB mutant has a temperature sensitive growth phenotype |CITS: [1328158]|.
Expression of cydAB is negatively regulated by Fnr, induced by anaerobiosis via the ArcA/ArcB
two-component regulatory system |CITS: [2172211][9302022]|, and repressed by H-NS under aerobic conditions,
resulting in maximal expression under microaerobic conditions |CITS: [11123679]|. Expression is induced by iron
limitation |CITS: [1478458]| and H2O2 exposure |CITS: [11016692]|, and is sensitive to the
level of DNA supercoiling |CITS: [11238966]|.)""","""NIL""",]},
'B3437' : {'ecocyc-rxns': {"""GLUCONOKIN-RXN""": """ATP + gluconate = ADP + 6-phospho-D-gluconate""",},'ucsd-rxns' : ['GNK',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B1125' : {'ecocyc-rxns': {"""ABC-25-RXN""": """ATP + putrescine[periplasmic space] + H2O =ADP + phosphate + putrescine[cytosol] ""","""ABC-24-RXN""": """ATP + spermidine[periplasmic space] + H2O =ADP + phosphate + spermidine[cytosol] """,},'ucsd-rxns' : ['PTRCabcpp','SPMDabcpp',], 'protein-comments' : ["""NIL""","""(PotABCD is an ATP-dependent polyamine transporter that is a member of the ATP-Binding
Cassette (ABC) Superfamily of transporters |CITS: [20053876]|. The transporter consists of a membrane
associated ATPase (PotA), two transmembrane proteins (PotB and PotC), and a periplasmic
substrate-binding protein (PotD) |CITS: [20053876]|. Knockout mutants in each of the four genes indicated
that they are all required for polyamine transport |CITS: [93374918] [20053876]|. PotA has been purified to homogeneity
and was shown to have magnesium and spermidine-dependent ATPase activity, with a Km
of 385 μM for ATP |CITS: [96029616] [20053876]|. Based on hydropathy analysis and sequence similarity, PotB and
PotC are the membrane components of the ABC transporter |CITS: [20053876]|. PotD is the periplasmic
substrate-binding protein that acts to recognize and facilitate the transport of the polyamines
|CITS: [20053876] [99315781]|. PotD preferentially binds spermidine, but will also bind putrescine with a lower affinity
(Km values of 0.1 μM and 1.5 μM for spermidine and putrescine, respectively |CITS: [20053876]|).
The dissociation constant for the binding of spermidine by PotD was found to be 3.2 μM
with an optimal spermidine concentration of 5-10 μM |CITS: [93374918]|. X-ray crystallography of
PotD showed that it has two domains with β-α -β topology, with four
acidic residues, used to recognize the positively charged nitrogen atoms of the spermidine
substrate, located in the central cleft between the two domains |CITS: [20053876] [99318982]|.
)""",]},
'B3580' : {'ecocyc-rxns': {"""LYXK-RXN""": """L-xylulose + ATP = L-xylulose-5-phosphate + ADP""","""RXN0-704""": """3-keto-L-gulonate + ATP = 3-keto-L-gulonate 6-phosphate + ADP""",},'ucsd-rxns' : ['XYLK2','3KGK',], 'protein-comments' : ["""(The lyxK gene appears to be cryptic in E. coli but can be activated through
some undefined mutation. |CITS: [95050816]|)""","""NIL""",]},
'B1123' : {'ecocyc-rxns': {"""ABC-25-RXN""": """ATP + putrescine[periplasmic space] + H2O =ADP + phosphate + putrescine[cytosol] ""","""ABC-24-RXN""": """ATP + spermidine[periplasmic space] + H2O =ADP + phosphate + spermidine[cytosol] """,},'ucsd-rxns' : ['PTRCabcpp','SPMDabcpp',], 'protein-comments' : ["""NIL""","""(PotABCD is an ATP-dependent polyamine transporter that is a member of the ATP-Binding
Cassette (ABC) Superfamily of transporters |CITS: [20053876]|. The transporter consists of a membrane
associated ATPase (PotA), two transmembrane proteins (PotB and PotC), and a periplasmic
substrate-binding protein (PotD) |CITS: [20053876]|. Knockout mutants in each of the four genes indicated
that they are all required for polyamine transport |CITS: [93374918] [20053876]|. PotA has been purified to homogeneity
and was shown to have magnesium and spermidine-dependent ATPase activity, with a Km
of 385 μM for ATP |CITS: [96029616] [20053876]|. Based on hydropathy analysis and sequence similarity, PotB and
PotC are the membrane components of the ABC transporter |CITS: [20053876]|. PotD is the periplasmic
substrate-binding protein that acts to recognize and facilitate the transport of the polyamines
|CITS: [20053876] [99315781]|. PotD preferentially binds spermidine, but will also bind putrescine with a lower affinity
(Km values of 0.1 μM and 1.5 μM for spermidine and putrescine, respectively |CITS: [20053876]|).
The dissociation constant for the binding of spermidine by PotD was found to be 3.2 μM
with an optimal spermidine concentration of 5-10 μM |CITS: [93374918]|. X-ray crystallography of
PotD showed that it has two domains with β-α -β topology, with four
acidic residues, used to recognize the positively charged nitrogen atoms of the spermidine
substrate, located in the central cleft between the two domains |CITS: [20053876] [99318982]|.
)""",]},
'B0469' : {'ecocyc-rxns': {"""ADENPRIBOSYLTRAN-RXN""": """diphosphate + AMP = 5-phosphoribosyl 1-pyrophosphate + adenine""",},'ucsd-rxns' : ['ADPT',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B3951' : {'ecocyc-rxns': {},'ucsd-rxns' : ['PFL',], 'protein-comments' : ["""(PflD was identified by sequence similarity as a homolog of pyruvate formate-lyase |CITS: [7773398]|. Effects of a gene
knockout have been studied; the fermentation pattern under microaerobic conditions is similar to wild type
|CITS: [14673546]|.)""",]},
'B1236' : {'ecocyc-rxns': {"""GLUC1PURIDYLTRANS-RXN""": """α-D-glucose 1-phosphate + UTP -> UDP-D-glucose + diphosphate""",},'ucsd-rxns' : ['GALUi',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B3428' : {'ecocyc-rxns': {"""GLYCOPHOSPHORYL-RXN""": """a glycogen + phosphate = maltodextrin + α-D-glucose 1-phosphate""","""GLYMALTOPHOSPHORYL-RXN""": """a glycogen + phosphate = maltotetraose + α-D-glucose 1-phosphate""",},'ucsd-rxns' : ['GLCP2','GLCP',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B3429' : {'ecocyc-rxns': {"""GLYCOGENSYN-RXN""": """(1,4-α-D-glucosyl)(N) + ADP-D-glucose = ADP + (1,4-α-D-glucosyl)(n+1)""",},'ucsd-rxns' : ['GLCS1',], 'protein-comments' : ["""NIL""","""(The active forms of the E. coli B glycogen synthase can
exist as dimers, trimers and tetramers. |CITS: [76114836]|)""",]},
'B2903' : {'ecocyc-rxns': {"""GCVMULTI-RXN""": """NAD+ + glycine + tetrahydrofolate = 5,10-methylene-THF + ammonia + CO2 + NADH""","""GCVP-RXN""": """H-protein-(lipoyl)lysine + glycine = CO2 + H-protein-S-(aminomethyldihydrolipoyl)lysine""",},'ucsd-rxns' : ['GLYCL',], 'protein-comments' : ["""NIL""","""NIL""","""(The glycine cleavage system is a multi-enzyme complex that
catalyzes the reversible oxidation of glycine and generates a C1 moiety. It is the second
major source of C1 units in the cell after serine hydroxymethyl
transferase.
One of the four
subunits, lipoamide dehydrogenase (E3), is shared with pyruvate
dehydrogenase and 2-oxoglutarate dehydrogenase.)""",]},
'B3425' : {'ecocyc-rxns': {"""THIOSULFATE-SULFURTRANSFERASE-RXN""": """hydrogen cyanide + thiosulfate = thiocyanate + sulfite""",},'ucsd-rxns' : ['CYANST',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B3426' : {'ecocyc-rxns': {"""GLYC3PDEHYDROG-RXN""": """sn-glycerol-3-phosphate + ubiquinone-8 = dihydroxy-acetone-phosphate + ubiquinol-8""",},'ucsd-rxns' : ['G3PD5',], 'protein-comments' : ["""NIL""","""(The aerobic glycerol 3-phosphate dehydrogenase is a homodimeric enzyme associated
with the cytoplasmic membrane through binding to negatively-charged phopholipids |CITS: [11955283]|. It is
essential for utilization of glycerol-3-phosphate or its precursors, glycerol and glycerophosphodiesters. Under
anaerobic conditions the anaerobic glycerol-3-phosphate dehydrogenase fulfills the same function. Optimal
intracellular levels of glycerol-3-phosphate are maintained for biosynthesis of phospholipids. Oxidation of
glycerol-3-phosphate results in concurrent reduction of its noncovalently-bound FAD cofactor, which passes
electrons on to ubiquinone.
GlpD is encoded by the glpD gene |CITS:[87109031] [91100269]|. Expression of glpD (along with other
members of the glp regulon |CITS: [825019]|) is repressed by GlpR and induced by glycerol-3-phosphate.
Anaerobically glpD expression is repressed by the two-component regulatory system arcA and
arcB.
)""",]},
'B4471' : {'ecocyc-rxns': {"""4.3.1.17-RXN""": """L-serine -> pyruvate + ammonia""",},'ucsd-rxns' : ['SERD_L',], 'protein-comments' : ["""(The sdhY gene product is 76% similar to the sdaA encoded deaminase and 75% similar to the sdaB
encoded deaminase.)""",]},
'B3844' : {'ecocyc-rxns': {"""FMNREDUCT-RXN""": """FMNH2 + NAD(P)+ = FMN + NAD(P)H + H+""",},'ucsd-rxns' : ['FE3Ri','FLVR(NAD)','FLVR','FMNRx2','FADRx','FMNRx',], 'protein-comments' : ["""NIL""",]},
'B3559' : {'ecocyc-rxns': {"""GLYCINE--TRNA-LIGASE-RXN""": """tRNAgly + glycine + ATP -> glycyl-tRNAgly + diphosphate + AMP""",},'ucsd-rxns' : ['GLYTRS',], 'protein-comments' : ["""(A β subunit cysteine thiol is not required for catalytic activity; however, C395 can be alkylated by NEM, resulting
in loss of GlyRS activity |CITS: [3536904]|. The N-terminal domain of the β subunit contains residues required
for adenylate synthesis, while the C-terminal domain appears to be dispensable for catalytic activity |CITS: [2404005]|.
The isolated β subunit binds tRNAGly; there is one binding site per monomer |CITS: [6374618]|.
)""","""(Glycyl-tRNA synthetase (GlyRS) is a member of the family of aminoacyl-tRNA synthetases, which interpret the
genetic code by covalently linking amino acids to their specific tRNA molecules. The reaction is driven by ATP
hydrolysis. GlyRS belongs to the Class II aminoacyl tRNA synthetases, which share three regions of homology
|CITS: [2203971][1852601]|.
GlyRS is a tetramer consisting of two α and two β subunits. Both subunits are required for catalytic activity
|CITS: [4923123][6992865]|. An enzyme in which the α and β subunits are fused into a single polypeptide
chain is catalytically active |CITS: [3009467]|.
Specificity determinants within tRNAGly that are important for recognition by GlyRS have been
identified |CITS: [167016][2068095][7664744][9171287]|. The tRNA binding site is located in the β subunit of
GlyRS |CITS: [6374618]|.
Review: |CITS: [10966471]|)""",]},
'B0335' : {'ecocyc-rxns': {},'ucsd-rxns' : ['ACCOAL',], 'protein-comments' : ["""(Acs appears to be more likely than PrpE to catalyze the first step in the propionate metabolism pathway |CITS: [12473114]|.
Regulation has been described |CITS: [12473114]|. Gene expression is induced by propionate, but protein is not observed during growth on propionate or acetate |CITS: [12473114]|.
)""",]},
'B0334' : {'ecocyc-rxns': {"""2-METHYLCITRATE-DEHYDRATASE-RXN""": """2-methylcitrate = H2O + 2-methyl-cis-aconitate""",},'ucsd-rxns' : ['MCITD',], 'protein-comments' : ["""(The prpD gene encodes 2-methylcitrate dehydratase activity |CITS: [11782506], [12473114]| and also encodes the minor aconitase activity, aconitase C |CITS: [11782506]|, which constitutes 5% or less of cellular activity and is observed in an acnA acnB double mutant |CITS: [9202458]|. Aconitase C activity does not substitute for aconitase A and B activities in vivo and appears not to be reversible, in contrast to true aconitase activity, and is therefore better described as a dehydratase activity |CITS: [11782506]|. The substrate specificity of the enzyme is examined |CITS: [11782506], [12473114]|.
PrpD is an iron-sulfur cluster protein of the [2Fe-2S] type |CITS: [11782506]|. The enzyme is monomeric |CITS: [11782506]|. Overproduction and purification of the enzyme is described |CITS: [12473114]|.
The Salmonella enterica PrpD protein has been crystallized for structural studies |CITS: [11807258]|. The Salmonella enterica PrpD enzyme has been characterized |CITS: [9006051], [10482501], [11294638]|.
Regulation has been described |CITS: [12473114]|. Gene expression is induced by propionate |CITS: [12473114]|. Protein production is observed during growth on propionate, but not acetate |CITS: [12473114]|.)""",]},
'B0337' : {'ecocyc-rxns': {"""CYTDEAM-RXN""": """H2O + cytosine -> ammonia + uracil""",},'ucsd-rxns' : ['CSND',], 'protein-comments' : ["""(Earlier characterization of the enzyme had found it to consist of two polypeptides of different molecular mass. Recent
studies did not confirm this observation, finding only a single polypeptide. |CITS: [92349961]|
Cytosine deaminase is present in prokaryotes and fungi, but not in multicellular eukaryotes. It is thus of interest for
the design of antimicrobial agents. Cytosine deaminase is also being used for suicide gene therapy against tumors
|CITS: [11948367]|.)""",]},
'B0369' : {'ecocyc-rxns': {"""PORPHOBILSYNTH-RXN""": """2 5-amino-levulinate = 2 H2O + porphobilinogen""",},'ucsd-rxns' : ['PPBNGS',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B0331' : {'ecocyc-rxns': {"""METHYLISOCITRATE-LYASE-RXN""": """methylisocitrate = succinate + pyruvate""",},'ucsd-rxns' : ['MCITL2',], 'protein-comments' : ["""(PrpB catalyzes the final step in the propionate metabolism pathway |CITS: [12473114]|. The prpB-encoded
2-methylisocitrate lyase is a homotetramer |CITS: [11422389]|. 2-Methylisocitrate lyase activity shows dependence
on Mg2+ (Km of 35 micromolar) and inhibition by Ca2+ |CITS: [11422389]|. The enzyme
(with 2 mM Mg2+) exhibits a Km of 19 micromolar for threo-2-methylisocitrate |CITS: [11422389]|.
The enzyme activity is sensitive to oxidation |CITS: [11422389]| and is inactivated by 3-bromopyruvate alkylation
|CITS: [11422389]|.
A crystal structure is presented at 1.9 A resolution |CITS: [12706720]|. Purification of the native enzyme is described,
as well as purification of overproduced, histidine-tagged enzyme |CITS: [11422389]|.
The Salmonella enterica PrpB enzyme has been characterized |CITS: [9006051], [10482501], [11294638]|.
Regulation has been described |CITS: [12473114], [11422389]|. Protein production is observed during growth on
propionate, but not acetate |CITS: [12473114]|. Activity is not observed during growth on glucose |CITS: [11422389]|.)""","""NIL""",]},
'B0333' : {'ecocyc-rxns': {"""2-METHYLCITRATE-SYNTHASE-RXN""": """oxaloacetate + H2O + propionyl-CoA = 2-methylcitrate + coenzyme A""","""CITSYN-RXN""": """oxaloacetate + acetyl-CoA + H2O = citrate + coenzyme A""",},'ucsd-rxns' : ['MCITS',], 'protein-comments' : ["""(Regulation has been described |CITS: [12473114]|. Protein production is observed during growth on propionate, but not acetate |CITS: [12473114]|.
)""","""NIL""",]},
'B0068' : {'ecocyc-rxns': {"""ABC-32-RXN""": """ATP + thiamine[periplasmic space] + H2O =ADP + phosphate + thiamine[cytosol] """,},'ucsd-rxns' : ['THMabcpp',], 'protein-comments' : ["""(The E. coli SufA/TbpA protein has been purified and characterized as a 34.2 kDa monomer.
It contains one tightly bound thiamin species, thiamin, thiamin monophosphate (TMP),
or thiamin diphosphate (TDP), per monomer |CITS:[12182833]|.)""","""(The ABC transporter ThiBPQ was functionally characterized in Salmonella typhimurium where it is
required for the uptake of thiamine and thiamine pyrophosphate |CITS:[9535878]|. Its ortholog in
E. coli, SfuABC, has not been functionally characterized yet but presumably also function in
thiamine uptake. thiB (sfuA) encodes periplasmic thiamine binding protein. thiP
(sfuB) encodes inner membrane permease, and thiQ(sfuC) encodes
energy-transducing ATPase.
)""",]},
'B0237' : {'ecocyc-rxns': {"""3.4.13.3-RXN""": """EC# 3.4.13.3""",},'ucsd-rxns' : ['AMPTASEPG','AMPTASECG','LALGP',], 'protein-comments' : ["""NIL""","""(Peptidase D is a dipeptidase capable of breaking down a number of dipeptides with unblocked
N termini, including cysteinylglycine |CITS: [7988883][11157967]|.
Peptidase D functions as a dimer of PepD monomers |CITS: [3540199]|.)""",]},
'B0339' : {'ecocyc-rxns': {"""CARBODEHYDRAT-RXN""": """H2CO3 = H2O + CO2""",},'ucsd-rxns' : ['HCO3E',], 'protein-comments' : ["""(The enzyme behaves as an oligomer, the precise number of
subunits in the active form has not yet been determined |CITS:[92156106]|.
Can has similarity to CynT, and induction of cynT expression suppresses phenotypes of a can mutant
|CITS: [14563877]|. A can cynT double mutant is only viable under high CO2 conditions
|CITS: [12784642]|.)""","""NIL""",]},
'B1646' : {'ecocyc-rxns': {"""SUPEROX-DISMUT-RXN""": """2 H+ + 2 O2- = H2O2 + O2""",},'ucsd-rxns' : ['SPODMpp',], 'protein-comments' : ["""(SodC is a periplasmic enzyme that converts superoxide radicals to hydrogen peroxide and water. It
is inactivated by hydrogen peroxide and diethyldithiocarbamate, suggesting that it contains both
copper and zinc |CITS: [4836277][7929223]|. Of the two metals, the presence of copper has
been demonstrated experimentally |CITS: [8791100]|.
SodC is monomeric even at high protein concentration and in a number of buffers. Charged residues
in portions of the protein that are typically hydrophobic dimer interfaces may explain this |CITS: [9003353]|.
SodC expression is repressed by Fnr during anaerobiosis and strongly induced during
aerobic growth |CITS: [10216871][7929223]|. SodC is induced in stationary
phase by RpoS, which helps diminished enhanced sensitivity to hydrogen peroxide that occurs
for several hours after entry into stationary phase following aerobic growth |CITS: [15489429][10216871][8626323]|.)""",]},
'B2813' : {'ecocyc-rxns': {},'ucsd-rxns' : ['MLTGY3pp','MLTGY4pp','MLTGY1pp','MLTGY2pp',], 'protein-comments' : ["""(MltA is one of three (along with MltB and Slt70) major lytic endotransglycosylases expressed in Escherichia coli.
MltA and MltB are expressed as membrane-bound lipoproteins. Overexpression of MltA resulted in elevated levels of
a membrane fraction protein with a molecular mass corresponding to the mass of the purified MltA protein |CITS:[8288527]|.
Expression of MltA in cells grown in the presence of H-3 palmitate followed by SDS-PAGE analysis resulted in
fluorographic visualization of a labeled band corresponding to the 39 kDa mass of MltA, demonstrating the lipoprotein
character of MltA |CITS:[6988430]|. Sucrose gradient centrifugation studies have shown that MltA is localized to the
outer membrane |CITS:[9287002]|. Induced overexpression of MltA resulted in lysis of cells grown at 30 degrees Celsius,
the optimal temperature for enzymatic activity, but not at 37 degrees. Furthermore the expressed activity was able to
hydrolyze both murein sacculi as well as isolated glycan strands |CITS:[9287002]|. A triple mltA, mltB, and
slt70 mutant resulted in a 72% reduction in murein turnover |CITS:[10572120]|.)""",]},
'B3633' : {'ecocyc-rxns': {"""KDOTRANS2-RXN""": """(KDO)-lipid IVA + CMP-3-deoxy-D-manno-octulosonate = KDO2-lipid IVA + CMP""","""KDOTRANS-RXN""": """CMP-3-deoxy-D-manno-octulosonate + lipid IVA = (KDO)-lipid IVA + CMP""",},'ucsd-rxns' : ['MOAT2','MOAT',], 'protein-comments' : ["""(The lipopolysaccharide of E. coli K-12 consists of two major components:
the hydrophobic lipid A moiety inserted into the outer membrane and the
phosphorylated core oligosaccharide |CITS:[12045108]|. E. coli K-12
does not produce O antigen to attach to the LPS core due to a defect in the
rfb gene cluster which can be complemented with genes from a second,
independent rfb mutant to produce an O16 type O antigen |CITS:[7517391]|.
E. coli K-12 may have two major pathways for LPS biosynthesis. One
generates LPS cores suitable for O antigen attachment, and a second generates
lipooligosaccharides (LOS) with modifications to the core structure which prevent
O antigen attachment |CITS:[1385388]|.
WaaA is responsible for attachment of the KDOI and KDOII residues to the Lipid A moiety.
Reviews: |CITS:[12045108],[9791168],[7504166]|
)""",]},
'B2987' : {'ecocyc-rxns': {"""TRANS-RXN-114""": """H+[periplasmic space] + phosphate[periplasmic space] =H+[cytosol] + phosphate[cytosol] """,},'ucsd-rxns' : ['PIt2rpp',], 'protein-comments' : ["""(PitB is a putative third (along with low-affinity phosphate transporter, PitA, and the phosphate ABC type
transporter system, PstSCAB) inorganic phosphate transporter. It has been shown that PitB forms a soluble
neutral metal phosphate (MeHPO4) proton symporter complex |CITS: [94153935]|. Cloning
and overexpression studies |CITS:[21382172]| demonstrate that pitB is a phosphate transporter whose
repression/inhibition is mediated through the pho regulon. It is thought that pitB expression is
regulated by the amount of available phosphate, unlike pitA, which is constitutively expressed.
Deletion studies suggest that pitB is inactivated or repressed through the pho regulon since
deletion of this regulon activated phosphate uptake by pitB |CITS:[21382172]|.)""",]},
'B3952' : {'ecocyc-rxns': {},'ucsd-rxns' : ['PFL',], 'protein-comments' : ["""(PflC was identified by sequence similarity as a homolog of pyruvate formate-lyase activating enzyme
|CITS: [7773398]|. Effects of a gene knockout have been studied; the fermentation pattern under microaerobic
conditions is similar to wild type |CITS: [14673546]|.)""",]},
'B2242' : {'ecocyc-rxns': {"""GLYC3PDEHYDROG-RXN""": """sn-glycerol-3-phosphate + ubiquinone-8 = dihydroxy-acetone-phosphate + ubiquinol-8""",},'ucsd-rxns' : ['G3PD7','G3PD6','G3PD5',], 'protein-comments' : ["""NIL""","""(The GlpABC enzyme is loosely associated with the cell membrane. A functional two subunit form, GlpAC, has been
isolated, and it is assumed that the third subunit (GlpB) is responsible for membrane anchoring.
The GlpA subunit contains noncovalently bound FAD, and the GlpC subunit is thought to bind flavin mononucleotide
|CITS: [3286606]|.
The GlpB subunit contains two iron-sulfur clusters, and does not contain any transmembrane helices, so
the mechanism by which it acts as the membrane anchor for the complex is not clear
|CITS: [3286606][7576488]|.
Please note: reference |CITS: [6363389]| and reference |CITS: [3286606]| utilize different terminologies for the
members of the glpACB operons. The former names the genes A,B,C, while the later names them A,C and B,
respectively. Throughout this discussion we have used the nomenclature of the later.
This three-subunit enzyme converts glycerol-3-phosphate to dihydroxyacetone phosphate (DHAP) using
electron acceptors other than oxygen, and functions mostly under anaerobic conditions.
The anaerobic dehydrogenase protein complex is encoded by the glpACB operon,
and is regulated by glycerol and catabolite repression |CITS: [6363389]|.
The reducing equivalents are passed through a simple electron transport chain which terminates with
fumarate or nitrate as the electron acceptor |CITS:[82007833]|.
Expression of glpABC (along with other members of the glp regulon |CITS: [825019]| is repressed by
GlpR and induced by glycerol-3-phosphate. Optimal intracellular levels of glycerol-3-phosphate are maintained for
biosynthesis of phospholipids. The glpTQ operon, which encodes glycerol-3-phosphate transporter and
phosphodiesterase is adjacent to glpABC. The two operons are divergently transcribed; the operators to
which GlpR binds overlap the ,glpA promoter |CITS: [9179845]|.
)""",]},
'B3648' : {'ecocyc-rxns': {"""GMKALT-RXN""": """ATP + dGMP = ADP + dGDP""","""GUANYL-KIN-RXN""": """GMP + ATP = GDP + ADP""",},'ucsd-rxns' : ['GK1','DGK1',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B0723' : {'ecocyc-rxns': {"""SUCCINATE-DEHYDROGENASE-(UBIQUINONE)-RXN""": """a ubiquinone + succinate = a ubiquinol + fumarate""",},'ucsd-rxns' : ['SUCDi',], 'protein-comments' : ["""(This is one of two catalytic subunits in the four subunit enzyme.
This subunit contains the FAD cofactor |CITS: [2659351]|. Analysis of
the nucleotide sequence suggests the location of the active site
and the site of FAD attachment |CITS: [6383359]|.
Succinate, fumarate, citrate, and isocitrate appear to cause increased flavinylation of overproduced SdhA in cell
extracts, indicating the existence of an activation mechanism involving TCA cycle intermediates |CITS: [2659351]|.
This protein has similarity to the FrdA subunit of fumarate reductase |CITS: [6383359]|. A 2.2 Å
crystal structure of L-aspartate oxidase suggests that an unusual tertiary structure is shared by L-aspartate
oxidase, the SdhA subunit of succinate dehydrogenase, and the FrdA subunit of fumarate
reductase |CITS: [10425677]|.
Regulation has been described |CITS: [11917098], [10423529], [9720032], [9383149], [9209026], [7860604], [7783618], [8132465], [1885542], [2644240], [3309132], [6388571], [9383149]|.)""","""(The complex containing only SdhA and SdhB is sometimes called "succinate dehydrogenase" |CITS: [COLISALII]|.
In vitro, SdhA and SdhB alone, devoid of the membrane-bound subunits SdhC and SdhD, exhibit
succinate dehydrogenase activity with non-physiological electron acceptors |CITS: [COLISALII]|.)""","""(The enzyme has two catalytic subunits (SdhA, SdhB) plus two membrane subunits (SdhC, SdhD).
The succinate oxidation reaction, which is part of the aerobic respiratory chain and part of the Krebs cycle, oxidizes
succinate to fummarate while reducing ubiquinone to ubiquinol. It is closely related to fumarate reductase, which
carries out the reverse reaction. The succinate dehydrogenase and fumarate reductase can replace each other |CITS: [GUEST81]|.
The quinone-binding domains of the two enzymes differ significantly |CITS: [12788489]|.
The enzyme exists as a trimer with a total molecular weight of 360 K Daltons.
The structure of Sdh has been determined at 2.6 Angstroms resolution |CITS: [12560550]|.
The enzyme is specific for the optical isomer fumarate. Electron transfer occurs among
neighboring membrane-bound components of the electron transport chain.
Succinate dehydrogenase is made under aerobic conditions with succinate or acetate
as a carbon source. Enzyme synthesis is regulated by catabolite repression
|CITS: [3309132]|. Activation of the enzyme by covalent attachment of FAD to the SdhA enzyme subunit is promoted
by intermediates of the TCA cycle |CITS: [2659351]|. Expression of the enzyme is negatively controlled, under
conditons of anaaerobic growth, by ArcA and Fnr. These two regulatory proteins act independently |CITS: [9383149]|.
The cytochrome b556 (SdhC and SdhD subunits and heme b) is reported to be required for membrane association and stable activity of the enzyme |CITS: [8550613]|. Proper assembly of the enzyme complex shows a specific requirement for heme iron that is not rescued by other metalloporphyrins |CITS: [11405622]|. One report suggests that mutations that disrupt heme coordination do not disrupt enzyme function |CITS: [9521736]|, whereas another report suggests that the mutant proteins in question do retain heme binding activity |CITS: [11259408]|.
The membrane-associated four-subunit enzyme uses the electron acceptor ubiquinone-8 in vitro |CITS:[2644269]|. SdhC is the ubiquinone binding subunit |CITS: [9822661]|.
A single-step purification of overproduced succinate dehydrogenase is
described |CITS: [2644269]|. The enzyme is purified and separated into a distinct catalytic subcomplex (SdhA and SdhB) and membrane-anchoring activity (SdhC and SdhD) |CITS: [9092498]|. The four-subunit enzyme has been crystallized for structural studies |CITS: [11803025]|.
Succinate dehydrogenase may may play a role in infection, as the enzyme is necessary for succinate-mediated protection of stationary-phase cells from killing by a derivative of a human antimicrobial peptide (BPI) |CITS: [10760151]|.
Fumarate reductase is a similar enzyme, but is made under different
physiological conditions. Fumarate reductase is made under anaerobic
conditions with glucose as a carbon source. Succinate dehydrogenase and
fumarate reductase functions are partially interchangeable if
their regulation is manipulated such that succinate dehydrogenase is produced under
anaerobic conditions or fumarate reductase is produced aerobically |CITS: [6274999] [9811659]|.
)""",]},
'B0720' : {'ecocyc-rxns': {"""CITSYN-RXN""": """oxaloacetate + acetyl-CoA + H2O = citrate + coenzyme A""",},'ucsd-rxns' : ['CS',], 'protein-comments' : ["""NIL""","""(The E. coli citrate synthase is a type II enzyme, which appears to be unique to the Gram-negative bacteria.
It behaves like a trimer of dimeric subunits; the dimer is the basic catalytic unit, but the hexameric form is required for
allosteric inhibition by NADH. By contrast, citrate synthase from animals, plants and some bacteria is a simple
dimer that is not allosterically regulated. |CITS:[89025711]|
Enzyme synthesis is subject to catabolite repression, is repressed by glucose and anaerobiosis, and induced by
acetate and oxygen. When acetate is the carbon source, citrate synthase is rate-limiting for the TCA cycle.
|CITS:[85216543][89076352]|
Crystal structures of citrate synthase have been solved, providing insight into the allosteric regulatory mechanism of
the enzyme |CITS: [11683626][12741811][12824188]|.)""",]},
'B0721' : {'ecocyc-rxns': {"""SUCCINATE-DEHYDROGENASE-(UBIQUINONE)-RXN""": """a ubiquinone + succinate = a ubiquinol + fumarate""",},'ucsd-rxns' : ['SUCDi',], 'protein-comments' : ["""(One of two membrane proteins in the four subunit enzyme. SdhC and SdhD are the large and small subunits of cytochrome
b556, respectively |CITS: [8550613]|. SdhC is the ubiquinone binding subunit of succinate-ubiquinone
oxidoreductase |CITS: [9822661]|. A characterization of S27A, S27C, S27T, R31A, R31K, R31H, S33T, and S33A
mutant proteins suggests that the S27 and R31 side chains in the wild-type protein may hydrogen-bond with
quinone ring carbonyls |CITS: [9822661]|.
The b556 type heme bridges both membrane
subunits |CITS: [99417502], [8550613]|. Published reports disagree
about whether mutation of SdhC-[His84] or SdhD-[His71] residues
eliminate coordination of the heme b |CITS: [11259408] [9521736]|.
SdhC-[His84] is involved in interaction with the quinone electron
acceptor |CITS: [11259408]|. SdhC-[His84] and SdhD-[His71] (with the associated heme b) are
reported to be dispensable for assembly, while SdhC-[His30] is required
for proper assembly of the membrane-bound enzyme |CITS: [9521736]|.
Mutants lacking SdhC and SdhD show cytoplasmic succinate dehydrogenase activity using artificial electron acceptors, in contrast to wild-type
membrane-associated succinate-ubiquinone oxidoreductase activity |CITS: [8550613], [COLISALII]|.
Despite similar function, hydrophobicity, and protein size, the SdhC
and SdhD subunits of succinate dehydrogenase do not share significant
sequence identity with the corresponding membrane-binding subunits of fumarate reductase, FrdC and FrdD |CITS: [6383359]|.
Regulation has been described |CITS: [11917098], [10423529], [9720032], [9383149], [9209026], [7860604], [7783618], [8132465], [1885542], [2644240], [3309132], [6388571], [9383149]|.)""","""(SdhA and SdhB alone, devoid of the membrane-bound subunits SdhC and SdhD, exhibit cytoplasmic
succinate dehydrogenase activity that does not use ubiquinone as the electron acceptor |CITS: [COLISALII]|.)""","""(The enzyme has two catalytic subunits (SdhA, SdhB) plus two membrane subunits (SdhC, SdhD).
The succinate oxidation reaction, which is part of the aerobic respiratory chain and part of the Krebs cycle, oxidizes
succinate to fummarate while reducing ubiquinone to ubiquinol. It is closely related to fumarate reductase, which
carries out the reverse reaction. The succinate dehydrogenase and fumarate reductase can replace each other |CITS: [GUEST81]|.
The quinone-binding domains of the two enzymes differ significantly |CITS: [12788489]|.
The enzyme exists as a trimer with a total molecular weight of 360 K Daltons.
The structure of Sdh has been determined at 2.6 Angstroms resolution |CITS: [12560550]|.
The enzyme is specific for the optical isomer fumarate. Electron transfer occurs among
neighboring membrane-bound components of the electron transport chain.
Succinate dehydrogenase is made under aerobic conditions with succinate or acetate
as a carbon source. Enzyme synthesis is regulated by catabolite repression
|CITS: [3309132]|. Activation of the enzyme by covalent attachment of FAD to the SdhA enzyme subunit is promoted
by intermediates of the TCA cycle |CITS: [2659351]|. Expression of the enzyme is negatively controlled, under
conditons of anaaerobic growth, by ArcA and Fnr. These two regulatory proteins act independently |CITS: [9383149]|.
The cytochrome b556 (SdhC and SdhD subunits and heme b) is reported to be required for membrane association and stable activity of the enzyme |CITS: [8550613]|. Proper assembly of the enzyme complex shows a specific requirement for heme iron that is not rescued by other metalloporphyrins |CITS: [11405622]|. One report suggests that mutations that disrupt heme coordination do not disrupt enzyme function |CITS: [9521736]|, whereas another report suggests that the mutant proteins in question do retain heme binding activity |CITS: [11259408]|.
The membrane-associated four-subunit enzyme uses the electron acceptor ubiquinone-8 in vitro |CITS:[2644269]|. SdhC is the ubiquinone binding subunit |CITS: [9822661]|.
A single-step purification of overproduced succinate dehydrogenase is
described |CITS: [2644269]|. The enzyme is purified and separated into a distinct catalytic subcomplex (SdhA and SdhB) and membrane-anchoring activity (SdhC and SdhD) |CITS: [9092498]|. The four-subunit enzyme has been crystallized for structural studies |CITS: [11803025]|.
Succinate dehydrogenase may may play a role in infection, as the enzyme is necessary for succinate-mediated protection of stationary-phase cells from killing by a derivative of a human antimicrobial peptide (BPI) |CITS: [10760151]|.
Fumarate reductase is a similar enzyme, but is made under different
physiological conditions. Fumarate reductase is made under anaerobic
conditions with glucose as a carbon source. Succinate dehydrogenase and
fumarate reductase functions are partially interchangeable if
their regulation is manipulated such that succinate dehydrogenase is produced under
anaerobic conditions or fumarate reductase is produced aerobically |CITS: [6274999] [9811659]|.
)""",]},
'B0726' : {'ecocyc-rxns': {"""2OXOGLUTARATEDEH-RXN""": """α-ketoglutarate + coenzyme A + NAD+ = succinyl-CoA + CO2 + NADH""","""RXN0-1144""": """α-ketoglutarate + SucB-lipoate -> SucB-S-succinyldihydrolipoate + CO2""",},'ucsd-rxns' : ['AKGDH',], 'protein-comments' : ["""NIL""","""(SucA is the E1(0) component of the oxoglutarate dehydrogenase complex.
REACTION: E1(o) + TPP = E1(o).TPP,
E1(o).TPP + 2-oxoglutarate = E1(o).hydroxycarboxypropylTPP + CO(2),
E1(o).hydroxycarboxypropylTPP + E2(o).lipoate(S2) = E1(o).TPP +
E2(o).lipoate(SH)(S-succinyl))""","""(One of the most complicated enzyme systems known.
A complex composed of multiple copies of 3 enzymes- E1, E2 and E3.
The E3 component is shared with the pyruvate dehydrogenase and glycine cleavage
multi-enzyme complexes. E1
and E2 differ slightly for 2oxoglutarate and pyruvate complexes,
designated (o) and (p) to distinguish them.
Substrate is channeled through the catalytic reactions by attachment
in thioester linkage to lipoyl groups via so-called 'swinging arm',
carrying substrate molecules to successive active sites.)""",]},
'B0727' : {'ecocyc-rxns': {"""2OXOGLUTARATEDEH-RXN""": """α-ketoglutarate + coenzyme A + NAD+ = succinyl-CoA + CO2 + NADH""","""RXN0-1147""": """succinyl-CoA + enzyme N6-(dihydrolipoyl)lysine -> coenzyme A + enzyme N6-(S-succinyldihydrolipoyl)lysine""",},'ucsd-rxns' : ['AKGDH',], 'protein-comments' : ["""(The SucB subunit (E2o) of the 2-oxoglutarate dehydrogenase complex is responsible for the dihydrolipoamide
succinyltransferase activity |CITS: [6376124]|.
The protein has a single lipoyl domain at the N terminus, and a domain with catalytic activity and subunit binding
activity at the C terminus |CITS: [6376124]|. The protein has areas that contain a large amount of alanine and proline
|CITS: [6376124]| with charged residues |CITS: [3297046]|. The domain structure has been examined by limited
proteolysis experiments |CITS: [3297046]|.
The SucB homomultimer constitutes the core of the 2-oxoglutarate dehydrogenase complex. Each peptide chain
contains one lipoyl domain, like many mammalian enzymes, whereas the E. coli pyruvate E2(p) component has
three. A 'swinging arm' mechanism carries the substrate to the active sites.
REACTION: E1(o).hydroxycarboxypropylTPP + E2(o).lipoate(S)2 = E1(o).TPP + E2(o).lipoate(SH)(S-succinyl),
E2(o).lipoate(SH)(S-succinyl) + CoA = E2(o).lip(SH)2 + succinylCoA
SucB (E2o) has similarity to the AceF (E2p) subunit of the pyruvate dehydrogenase multienzyme complex; however,
the N-terminal domain of AceF contains three lipoyl repeats, whereas SucB contains only one of these sequences
|CITS: [6376124]|. SucB has similarity to Coxiella burnetii SucB, which elicits an immune response in infected
humans |CITS: [10524791]|. The Mycobacterium tuberculosis SucB is involved in a protective antioxidant
response to attack by the immune system |CITS: [11799204]|.
Regulation has been described |CITS: [6376124], [3897791], [3002435], [3543212], [12107143]|.
The initial sequence of the gene has been corrected |CITS: [3297046]|.)""","""NIL""","""NIL""","""NIL""","""NIL""","""(One of the most complicated enzyme systems known.
A complex composed of multiple copies of 3 enzymes- E1, E2 and E3.
The E3 component is shared with the pyruvate dehydrogenase and glycine cleavage
multi-enzyme complexes. E1
and E2 differ slightly for 2oxoglutarate and pyruvate complexes,
designated (o) and (p) to distinguish them.
Substrate is channeled through the catalytic reactions by attachment
in thioester linkage to lipoyl groups via so-called 'swinging arm',
carrying substrate molecules to successive active sites.)""",]},
'B0724' : {'ecocyc-rxns': {"""SUCCINATE-DEHYDROGENASE-(UBIQUINONE)-RXN""": """a ubiquinone + succinate = a ubiquinol + fumarate""",},'ucsd-rxns' : ['SUCDi',], 'protein-comments' : ["""(This is one of two catalytic subunits of the four subunit enzyme.
This subunit contains three iron-sulfur clusters: a 2Fe-2S, a 4Fe-4S
and a 3Fe-4S.
This subunit has 38% identity to the fumarate reductase iron-sulfur cluster subunit, FrdB |CITS: [6388571]|.
Regulation has been described |CITS: [11917098], [10423529], [9720032], [9383149], [9209026], [7860604], [7783618], [8132465], [1885542], [2644240], [3309132], [6388571], [9383149]|.)""","""(The complex containing only SdhA and SdhB is sometimes called "succinate dehydrogenase" |CITS: [COLISALII]|.
In vitro, SdhA and SdhB alone, devoid of the membrane-bound subunits SdhC and SdhD, exhibit
succinate dehydrogenase activity with non-physiological electron acceptors |CITS: [COLISALII]|.)""","""(The enzyme has two catalytic subunits (SdhA, SdhB) plus two membrane subunits (SdhC, SdhD).
The succinate oxidation reaction, which is part of the aerobic respiratory chain and part of the Krebs cycle, oxidizes
succinate to fummarate while reducing ubiquinone to ubiquinol. It is closely related to fumarate reductase, which
carries out the reverse reaction. The succinate dehydrogenase and fumarate reductase can replace each other |CITS: [GUEST81]|.
The quinone-binding domains of the two enzymes differ significantly |CITS: [12788489]|.
The enzyme exists as a trimer with a total molecular weight of 360 K Daltons.
The structure of Sdh has been determined at 2.6 Angstroms resolution |CITS: [12560550]|.
The enzyme is specific for the optical isomer fumarate. Electron transfer occurs among
neighboring membrane-bound components of the electron transport chain.
Succinate dehydrogenase is made under aerobic conditions with succinate or acetate
as a carbon source. Enzyme synthesis is regulated by catabolite repression
|CITS: [3309132]|. Activation of the enzyme by covalent attachment of FAD to the SdhA enzyme subunit is promoted
by intermediates of the TCA cycle |CITS: [2659351]|. Expression of the enzyme is negatively controlled, under
conditons of anaaerobic growth, by ArcA and Fnr. These two regulatory proteins act independently |CITS: [9383149]|.
The cytochrome b556 (SdhC and SdhD subunits and heme b) is reported to be required for membrane association and stable activity of the enzyme |CITS: [8550613]|. Proper assembly of the enzyme complex shows a specific requirement for heme iron that is not rescued by other metalloporphyrins |CITS: [11405622]|. One report suggests that mutations that disrupt heme coordination do not disrupt enzyme function |CITS: [9521736]|, whereas another report suggests that the mutant proteins in question do retain heme binding activity |CITS: [11259408]|.
The membrane-associated four-subunit enzyme uses the electron acceptor ubiquinone-8 in vitro |CITS:[2644269]|. SdhC is the ubiquinone binding subunit |CITS: [9822661]|.
A single-step purification of overproduced succinate dehydrogenase is
described |CITS: [2644269]|. The enzyme is purified and separated into a distinct catalytic subcomplex (SdhA and SdhB) and membrane-anchoring activity (SdhC and SdhD) |CITS: [9092498]|. The four-subunit enzyme has been crystallized for structural studies |CITS: [11803025]|.
Succinate dehydrogenase may may play a role in infection, as the enzyme is necessary for succinate-mediated protection of stationary-phase cells from killing by a derivative of a human antimicrobial peptide (BPI) |CITS: [10760151]|.
Fumarate reductase is a similar enzyme, but is made under different
physiological conditions. Fumarate reductase is made under anaerobic
conditions with glucose as a carbon source. Succinate dehydrogenase and
fumarate reductase functions are partially interchangeable if
their regulation is manipulated such that succinate dehydrogenase is produced under
anaerobic conditions or fumarate reductase is produced aerobically |CITS: [6274999] [9811659]|.
)""",]},
'B3526' : {'ecocyc-rxns': {"""DEOXYGLUCONOKIN-RXN""": """2-dehydro-3-deoxy-D-gluconate + ATP = 2-keto-3-deoxy-6-phospho-gluconate + ADP""",},'ucsd-rxns' : ['DDGLK',], 'protein-comments' : ["""NIL""",]},
'B3640' : {'ecocyc-rxns': {"""DUTP-PYROP-RXN""": """dUTP + H2O -> dUMP + diphosphate""",},'ucsd-rxns' : ['DUTPDP',], 'protein-comments' : ["""NIL""","""(Deoxyuridine triphosphatase (dUTPase) catalyzes the hydrolysis of dUTP, maintaining a
low intracellular concentration of dUTP so that uracil cannot be
incorporated into DNA. dUTPase is specific for dUTP as a substrate,
the active site discriminating between nucleotides with respect to the
sugar moiety as well as the pyrimidine base. The enzyme has been
crystallized |CITS: [92158084] [78150962]|.
dut mutants fail to replicate the chromosomal terminus, resulting
in the accumulation of subchromosomal fragments containing an
origin of replication |CITS: [16297932]|.)""",]},
'B3528' : {'ecocyc-rxns': {"""TRANS-RXN-121C""": """Na+[periplasmic space] + orotate[periplasmic space] =Na+[cytosol] + orotate[cytosol] ""","""TRANS-RXN-121B""": """Na+[periplasmic space] + fumarate[periplasmic space] =Na+[cytosol] + fumarate[cytosol] ""","""TRANS-RXN-121A""": """Na+[periplasmic space] + malate[periplasmic space] =Na+[cytosol] + malate[cytosol] ""","""TRANS-RXN-121""": """Na+[periplasmic space] + succinate[periplasmic space] =Na+[cytosol] + succinate[cytosol] """,},'ucsd-rxns' : ['ASPt2_2pp','MALDt2_2pp','SUCCt2_2pp','FUMt2_2pp','MALt2_2pp','OROTt2_2pp',], 'protein-comments' : ["""(DctA is a sodium-dependent dicarboxylate transporter, responsible
for the uptake of fumarate, succinate and malate under aerobic
conditions, and also for the uptake of orotate, a pyrmidine precursor.
Mutants defective in dctA were unable to grow on fumarate
or malate and showed decreased growth on succinate and were unable
to utilise orotate as a pyrimidine source |CITS: [97113529]|. These
defects could be complemented by the cloned dctA gene. DctA
is highly similar to the Rhizobium meliloti dicarboxylate
transporter DctA and is a member of the DAACS family of dicarboxylate
and amino acid transporters |CITS: [94304911]|. It seems likely that
DctA functions as a sodium/dicarboxylate and sodium/orotate symporter.)""",]},
'B0728' : {'ecocyc-rxns': {"""SUCCCOASYN-RXN""": """succinate + coenzyme A + ATP = succinyl-CoA + ADP + phosphate""",},'ucsd-rxns' : ['SUCOAS',], 'protein-comments' : ["""(ACTIVE.SITES: 1 succinate, 1 CoA binding site per monomer)""","""(There are two classes of this enzyme. One like the pig heart enzyme are dimers, others
like E coli are tetramers. Genes for the 2 subunits are coordinately
expressed, so alpha and beta subunits are produced in equimolar
proportions |CITS: [WolodkoetalJB143-231(80)]| Adjacent on genetic map is
gene g30, which may have a regulatory function |CITS:[89350876]|
There is one ATP binding site and one phosphorylation
histidine per monomer, but in the dimer, an alternating mode utilizes only one
at a time.)""",]},
'B0729' : {'ecocyc-rxns': {"""SUCCCOASYN-RXN""": """succinate + coenzyme A + ATP = succinyl-CoA + ADP + phosphate""",},'ucsd-rxns' : ['SUCOAS',], 'protein-comments' : ["""(contains the his residue that is phosphorylated.
Catalyses its own phosphorylation.)""","""(There are two classes of this enzyme. One like the pig heart enzyme are dimers, others
like E coli are tetramers. Genes for the 2 subunits are coordinately
expressed, so alpha and beta subunits are produced in equimolar
proportions |CITS: [WolodkoetalJB143-231(80)]| Adjacent on genetic map is
gene g30, which may have a regulatory function |CITS:[89350876]|
There is one ATP binding site and one phosphorylation
histidine per monomer, but in the dimer, an alternating mode utilizes only one
at a time.)""",]},
'B2817' : {'ecocyc-rxns': {"""NACMURLALAAMI-RXN""": """EC# 3.5.1.28""",},'ucsd-rxns' : ['AGM3PApp','AGM4PApp',], 'protein-comments' : ["""(AmiC is an N-acetylmuramyl-L-alanine amidase, which cleaves the peptide moiety from N-acetylmuramic acid,
removing murein crosslinks. AmiC is active toward the murein located at the septum and thereby important for cell
separation upon cell division |CITS: [11454209]|. AmiA, AmiB, and AmiC appear to have overlapping functions
|CITS: [11454209]|. AmiC is involved in wild-type stability of the cell envelope |CITS: [12787348]|.
AmiC is translocated from the cytoplasm to the periplasm by the twin-arginine transport (Tat) system
|CITS: [12787347][12787348]|. During cell division, AmiC specifically localizes to the septal ring; localization is
mediated by an N-terminal targeting domain and dependent on FtsN. In small cells that have not begun deviding,
AmiC is located throughout the periplasm |CITS: [12787347]|.
An amiC mutant forms cell chains |CITS: [11454209]| and a mutant lacking all three
N-acetylmuramyl-L-alanine amidases (AmiA, AmiB, and AmiC) forms even more extensive cell chains and shows
morphological abnormalities consistent with a defect in murein degradation |CITS: [11454209]|. The triple mutant is
also less sensitive than wild type to the antibiotics aztreonam and bulgecin |CITS: [11454209]|.
Review: |CITS: [15491352]|
)""",]},
'B4322' : {'ecocyc-rxns': {"""MANNONDEHYDRAT-RXN""": """D-mannonate -> H2O + 2-dehydro-3-deoxy-D-gluconate""",},'ucsd-rxns' : ['MNNH',], 'protein-comments' : ["""NIL""",]},
'B4323' : {'ecocyc-rxns': {"""MANNONOXIDOREDUCT-RXN""": """NAD+ + D-mannonate = NADH + fructuronate""",},'ucsd-rxns' : ['MANAO',], 'protein-comments' : ["""NIL""",]},
'B1638' : {'ecocyc-rxns': {"""PNPOXI-RXN""": """O2 + pyridoxine-5'-phosphate = H2O2 + pyridoxal 5'-phosphate""","""PMPOXI-RXN""": """O2 + H2O + pyridoxamine 5'-phosphate = H2O2 + ammonia + pyridoxal 5'-phosphate""",},'ucsd-rxns' : ['PDX5POi','PYAM5PO',], 'protein-comments' : ["""NIL""","""(The pdxH gene codes for a monofunctional flavoprotein enzyme
that can accept either pyridoxine 5'-phosphate (PNP) or pyridoxamine
5'-phosphate (PMP) as substrates. The PNP/PMP oxidase is a key
committed enzyme in the biosynthesis of the coenzyme pyridoxal
5'-phosphate. The enzyme also functions in the salvage pathway. Since the
oxidase uses molecular oxygen, there may be a
second pathway in anaerobically growing E. coli. |CITS: [95164519] [98196726]|)""",]},
'B2066' : {'ecocyc-rxns': {"""URKI-RXN""": """uridine + GTP = UMP + GDP""","""CYTIDINEKIN-RXN""": """cytidine + GTP = CMP + GDP""",},'ucsd-rxns' : ['URIK2','CYTDK2',], 'protein-comments' : ["""NIL""",]},
'B2065' : {'ecocyc-rxns': {"""DCTP-DEAM-RXN""": """H2O + dCTP -> ammonia + dUTP""",},'ucsd-rxns' : ['DCTPD',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B3359' : {'ecocyc-rxns': {"""SUCCINYLDIAMINOPIMTRANS-RXN""": """α-ketoglutarate + N-succinyl-L,L-2,6-diaminopimelate = L-glutamate + N-succinyl-2-amino-6-ketopimelate""","""ACETYLORNTRANSAM-RXN""": """N-acetyl-L-ornithine + α-ketoglutarate = N-acetyl-L-glutamate 5-semialdehyde + L-glutamate""",},'ucsd-rxns' : ['ACOTA','SDPTA',], 'protein-comments' : ["""NIL""","""(The is a dual function enzyme, which participates in the biosynthesis of both lysine and arginine.
The enzyme was initially purified by Peterkofsky and Gilvarg |CITS: [13734750]|, and later by Cox et al |CITS: [Cox96]|,
as the dapC-encoded N-succinyldiaminopimelate-aminotransferase. However, searches for the
dapC gene were unsuccessful.
The gene has been independently cloned and sequenced as argD, encoding acetylornithine
transaminase, by Heimberg et al |CITS: [2199330]|. In 1999 Ledwidge and Blanchard |CITS: [10074354]|
purified and sequenced the N-succinyldiaminopimelate-aminotransferase protein,
showing that it is identical to the argD gene product.
Interestingly, the E. coli argD gene does not share sequence similarity with the dapC gene of other
organisms (such as Bordetella pertusis), even though both gene products catalyze the same reaction
|CITS: [10850974]|.)""",]},
'B2867' : {'ecocyc-rxns': {"""RXN0-901""": """xanthine + NAD+ + H2O = urate + NADH + H+""","""RXN0-902""": """hypoxanthine + H2O = 2 H+ + xanthine""",},'ucsd-rxns' : ['HXAND','XAND',], 'protein-comments' : ["""(XdhB has similarity to YagS |CITS: [10986234]|. XdhB has similarity to the FAD-binding domain of Drosophila melanogaster xanthine dehydrogenase |CITS: [10986234]|.)""","""(XdhA-XdhB-XdhC is a putative heterotrimeric xanthine dehydrogenase |CITS: [10986234]|.
Degradation of hypoxanthine, xanthosine, inosine, or allantoin does not provide adequate nitrogen to support cell growth under aerobic conditions, in contrast to degradation of adenine or adenosine, which does support cell growth |CITS: [10986234]|. Hypoxanthine, guanosine, inosine, or xanthosine (but not allantoin) speeds the growth of cells utilizing aspartate as the nitrogen source |CITS: [10986234]|.
Xanthine degradation to allantoin has been observed |CITS: [10986234]|.
It is suggested that xanthine dehydrogenase plays a role in purine salvage, perhaps by favoring production of GMP rather than AMP |CITS: [10986234]|.)""",]},
'B3957' : {'ecocyc-rxns': {"""ACETYLORNDEACET-RXN""": """N-acetyl-L-ornithine + H2O = L-ornithine + acetate""",},'ucsd-rxns' : ['NACODA','ACODA',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B1637' : {'ecocyc-rxns': {"""TYROSINE--TRNA-LIGASE-RXN""": """tRNAtyr + L-tyrosine + ATP -> L-tyrosyl-tRNAtyr + diphosphate + AMP""",},'ucsd-rxns' : ['TYRTRS',], 'protein-comments' : ["""(Tyrosyl-tRNA synthetase (TyrRS) is a member of the family of aminoacyl-tRNA synthetases, which interpret the
genetic code by covalently linking amino acids to their specific tRNA molecules. The reaction is driven by ATP
hydrolysis. TyrRS belongs to the Class I aminoacyl tRNA synthetases |CITS: [2203971][7647112]|.
The enzyme is a homodimer in solution |CITS: [4626368][4579631][6754952]|. TyrRS binds one molecule of
tRNATyr per TyrRS dimer and has two binding sites for tyrosine with different dissociation constants
|CITS: [1096941][9287][6754952]|. Other reports find two equivalent tyrosinyl-5'-AMP binding sites |CITS: [377229]|;
the binding data may require more complex analysis |CITS: [511381]|.
The reaction mechanism of TyrRS has been studied |CITS: [1096942][399325]|. Aminoacylation proceeds via the
aminoacyl adenylate pathway |CITS: [764868]|. TyrRS also aminoacylates tRNATyr with D-tyrosine
|CITS: [4289778][4292198][329276]|; the resulting D-Tyr-tRNATyr can be hydrolyzed by
D-Tyr-tRNATyr deacylase |CITS: [4292198][10918062]|. Discrimination by TyrRS against phenylalanine
appears to be at the level of amino acid recognition |CITS: [7006687]|.
Specificity determinants within tRNATyr that are important for recognition by TyrRS were found to consist
of the discriminator base at position 73 and the first base of the anticodon of tRNATyr
|CITS: [1377381][12903187]|. Residues within TyrRS that interact with tRNATyr have been identified
|CITS: [3513822]|, and the Lys237 residue has been implicated in ATP binding |CITS: [8031903]|. An F130S mutation
allows efficient charging of azatyrosine onto tRNATyr |CITS: [11006270]|.
Crystal structures of the catalytic domain of TyrRS in complex with L-tyrosine and Tyr-AMS have been solved at 2
and 2.7 Å resolution |CITS: [15663931]|. Crystal structures of a mutant protein which recognizes
3-iodo-L-tyrosine have been solved |CITS: [15671170]|.
Reviews: |CITS: [10966471][2126463][8199245]|
)""","""NIL""",]},
'B1636' : {'ecocyc-rxns': {"""PYRIDOXKIN-RXN""": """ATP + pyridoxal -> ADP + pyridoxal 5'-phosphate""",},'ucsd-rxns' : ['PYDXK',], 'protein-comments' : ["""NIL""",]},
'B2744' : {'ecocyc-rxns': {"""3-NUCLEOTID-RXN""": """a nucleoside 3'-phosphate + H2O = a ribonucleoside + phosphate""","""5'-NUCLEOTID-RXN""": """a ribonucleoside monophosphate + H2O = a ribonucleoside + phosphate""",},'ucsd-rxns' : ['NTD10','NTD11','NTD12','PPA2','NTD8','NTD9','NTD6','NTD7','NTD4','NTD5','NTD2','NTD3','NTD1','PPA',], 'protein-comments' : ["""(SurE is a phosphatase with broad substrate specificity. A substrate profile has been determined; the enzyme has
the highest Km (20 micromolar) with polyphosphate |CITS: [15489502]|.
SurE was initially thought to be involved in cell survival during stationary phase |CITS: [7928962]|, but it has since
been shown that the phenotype was due to the presence of an amber mutation in rpoS |CITS: [9209028]|.
SurE and Pcm may act in parallel protein damage response pathways |CITS: [9785447]|.
Transcriptional fusions showed an RpoS-independent increase in surE transcription during stationary phase
|CITS: [9387229]|.)""",]},
'B2866' : {'ecocyc-rxns': {"""RXN0-901""": """xanthine + NAD+ + H2O = urate + NADH + H+""","""RXN0-902""": """hypoxanthine + H2O = 2 H+ + xanthine""",},'ucsd-rxns' : ['HXAND','XAND',], 'protein-comments' : ["""(XdhA has similarity to the molybdenum cofactor-containing domains of Drosophila melanogaster xanthine dehydrogenase and Desulfovibrio gigas aldehyde oxidoreductase |CITS: [10986234]|.
An xdhA mutant exhibits a defect in an indirect assay of xanthine dehydrogenase activity and exhibits sensitivity to adenine, which is indicative of a defect in purine salvage |CITS: [10986234]|. The mutant exhibits more rapid growth than wild type utilizing aspartate as the source of nitrogen and growth under these conditions is stimulated by hypoxanthine |CITS: [10986234]|. The mutant shows wild-type growth utilizing abundant ammonia as the nitrogen source |CITS: [10986234]|.)""","""(XdhA-XdhB-XdhC is a putative heterotrimeric xanthine dehydrogenase |CITS: [10986234]|.
Degradation of hypoxanthine, xanthosine, inosine, or allantoin does not provide adequate nitrogen to support cell growth under aerobic conditions, in contrast to degradation of adenine or adenosine, which does support cell growth |CITS: [10986234]|. Hypoxanthine, guanosine, inosine, or xanthosine (but not allantoin) speeds the growth of cells utilizing aspartate as the nitrogen source |CITS: [10986234]|.
Xanthine degradation to allantoin has been observed |CITS: [10986234]|.
It is suggested that xanthine dehydrogenase plays a role in purine salvage, perhaps by favoring production of GMP rather than AMP |CITS: [10986234]|.)""",]},
'B3222' : {'ecocyc-rxns': {"""NANK-RXN""": """N-acetylmannosamine + ATP = N-acetyl-D-mannosamine-6-phosphate + ADP""",},'ucsd-rxns' : ['AMANK',], 'protein-comments' : ["""(The initial assignment of function to this gene product was based on homology |CITS: [9864311]|.
The subunit structure is unknown.
Overexpression of nanK rescues the glucose auxotrophy of a glucokinase mutant, and the NanK protein functions
as a rudimentary glucokinase in vitro |CITS: [15157072]|.
Regulation has been described |CITS: [12897000]|. Transcription of nanATEK-yhcH (sialic acid catabolic operon) is
repressed by a NanR homodimer |CITS: [12897000]|.)""",]},
'B3223' : {'ecocyc-rxns': {"""NANE-RXN""": """N-acetyl-D-mannosamine-6-phosphate = N-acetyl-D-glucosamine-6-phosphate""",},'ucsd-rxns' : ['AMANAPEr',], 'protein-comments' : ["""(The assignment of function to the nanE gene product is based on
homology and biochemistry. The subunit structure is unknown.
Regulation has been described |CITS: [12897000]|. Transcription of nanATEK-yhcH (sialic acid catabolic operon) is repressed by a NanR homodimer |CITS: [12897000]|.)""",]},
'B3966' : {'ecocyc-rxns': {"""RXN0-2121""": """cob(I)alamin[extracellular space] =cob(I)alamin[cytosol] ""","""RXN0-1565""": """cob(I)alamin[extracellular space] =cob(I)alamin[periplasmic space] """,},'ucsd-rxns' : ['CBItonex','CBL1tonex','ADOCBLtonex',], 'protein-comments' : ["""(Regulation has been described |CITS: [12323379]|. Translation is down-regulated by coenzyme B(12)
via a direct interaction between the compound and the 5'-untranslated region of the mRNA
|CITS: [12323379]|. BtuB is an outer membrane porin that mediates high affinity binding and TonB-
dependent active transport of vitamin B12 (cyanocobalamin) across the outer membrane.Calcium binding to
BtuB induces high-affinity binding of cyanocobalamin. Several structures of this 22 strand beta barrel
protein have been elcudiated including a structure with bound calcium and cyanocobalamin
|CITS: [12652322]| . BtuB is also the receptor for A and E colicins which enter by way of the Tol system.
)""","""NIL""","""NIL""","""NIL""",]},
'B2818' : {'ecocyc-rxns': {"""N-ACETYLTRANSFER-RXN""": """L-glutamate + acetyl-CoA = N-acetyl-L-glutamate + coenzyme A""",},'ucsd-rxns' : ['ACGS',], 'protein-comments' : ["""NIL""","""(N-acetylglutamate synthase (ArgA) catalyzes the synthese of N-acetylglutamate from L-glutamate and acetyl-CoA.
Though the molecular weight of ArgA multimers can vary from 144-224 kD with concentration of ArgA, the
presence of the reactant L-arginine and the product N-acetyl-L-glutamate stabilizes the molecular
weight at 300 kD, indicating that the active form is a hexamer |CITS: [16890]|. ArgA is optimally
stable at pH 7, though it has maximal activity at pH 10 |CITS: [16890]|.)""",]},
'B3288' : {'ecocyc-rxns': {"""METHIONYL-TRNA-FORMYLTRANSFERASE-RXN""": """N10-formyl-THF + L-methionyl-tRNAfmet + H2O = tetrahydrofolate + N-formyl-L-methionyl-tRNAfmet""",},'ucsd-rxns' : ['FMETTRS',], 'protein-comments' : ["""(The fmt gene encodes 10-formyltetrahydrofolate:L-methionyl-tRNA(fMet) N-formyltransferase |CITS: [1624424]|. The formylation of the methionylated initiator tRNA that is catalyzed by this enzyme is important in restricting the use of the methionylated initiator tRNA specifically for initiation, rather than chain elongation |CITS: [8331078]|.
The enzyme activity has been characterized |CITS: [6989606], [6995120], [6387369], [9843398], [10694387]|. Substrate recognition and specificity have been studied |CITS: [1917939], [1373194], [1409632], [7515283], [8346229], [7779813], [9030604], [9391059], [9843398], [9927661], [10694387], [10891086], [12087168]|. The protein structure is discussed with respect to substrate binding |CITS: [8887566], [9843487]|.
fmt mutations result in a growth defects and heat sensitivity |CITS: [1624424][10428776]|.
Fmt is monomeric |CITS: [8727328]|.
A crystal structure is presented at 2.0 Å resolution |CITS: [8887566]|. A crystal structure of the
enzyme-substrate complex is presented at 2.8 Å resolution |CITS: [9843487]|.
Fmt has amino-terminal structural similarity to glycinamide ribonucleotide
formyltransferase |CITS: [8887566]|.
Regulation has been described |CITS: [8432722], [8112305]|.
Reviews: |CITS: [8199241], [7507918], [8955898], [11860363]|.)""",]},
'B3380' : {'ecocyc-rxns': {},'ucsd-rxns' : ['PPM',], 'protein-comments' : ["""(No information about this protein was found by a literature search conducted on December 22, 2005.)""",]},
'B2752' : {'ecocyc-rxns': {"""SULFATE-ADENYLYLTRANS-RXN""": """sulfate + ATP = APS + diphosphate""",},'ucsd-rxns' : ['SADT2',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B1281' : {'ecocyc-rxns': {"""OROTPDECARB-RXN""": """orotidine-5'-phosphate = CO2 + UMP""",},'ucsd-rxns' : ['OMPDC',], 'protein-comments' : ["""NIL""","""(Orotidine-5'-phosphate-decarboxylase (PyrF) catalyzes the synthesis of |FRAME: UMP|.
PyrF dimerizes to become active orotidine-5'-phosphate-decarboxylase, catalyzing
the conversion of orotidine-5'-phosphate to UMP |CITS: [6355062]|. It does
this with a specific activity of 220 U/mg protein |CITS: [6355062]|.
pyrF mutants excrete orotic acid under conditions when normal
strains excrete uracil |CITS: [361725]|. Strains deficient in |FRAME: CPLX0-3521|
show higher PyrF activity than wild-type strains |CITS: [6319231]|.)""",]},
'B2169' : {'ecocyc-rxns': {"""TRANS-RXN-158""": """phosphoenolpyruvate + fructose[periplasmic space] =fructose-1-phosphate[cytosol] + pyruvate """,},'ucsd-rxns' : ['FRUptspp',], 'protein-comments' : ["""(contains PTS Enzyme IIA and FPr domains)""","""(FruAB, the fructose PTS permease, belongs to the functional superfamily
of the phosphoenolpyruvate (PEP)-dependent, sugar transporting
phosphotransferase system (PTS). The PTS transports and simultaneously
phosphorylates its sugar substrates in a process called group
translocation. FruAB takes up exogenous fructose, releasing the
1-phosphate ester into the cell cytoplasm in preparation for metabolism,
primarily via glycolysis |CITS: [8246840]|.
FruAB, the Enzyme IIFru complex, possesses
three domains in the FruA protein with the domain order IIB'-IIB-IIC
|CITS: [89341690]| and three domains in its FruB protein, also named diphosphoryl
transfer protein (DTP), with the domain order IIA-M-H where IIA
is the first phosphorylation site domain, M is a central domain
of unknown function, and H is an HPr-like domain called FPr (fructose-inducible
HPr) |CITS: [2546043]|. FruAB is homologous to MtlA (the mannitol-specific
PTS Enzyme II) which has been reported to possess 6 transmembrane
α-helical segments in its IIC domain.
The IIA, IIB and IIB' domains are localized to the cytoplasmic
side of the membrane. IIB' is required for high affinity binding
of FruB to FruA but does not participate in phosphoryl transfer
|CITS: [8626640]|. The overall PTS-mediated phosphoryl transfer reaction, requiring
the two general energy coupling proteins of the PTS, Enzyme I
and HPr, as well as the three domains of the Enzyme II complex
is:
PEP --> Enzyme I(his~~P)
--> HPr(his~~P)
--> IIA(his~~P) -->
IIB(cys~~P) -(IIC)-> fructose-1-P.
FruAB transports fructose with low micromolar affinity.
The fru operon is inducible in wild type E. coli K12
due to the presence of the fructose repressor, FruR, also known
as the catabolite repressor/activator (Cra) protein. Cra is a
member of the LacI-GalR family |CITS: [2203752] [8230205]|. The fru operon
is also subject to positive control by the cyclic AMP-cyclic AMP
receptor protein (CRP) complex. The fru operon contains
the fruB gene, the fruK gene (encoding fructose-1-P
kinase) and the fruA gene in that order. The fruR gene
does not map near the fru operon. FruK is a homologue
of phosphofructokinase.)""",]},
'B4374' : {'ecocyc-rxns': {"""5'-NUCLEOTID-RXN""": """a ribonucleoside monophosphate + H2O = a ribonucleoside + phosphate""",},'ucsd-rxns' : ['NTD5','NTD2','NTD1',], 'protein-comments' : ["""(YjjG has phosphatase activity towards UMP, dUMP, and dTMP, and the activity is inhibited by nucleoside di- and
triphosphates |CITS: [15489502]|. Phosphatase activity of YjjG was also shown in a high-throughput screen of
purified proteins |CITS: [15808744]|.
YjjG is oligomeric in solution |CITS: [15489502]|.
)""",]},
'B0151' : {'ecocyc-rxns': {"""RXN0-2241""": """iron (III) hydroxamate complex[extracellular space] =iron (III) hydroxamate complex[cytosol] ""","""ABC-11-RXN""": """ATP + iron (III) hydroxamate complex[periplasmic space] + H2O =ADP + phosphate + iron (III) hydroxamate complex[cytosol] """,},'ucsd-rxns' : ['FE3HOXabcpp','CPGNabcpp','ARBTNabcpp','FEOXAMabcpp','FECRMabcpp',], 'protein-comments' : ["""NIL""","""(The FhuBCD ATP-dependent iron (III) hydroxamate transporter is a member of the ATP-Binding Cassette
(ABC) Superfamily of transporters |CITS: [96381453]|. FhuBCD catalyzes transport of iron (III)-hydroxamate
compounds across the inner membrane into the cytoplasm of E. coli. Hydroxamates, or siderophores,
are used to increase the solubility of iron (III), which is normally insoluble at pH 7 |CITS: [88038363]|.
Based on sequence similarity, FhuB is the transmembrane component |CITS: [98086115]|, FhuC is the
ATP-binding subunit |CITS: [87279948]|, and FhuD is the periplasmic siderophore-binding component of
the ABC transporter |CITS: [98273640]|. A mutant with overproduced periplasmic FhuD protein was shown
to bind to radioactively labeled iron (III) ferrichrome |CITS: [91307893]|. Resistance of FhuD to protease K
in the presence of ferrichrome, aerobactin, and coprogen also indicated binding of these substrates to
FhuD |CITS: [91307893]|. In E. coli, hydroxamate transport across the outer membrane (via FhuA
and the TonB-ExbB-ExbD complex), coupled with the FhuBCD-mediated hydroxamate transport across
the cytoplasmic membrane completes the uptake of iron (III) hydroxamates into the cell. fhuA-fhuB
mutants exhibited completely abolished growth promotion by natural hydroxamates |CITS: [20048384]|.)""","""NIL""",]},
'B0150' : {'ecocyc-rxns': {"""RXN0-2241""": """iron (III) hydroxamate complex[extracellular space] =iron (III) hydroxamate complex[cytosol] ""","""RXN0-1701""": """iron (III) hydroxamate complex[extracellular space] =iron (III) hydroxamate complex[periplasmic space] """,},'ucsd-rxns' : ['FEOXAMtonex','FECRMtonex','FE3HOXtonex',], 'protein-comments' : ["""(FhuA is involved with the transport of ferrichrome across the outer membrane. |CITS: [9865695]| It forms a monomeric
channel consisting of a 22-strand, antiparallel β-barrel, obstructed by a "plug" formed by residues 19-159. |CITS: [9865695]|
FhuA interacts with TonB to move siderophore-iron complexes across the outer membrane. |CITS: [10209114]| TonB
combined with ExbB and ExbD, also serves to couple this transport with the electrochemical gradient across the inner
membrane, allowing for the accumulation of siderophore-iron against the concentration gradient, thereby making it an
active process. |CITS: [10209114]| In addition to siderophore transport, FhuA also transports albomycin and rifamycin
CGP 4832, and serves as a receptor for phages T5, T1, φ80, UC-1, and the peptides colicin M and microncin J25. |CITS: [12383253]|
The three dimensional crystal structure of FhuA, in its native and substrate associated conformations, has been determined
to 2.7 and 2.5 A resolution, respectively |CITS:[9856937]|.
Targeting of FhuA to the Sec-translocase for transport across the inner membrane is
SecB-dependent |CITS:[16352602]|.)""","""NIL""","""NIL""",]},
'B0153' : {'ecocyc-rxns': {"""RXN0-2241""": """iron (III) hydroxamate complex[extracellular space] =iron (III) hydroxamate complex[cytosol] ""","""ABC-11-RXN""": """ATP + iron (III) hydroxamate complex[periplasmic space] + H2O =ADP + phosphate + iron (III) hydroxamate complex[cytosol] """,},'ucsd-rxns' : ['FE3HOXabcpp','CPGNabcpp','ARBTNabcpp','FEOXAMabcpp','FECRMabcpp',], 'protein-comments' : ["""NIL""","""(The FhuBCD ATP-dependent iron (III) hydroxamate transporter is a member of the ATP-Binding Cassette
(ABC) Superfamily of transporters |CITS: [96381453]|. FhuBCD catalyzes transport of iron (III)-hydroxamate
compounds across the inner membrane into the cytoplasm of E. coli. Hydroxamates, or siderophores,
are used to increase the solubility of iron (III), which is normally insoluble at pH 7 |CITS: [88038363]|.
Based on sequence similarity, FhuB is the transmembrane component |CITS: [98086115]|, FhuC is the
ATP-binding subunit |CITS: [87279948]|, and FhuD is the periplasmic siderophore-binding component of
the ABC transporter |CITS: [98273640]|. A mutant with overproduced periplasmic FhuD protein was shown
to bind to radioactively labeled iron (III) ferrichrome |CITS: [91307893]|. Resistance of FhuD to protease K
in the presence of ferrichrome, aerobactin, and coprogen also indicated binding of these substrates to
FhuD |CITS: [91307893]|. In E. coli, hydroxamate transport across the outer membrane (via FhuA
and the TonB-ExbB-ExbD complex), coupled with the FhuBCD-mediated hydroxamate transport across
the cytoplasmic membrane completes the uptake of iron (III) hydroxamates into the cell. fhuA-fhuB
mutants exhibited completely abolished growth promotion by natural hydroxamates |CITS: [20048384]|.)""","""NIL""",]},
'B0152' : {'ecocyc-rxns': {"""RXN0-2241""": """iron (III) hydroxamate complex[extracellular space] =iron (III) hydroxamate complex[cytosol] ""","""ABC-11-RXN""": """ATP + iron (III) hydroxamate complex[periplasmic space] + H2O =ADP + phosphate + iron (III) hydroxamate complex[cytosol] """,},'ucsd-rxns' : ['FE3HOXabcpp','CPGNabcpp','ARBTNabcpp','FEOXAMabcpp','FECRMabcpp',], 'protein-comments' : ["""NIL""","""(The FhuBCD ATP-dependent iron (III) hydroxamate transporter is a member of the ATP-Binding Cassette
(ABC) Superfamily of transporters |CITS: [96381453]|. FhuBCD catalyzes transport of iron (III)-hydroxamate
compounds across the inner membrane into the cytoplasm of E. coli. Hydroxamates, or siderophores,
are used to increase the solubility of iron (III), which is normally insoluble at pH 7 |CITS: [88038363]|.
Based on sequence similarity, FhuB is the transmembrane component |CITS: [98086115]|, FhuC is the
ATP-binding subunit |CITS: [87279948]|, and FhuD is the periplasmic siderophore-binding component of
the ABC transporter |CITS: [98273640]|. A mutant with overproduced periplasmic FhuD protein was shown
to bind to radioactively labeled iron (III) ferrichrome |CITS: [91307893]|. Resistance of FhuD to protease K
in the presence of ferrichrome, aerobactin, and coprogen also indicated binding of these substrates to
FhuD |CITS: [91307893]|. In E. coli, hydroxamate transport across the outer membrane (via FhuA
and the TonB-ExbB-ExbD complex), coupled with the FhuBCD-mediated hydroxamate transport across
the cytoplasmic membrane completes the uptake of iron (III) hydroxamates into the cell. fhuA-fhuB
mutants exhibited completely abolished growth promotion by natural hydroxamates |CITS: [20048384]|.)""","""NIL""",]},
'B3730' : {'ecocyc-rxns': {"""NAG1P-URIDYLTRANS-RXN""": """N-acetyl-glucosamine-1-phosphate + UTP = UDP-N-acetyl-D-glucosamine + diphosphate""","""2.3.1.157-RXN""": """D-glucosamine 1-phosphate + acetyl-CoA -> N-acetyl-glucosamine-1-phosphate + coenzyme A""",},'ucsd-rxns' : ['UAGDP','G1PACT',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B3224' : {'ecocyc-rxns': {"""TRANS-RXN-25""": """H+[periplasmic space] + N-acetylneuraminate[periplasmic space] =H+[cytosol] + N-acetylneuraminate[cytosol] """,},'ucsd-rxns' : ['ACNAMt2pp',], 'protein-comments' : ["""(NanT is a probable sialic acid transporter. The cloned nanT
gene restored sialic acid transport and utilisation in
mutants unable to transport sialic acid |CITS: [96011396]|. Whole cell
transport experiments indicated that sialic acid is transported with
an affinity of 30 μM and uptake is non-competitively inhibited
by N-acetylglucosamine |CITS: [88076791]|. Sialic acid transport was
inhibited by 2,4-dinitrophenol, but not by sodium arsenate, suggesting
that NanT is a sugar/proton symporter |CITS: [88076791]|.
Consistent with this, NanT is a member of the major facilitator
superfamily and has fourteen predicted transmembrane segments
|CITS: [96011396]|. Expression of nanT is induced by sialic acid,
and the transporter gene is located in a probable operon with nanA,
encoding sialic acid lyase. Imported sialic acid is cleaved by NanA
to yield N-acetylmannosamine and pyruvate.
Regulation has been described |CITS: [12897000]|. Transcription of nanATEK-yhcH (sialic acid catabolic operon) is repressed by a NanR homodimer |CITS: [12897000]|.)""",]},
'B3732' : {'ecocyc-rxns': {"""ATPSYN-RXN""": """H+[cytosol] + H2O + ATP =H+[periplasmic space] + phosphate + ADP """,},'ucsd-rxns' : ['ATPS4rpp','ATPS4rpp',], 'protein-comments' : ["""NIL""","""(The beta subunit contains the catalytic site. The complex is a homotrimer.
|CITS: [91358411] [90303438]|)""","""(The F-1 complex of ATP synthase contains the catalytic sites. The complex
consists of five subunits, each of which is required for activity.
|CITS: [90303438] [89372792]|)""","""(The enzyme is made up of two subcomplexes, the F-1 complex and the F-O complex.
There are eight total subunits all required for activity. The F-1 complex is
the catalytic unit. The F-O complex anchors the F-1 complex to the membrane
and also forms the proton channel. |CITS: [89123355] [90303438] [93252965]|)""",]},
'B3733' : {'ecocyc-rxns': {"""ATPSYN-RXN""": """H+[cytosol] + H2O + ATP =H+[periplasmic space] + phosphate + ADP """,},'ucsd-rxns' : ['ATPS4rpp','ATPS4rpp',], 'protein-comments' : ["""(The gamma subunit appears to play an important role in coupling the catalytic
site events with proton translocation in association with the epsilon subunit.
The coupling involves conformational changes and probable translocations of
one or both subunits. |CITS: [96216373]|)""","""(The F-1 complex of ATP synthase contains the catalytic sites. The complex
consists of five subunits, each of which is required for activity.
|CITS: [90303438] [89372792]|)""","""(The enzyme is made up of two subcomplexes, the F-1 complex and the F-O complex.
There are eight total subunits all required for activity. The F-1 complex is
the catalytic unit. The F-O complex anchors the F-1 complex to the membrane
and also forms the proton channel. |CITS: [89123355] [90303438] [93252965]|)""",]},
'B0090' : {'ecocyc-rxns': {"""NACGLCTRANS-RXN""": """N-acetylmuramoyl-pentapeptide-diphosphoundecaprenol + UDP-N-acetyl-D-glucosamine = UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol + UDP""",},'ucsd-rxns' : ['UAGPT3',], 'protein-comments' : ["""NIL""",]},
'B0842' : {'ecocyc-rxns': {"""TRANS-RXN-92""": """H+[periplasmic space] + multidrug[cytosol] =H+[cytosol] + multidrug[periplasmic space] """,},'ucsd-rxns' : ['Kt3pp','NAt3pp',], 'protein-comments' : ["""(The MdfA protein, also known as Cmr, is a multidrug efflux protein belonging to
the major facilitator superfamily (MFS) |CITS: [97140959]|. Overexpression of MdfA
has demonstrated that it confers resistance to tetracycline, chloramphenicol, erythromycin,
some aminoglycosides and fluoroquinolones, and organic cations such as ethidium
bromide |CITS: [97234639]|. Deletion of mdfA resulted in increased susceptibility to ethidium bromide
and benzalkonium chloride |CITS:[11257026]|. Transport experiments in an E. coli unc mutant
have indicated that MdfA confers resistance via an efflux mechanism dependent on the
proton motive force |CITS: [97234639]|. Consistent with this, chloramphenicol/proton
antiport was observed in membrane vesicles prepared from cells overexpressing
mdfA |CITS: [98309866]|.
Overexpression of mdfAA also results in spectinomycin sensisitivity and
isopropyl-Β-D-thiogalactopyranoside (IPTG) exclusion due to unknown mechanisms
|CITS: [99030337]|. 12 transmembrane domains (TMs) has been predicted from the hydropathy
plot of the protein and confirmed by gene fusion analysis |CITS:[10022825][12029048]|.
MdfA catalyzes both electrogenic and electroneutral transport. MdfA-catalyzed transport of neutral
substrates is electrogenic, resulting in a net movement of electric charges, whereas transport of
cationic substrates is electroneutral with no net movement of charges, driven primarily by proton
chemical gradient |CITS:[12578981]|. Mutagenesis of MdfA has indicated that residue E-26,
located in the periplasmic half of the TM1, is important for the recognition of a variety of positively
charged substrates but not for neutral compounds |CITS: [10022825] [97140959] [14717607]|. Replacement
of E26 with a lysine abolished multidrug resistance activity against positively charged drugs.
In addition to its role as a multidrug resistance transporter, MdfA also mediates alkaline resistance. In deletion
mutation experiments mdfA mutants were sensitive even to mild alkaline conditions, and the wild-type
phenotype is restored fully by MdfA expressed from a plasmid. MdfA expressed from a multicopy plasmid
was found to confer extreme alkaline pH resistance, allowing the growth of cells under conditions that are
close to those used normally by alkaliphiles (up to pH 10). Inverted vesicle fluorescence studies demonstrated
that MdfA catalyzes Na(+)- or K(+)-dependent proton transport |CITS:[15371593]|.)""",]},
'B0092' : {'ecocyc-rxns': {"""DALADALALIG-RXN""": """2 D-alanine + ATP = D-alanyl-D-alanine + phosphate + ADP""",},'ucsd-rxns' : ['ALAALAr',], 'protein-comments' : ["""NIL""","""(The protein has been crystallized. |CITS: [95025939]|)""",]},
'B2965' : {'ecocyc-rxns': {"""ORNDECARBOX-RXN""": """L-ornithine = CO2 + putrescine""",},'ucsd-rxns' : ['ORNDC',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B3738' : {'ecocyc-rxns': {"""ATPSYN-RXN""": """H+[cytosol] + H2O + ATP =H+[periplasmic space] + phosphate + ADP """,},'ucsd-rxns' : ['ATPS4rpp','ATPS4rpp',], 'protein-comments' : ["""(The a subunit of the F0 complex plays a critical role in the proton
translocation mechanism. |CITS: [89123453] [93147708]|)""","""(The F-O complex of ATP synthase functions as the proton channel and consists of
three subunits. All are required for a functional F-O complex. The F-O complex
is membrane-bound. |CITS: [90303438] [93147708]|)""","""(The enzyme is made up of two subcomplexes, the F-1 complex and the F-O complex.
There are eight total subunits all required for activity. The F-1 complex is
the catalytic unit. The F-O complex anchors the F-1 complex to the membrane
and also forms the proton channel. |CITS: [89123355] [90303438] [93252965]|)""",]},
'B3739' : {'ecocyc-rxns': {},'ucsd-rxns' : ['ATPS4rpp',], 'protein-comments' : ["""(A nonpolar mutation in the atpI gene shows that the AtpI protein is not an essential component of the H+-ATPase
complex |CITS: [6327640]|.
Expression of AtpI is 10 to 20-fold lower than expression of AtpB, which is encoded by
the second open reading frame of the atp operon |CITS: [2524469]|. RNA processing and low efficiency of translation
initiation may account for lower levels of atpI transcript and AtpI protein |CITS: [2472380][8679701][1373327][1834655]|.
AtpI appears to affect AtpB expression at a post-translation initiation step |CITS: [7672111]|.)""",]},
'B2601' : {'ecocyc-rxns': {"""DAHPSYN-RXN""": """phosphoenolpyruvate + D-erythrose-4-phosphate + H2O = 3-deoxy-D-arabino-heptulosonate-7-phosphate + phosphate""",},'ucsd-rxns' : ['DDPA',], 'protein-comments' : ["""(aroF and tyrA encoding the bifunctional chorismate mutase
prephenate dehydrogenase form the tyrosine operon. The tyrosine operon
is repressed by tyrosine and phenylalanine. This repression is
mediated by the tyrR gene product postulated to bind at a regulatory
region preceding the aroF coding sequence.)""","""NIL""",]},
'B2600' : {'ecocyc-rxns': {"""CHORISMATEMUT-RXN""": """chorismate = prephenate""","""PREPHENATEDEHYDROG-RXN""": """prephenate + NAD+ -> p-hydroxyphenylpyruvate + CO2 + NADH""",},'ucsd-rxns' : ['CHORM','PPND',], 'protein-comments' : ["""NIL""","""(This enzyme catalyzes the first and second steps in the
biosynthesis of tyrosine.
The enzyme occurs in two aggregation states, a dimer and a tetramer.
The tetrameric species is only observed in the presence of the
co-factor NAD+ and/or the end product inhibitor tyrosine.
|CITS:[83135765]|
Investigations on the sulfhydryl groups of chorismate mutase/prephenate
dehydrogenase have indicated that modification of these groups is associated
with a parallel loss of both enzymic activities. Thus, the two activities of
this enzyme may be catalyzed at the same site or at closely situated
active sites.
The two activities of the enzyme from coli
appear to be interdependent. NAD+ activates chorismate mutase
activity, and conversely, chorismate stimulates prephenate
dehydrogenase activity. Prephenate formed at the chorismate mutase
site is more accessible for subsequent conversion to
(4-hydroxyphenyl)-pyruvate than would be expected if there were an
intervening dissociation and reassociation.|CITS:[85122698]|
In contrast, the two active sites of the closely related enzyme
chorismate mutase/prephenate dehydratase has two separate active sites.
|CITS: [85122698]|)""",]},
'B1704' : {'ecocyc-rxns': {"""DAHPSYN-RXN""": """phosphoenolpyruvate + D-erythrose-4-phosphate + H2O = 3-deoxy-D-arabino-heptulosonate-7-phosphate + phosphate""",},'ucsd-rxns' : ['DDPA',], 'protein-comments' : ["""(The aroH gene has two promoters. One is regulated by the trp
repressor and is favored by growth on minimal media. The other
promoter is activated under conditions of growth in rich medium by an
unknown mechanism. The presence of a second promoter that is active
during growth in the presence of high levels of aromatic amino acid could allow
aroH to escape from repression and ensure a low level of metabolic flux
through the shikimate pathway for the biosynthesis of aromatic
vitamins not present in the growth medium. Of
the three isozymes, DAHP synthase (Trp) is only moderately
feedback-inhibited and will function despite high levels of
intracellular tryptophan |CITS:[91323737]|. In wild-type
cells grown in minimal medium,
the aroG isozyme makes up about 80% of the total DAHPS activity, the
aroF isozyme makes up 20%, and the aroH isozyme makes up
about 1%.)""","""NIL""",]},
'B3639' : {'ecocyc-rxns': {"""P-PANTOCYSLIG-RXN""": """D-4'-phosphopantothenate + L-cysteine + CTP = diphosphate + CMP + R-4'-phosphopantothenoyl-L-cysteine""","""P-PANTOCYSDECARB-RXN""": """R-4'-phosphopantothenoyl-L-cysteine = pantetheine 4'-phosphate + CO2""",},'ucsd-rxns' : ['PPCDC','PPNCL2',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B1702' : {'ecocyc-rxns': {"""PEPSYNTH-RXN""": """H2O + pyruvate + ATP = phosphate + phosphoenolpyruvate + AMP""",},'ucsd-rxns' : ['PPS',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B1701' : {'ecocyc-rxns': {"""ACYLCOASYN-RXN""": """coenzyme A + a fatty acid + ATP = an acyl-CoA + diphosphate + AMP""",},'ucsd-rxns' : ['FACOAL160t2pp','FACOAL140t2pp','FACOAL60t2pp','FACOAL161t2pp','FACOAL180t2pp','FACOAL100t2pp','FACOAL141t2pp','FACOAL80t2pp','FACOAL120t2pp','FACOAL181t2pp',], 'protein-comments' : ["""(FadK is an acyl-CoA synthetase that is primarily active on short chain fatty acids and acts in anaerobic
β-oxidation of fatty acids |CITS: [12535077][15213221]|. During anaerobic β-oxidation of fatty acids, FadI, FadJ, and FadK
serve functions parallel to those of FadA, FadB, and FadD in the aerobic pathway |CITS: [12535077]|.
A fadK mutant exhibits a defect in anaerobic growth on short chain fatty acids |CITS: [12535077]|. A fadD
fadK double mutant exhibits a complete defect in anaerobic growth on fatty acids, indicating that FadD acyl-CoA
synthetase activity partially complements FadK activity under anaerobic growth conditions |CITS: [12535077]|. The
failure of FadK to complement a fadD mutant under aerobic conditions is likely due to poor expression of FadK
under those conditions |CITS: [15213221]|.
FadK has a FACS (fatty acyl-CoA-binding) motif and an ATP/AMP binding motif |CITS: [12535077]|.
FadK is not expressed under aerobic conditions, and the level of expression under anaerobic conditions depends on
the terminal electron acceptor: in the presence of nitrate, expression is low, while in the presence of fumarate,
expression is high |CITS: [15213221]|.
Based on sequence similarity, YdiD has been predicted to be a hydroxycinnamate-CoA ligase |CITS: [12952533]|.
)""","""NIL""",]},
'B0657' : {'ecocyc-rxns': {},'ucsd-rxns' : ['ALPATG160pp','ALPATE160pp',], 'protein-comments' : ["""(Apolipoprotein N-acyltransferase activity transfers palmitate to apolipoproteins, resulting in the maturation of lipoproteins from apolipoprotein precursors |CITS: [2032623]|. Aminoacylation of lipoproteins bound for the outer membrane is required for proper localization of these lipoproteins via the Lol pathway |CITS: [12198129]|.
The enzyme activity has been characterized |CITS: [2032623]|. The enzyme can utilize the phospholipids phosphatidylethanolamine, phosphatidylglycerol, or cardiolipin in vitro |CITS: [2032623]|. A pss mutant exhibits apolipoprotein N-acyltransferase activity, indicating that the enzyme is not specific for a phosphatidylethanolamine donor in vivo |CITS: [2033085]|.
Apolipoprotein N-acyltransferase localizes to inner membrane or inner-plus-outer membrane fractions |CITS: [2032623]|.
A cutE mutant exhibits copper sensitivity |CITS: [1938881]|.
CutE has a region with similarity to copper binding sites |CITS: [1938881]|.
CutE functionally complements the heat sensitivity, copper sensitivity, and apolipoprotein N-acyltransferase defect of a Salmonella typhimurium SE5312 mutant |CITS: [8344936]|. CutE overproduction in Salmonella typhimurium results in increased apolipoprotein N-acyltransferase activity |CITS: [8344936]|.
CutE has similarity to Rhizobium meliloti ActA |CITS: [8868435]|.
Regulation has been described |CITS: [1938881]|.
Review: |CITS: [7651187]|.)""",]},
'B0654' : {'ecocyc-rxns': {"""ABC-13-RXN""": """ATP + L-glutamate[periplasmic space] + H2O =ADP + phosphate + L-glutamate[cytosol] """,},'ucsd-rxns' : ['GLUabcpp','ASPabcpp',], 'protein-comments' : ["""NIL""","""(The GltIJKL glutamate transporter is a member of the ATP Binding Cassette (ABC) transporter superfamily
|CITS:[98254124]|. Sequence similarity with known ABC transporter components suggests that GltJK are
integral membrane components and GltL is the ABC protein. GltI (also known as YbeJ) is the presumed
periplasmic binding protein.)""",]},
'B0655' : {'ecocyc-rxns': {},'ucsd-rxns' : ['GLUabcpp','ASPabcpp',], 'protein-comments' : ["""(GltI is the periplasmic-binding component of the GltJKL glutamate ABC transporter |CITS:[10972807],[9593292]|.
gltI was shown to be regulated by the FlhDC flagellar transcriptional regulator |CITS:[15941987]|.
)""",]},
'B0652' : {'ecocyc-rxns': {"""ABC-13-RXN""": """ATP + L-glutamate[periplasmic space] + H2O =ADP + phosphate + L-glutamate[cytosol] """,},'ucsd-rxns' : ['GLUabcpp','ASPabcpp',], 'protein-comments' : ["""NIL""","""(The GltIJKL glutamate transporter is a member of the ATP Binding Cassette (ABC) transporter superfamily
|CITS:[98254124]|. Sequence similarity with known ABC transporter components suggests that GltJK are
integral membrane components and GltL is the ABC protein. GltI (also known as YbeJ) is the presumed
periplasmic binding protein.)""",]},
'B1521' : {'ecocyc-rxns': {"""ALTRO-OXIDOREDUCT-RXN""": """NAD+ + D-altronate = NADH + D-tagaturonate""",},'ucsd-rxns' : ['TAGURr',], 'protein-comments' : ["""NIL""",]},
'B1709' : {'ecocyc-rxns': {"""RXN0-2121""": """cob(I)alamin[extracellular space] =cob(I)alamin[cytosol] ""","""ABC-5-RXN""": """ATP + cob(I)alamin[periplasmic space] + H2O =ADP + phosphate + cob(I)alamin[cytosol] """,},'ucsd-rxns' : ['CBL1abcpp','CBIuabcpp','ADOCBLabcpp',], 'protein-comments' : ["""(BtuD is the ATP-binding component of the BtuCD, an ABC-type vitamin B12 uptake system.)""","""(BtuCDF is a vitamin B12 transport system that is a member of the ATP-Binding Cassette
(ABC) Superfamily of transporters |CITS: [96381453]|. Based on sequence similarity, BtuD is the ATP-binding
component, BtuC is the integral membrane component, and BtuF is the periplasmic substrate-binding
component of the ABC transporter |CITS: [12475936]| . Transposon insertions in the btuCand regions
conferred a deficiency in vitamin B12 utilization and transport |CITS: [86304183]|. However, there are
indications that BtuE (residing within the operon) is not required for transport. Transposon insertions in btuE were not
complemented by plasmids carrying btuE alone, whereas insertions in btuC and
btuD were effectively complemented by plasmids carrying the corresponding functional gene |CITS: [86304183] [89364713]|.
btuE mutants were also shown to have little effect on vitamin B12 binding and
transport and did not affect the utilization of vitamin B12 or other cobalamins for
methionine biosynthesis |CITS: [89364713]|.
The crystal structure of the Escherichia coli BtuCD protein has been resolved to 3.2 angstrom resolution |CITS:[12004122]|.)""","""NIL""",]},
'B0651' : {'ecocyc-rxns': {"""URIDINE-NUCLEOSIDASE-RXN""": """uridine + H2O -> uracil + D-ribose""","""RXN0-361""": """cytidine + H2O -> cytosine + D-ribose""",},'ucsd-rxns' : ['URIH','CYTDH',], 'protein-comments' : ["""(The rihA gene encodes a ribonucleoside hydrolase that preferentially utilizes cytidine and uridine
|CITS: [11027694]|. The kcat/KM for uridine is approximately 10 times higher than for
cytidine, largely due to a lower KM value for uridine |CITS: [16411753]|. There are two other nucleoside
hydrolases with differing specificities encoded by the rihB and rihC genes |CITS: [11027694]|.
A crystal structure of RihA bound to the reaction product D-ribose has been solved at 1.8 Å resolution
|CITS: [16411753]|.
An rihA null mutant can not use cytidine as a source of pyrimidine |CITS: [11027694]|. The rihA and
rihC genes are subject to catabolite repression |CITS: [11027694]|.
)""",]},
'B3579' : {'ecocyc-rxns': {},'ucsd-rxns' : ['XYLUt2pp',], 'protein-comments' : ["""(Based on sequence similarity, YiaO is the periplasmic solute-binding component of the YiaMNO Binding Protein-dependent Secondary (TRAP) transporter)""","""(Based on sequence similarity, the yiaMNO genes encode the only tri-partite
ATP-independent periplasmic (TRAP) transporter in Escherichia coli. The TRAP
transporters share characteristics of both the ATP-binding cassette (ABC) and secondary
families of transporters |CITS:[11524131]|. Like the ABC transporters TRAP
transporters use an extracytoplasmic solute-binding protein but rather than ATP hydrolysis
the driving force is provided by either proton-(pmf) and/or sodium ion motive
force (smf) |CITS:[11524131]|. Based on sequence similarity, YiaO is the periplasmic
solute-binding protein and YiaM and YiaN are membrane-spanning proteins.
Deletion mutation experiments |CITS:[14668138]| showed that deletion of the yiaMNO
genes affected the ability of E.coli to utilize L-xylulose when
growth was measured using various carbon substrates. Solute transport studies
|CITS:[14668138]| determined that the yiaMNO deletion strain was capable
of utilizing L-xylulose but at a lower rate, indicating that the YiaMNO transporter is
involved in, but not essential for L-xylulose utilization. Purification and binding
studies |CITS:[14668138]| using YiaO showed that YiaO was able to bind L-xylulose.
Furthermore, spheroblasts expressing the YiaMN membrane domains were
stimulated to increase uptake of L-xylulose when incubated with the periplasmic
substrate-binding YiaO while those spheroblasts not expressing YiaMN showed no
such stimulation. Deletion of yiaMNO resulted in a delay of entry into stationary phase of cells
grown in LB with glucose, or minimal medium with glucose or other compounds. These cultures obtained a
higher stationary phase OD660 and higher c.f.u. numbers. Deletion of yiaMNO also
resulted in an increased lag time in cultures with high NaCl concentrations, and a reduction in biofilm
formation in minimal medium with glucose |CITS:[15870475]|.)""",]},
'B4395' : {'ecocyc-rxns': {"""3PGAREARR-RXN""": """3-phosphoglycerate = 2-phosphoglycerate""",},'ucsd-rxns' : ['PGM',], 'protein-comments' : ["""(The enzyme has not been characterized and the subunit
structure is unknown. However, phosphoglycerate mutase 1 is a
homodimer.)""",]},
'B4394' : {'ecocyc-rxns': {"""RXN0-5074""": """XTP + H2O -> XDP + phosphate""","""RXN0-5073""": """ITP + H2O -> IDP + phosphate""",},'ucsd-rxns' : ['NTP10','NTP11','NTP12',], 'protein-comments' : ["""(YjjX is a phosphatase that preferentially hydrolyzes inosine triphosphate (ITP) and xanthosine triphosphate (XTP).
Both ITP and XTP can be formed by oxidative deamination damage, converting an amino group of adenine or guanine
to a keto group. By hydrolyzing these damaged nucleotides, YjjX may thus prevent their incorporation into RNA
|CITS: [16216582]|.
A crystal structure of YjjX has been solved at 2.3 Å resolution; the protein forms a dimer in the crystal structure
as well as in solution |CITS: [16216582]|.
Overexpression of YjjX from a multicopy plasmid leads to resistance to the HMP
(4-amino-2-methyl-5-hydroxymethylpyrimidine) analog CF3-HMP
(4-amino-2-trifluoromethyl-5-hydroxymethylpyrimidine). The resistance mechanism is undetermined, but does not
involve biosynthesis of HMP |CITS: [15292217]|.
Review: |CITS: [16216571]|)""","""NIL""",]},
'B4392' : {'ecocyc-rxns': {},'ucsd-rxns' : ['MLTGY3pp','MLTGY4pp','MLTGY1pp','MLTGY2pp',], 'protein-comments' : ["""(Slt70 is involved in growth and recycling of peptidoglycan by catalyzing
the lysis of the β-1,4 glycosidic bond between N-acetylmuramic
acid and N-acetylglucosamine, producing 1,6-anhydromuropeptides at
an optimal pH of 4.5 with a Km of 200 mg/L |CITS:[357]|.
Slt70 forms a murein-metabolizing multi-enzyme complex with PBP3 and
PBP7/8 |CITS:[8063800]|. PBP7/8 was shown to stabilize and stimulate the
activity of Slt70 |CITS:[8063800]|. Slt70 activity is also modulated by the
stringent response |CITS:[1970319]|.
The structure of Slt70 has been determined by X-ray crystallography
revealing a α-superhelix structure with the catalytic domain on
top |CITS:[2184239],[8107871]|. The structure has also been determined
to a resolution of 1.65 Å for its native form, 1.90 Å as a
complex with 1,6-anhydromuropeptide |CITS:[10452894]|, and 2.8 Å
as a complex with bulgecin A |CITS:[7548026]|, its inhibitor |CITS:[1400320]|.
Overproduction of Slt70 resulted in growth inhibition and lysis of some cells,
but a deletion mutant had no observable phenotype |CITS:[1938883]|.
Review: |CITS:[9529891]|
)""",]},
'B4258' : {'ecocyc-rxns': {"""VALINE--TRNA-LIGASE-RXN""": """tRNAval + L-valine + ATP -> L-valyl-tRNAval + diphosphate + AMP""",},'ucsd-rxns' : ['VALTRS',], 'protein-comments' : ["""(Valyl-tRNA synthetase (ValRS) is a member of the family of aminoacyl-tRNA synthetases, which interpret the
genetic code by covalently linking amino acids to their specific tRNA molecules. The reaction is driven by ATP
hydrolysis. ValRS belongs to the Class I aminoacyl tRNA synthetases |CITS: [2203971][7647112]|.
ValRS is a monomer in solution |CITS: [4897802]|. A single binding site for tRNAVal was thought to exist
|CITS: [4897800]|, but evidence for a second binding site has been reported |CITS: [11434781]|. The reaction
mechanism of ValRS includes the formation of an aminoacyl adenylate intermediate, which then serves as the animo
acid donor in the aminoacyl-tRNA synthetase reaction |CITS: [165186][320199][199234][391274]|. The enzyme
rapidly forms a valyl-adenylate and binds a second molecule of valine slowly |CITS: [199234]|. Residues in contact
with valine and residues that may be part of the editing site have been determined |CITS: [10903513]|. The ATP
binding site of ValRS was determined by affinity labeling |CITS: [2271710]|.
Specificity determinants within tRNAVal that are important for recognition by ValRS have been identified
|CITS: [1847071][2049085][8071341][7937960][9396792][10387013][11434781]|. The anticodon is sufficient for
distinguishing tRNAMet and tRNAVal |CITS: [3055296][2023934]|.
Many aminoacyl tRNA synthetases have been shown to have editing functions. ValRS misactivates threonine,
cysteine and α-aminobutyrate (αBut) |CITS: [4897802][329276][371673]|, but has a post-transfer editing
mechanism which hydrolyzes a mischarged αBut-tRNAVal and others |CITS: [371673][2261451]|.
Only substrates that can be (mis)charged by ValRS appear to be able to undergo editing |CITS: [12034843]|. The
editing site of ValRS recognizes adenosine at the 3' end of tRNA |CITS: [11434781]|; further requirements for editing
have been determined |CITS: [14596614][14970394]|. The nature of the mischarged tRNA does not influence its
transfer to the editing site on ValRS |CITS: [10792042]|. Mutations that allow charging of tRNAVal with
cysteine have been identified and lie in the editing site of ValRS |CITS: [11313495]|; the Lys277 residue is important
for the editing activity |CITS: [12475234]|. Isoleucine is selected against by a steric exclusion mechanism
|CITS: [375976]|. The β-phosphate-γ-phosphate interchange reaction of ATP contributes to the
prevention of tRNA aminoacylation by non-cognate amino acids |CITS: [6258639]|.
During infection of E. coli with bacteriophage T4, ValRS is modified by the tau peptide, changing its properties
|CITS: [19475][330535][6992274]|.
Reviews: |CITS: [10966471][11330299]|
)""",]},
'B4390' : {'ecocyc-rxns': {"""RIBOSYLNICOTINAMIDE-KINASE-RXN""": """nicotinamide riboside + ATP -> nicotinamide mononucleotide + ADP""","""2.7.7.1-RXN""": """nicotinamide mononucleotide + ATP = NAD+ + diphosphate""",},'ucsd-rxns' : ['NMNAT',], 'protein-comments' : ["""(The nadR gene product has enzymatic as well as regulator activity. Previously know as a repressor and for controlling the transport of exogenous NMN across the cytoplasmic membrane, NadR has also been shown to be an
NMN adenylyltransferase and predicted to have ribosylnicotinamide kinase activity |CITS: [99395064][12446641]|.
The full-size multifunctional NadR protein is composed of three different domains:
(i) an N-terminal DNA-binding domain involved in the transcriptional regulation of NAD biosynthesis
(ii) a central nicotinamide mononucleotide (NMN) adenylyltransferase domain
(iii) a C-terminal ribosylnicotinamide kinase domain.
Most studies on the transcription regulation properties of NadR were done in Salmonella typhimurium. NadR
participates in controlling several genes involved in de novo synthesis of NAD, including nadB and
pncB |CITS: [4349027][3934331][3275606][9882682]|.)""","""NIL""","""NIL""",]},
'B1453' : {'ecocyc-rxns': {"""TRANS-RXN-262""": """L-asparagine[periplasmic space] + H+[periplasmic space] =H+[cytosol] + L-asparagine[cytosol] """,},'ucsd-rxns' : ['ASNt2rpp',], 'protein-comments' : ["""(AnsP is a probable L-asparagine transporter. The equivalent gene to
ansP in Salmonella enterica has been expressed and shown
to confer L-asparagine uptake |CITS: [95202072]|. AnsP is a member of
the APC superfamily of transporters and based on sequence similarity
probably functions as an L-asparagine/proton symporter.)""",]},
'B4254' : {'ecocyc-rxns': {"""ORNCARBAMTRANSFER-RXN""": """L-ornithine + carbamoyl-phosphate = citrulline + phosphate""",},'ucsd-rxns' : ['OCBT',], 'protein-comments' : ["""NIL""","""(In the test tube, not in the cell, a family of four isoenzymes forms by
assortment of two closely similar polypeptides, the chain F-monomer
and chain I-monomer, to give active trimers FFF, FFI, FII, and III.
|CITS: [77028751]|)""",]},
'B4006' : {'ecocyc-rxns': {"""AICARTRANSFORM-RXN""": """N10-formyl-THF + AICAR = tetrahydrofolate + phosphoribosyl-formamido-carboxamide""","""IMPCYCLOHYDROLASE-RXN""": """inosine-5'-phosphate + H2O = phosphoribosyl-formamido-carboxamide""",},'ucsd-rxns' : ['AICART','IMPC',], 'protein-comments' : ["""(From the earliest studies an association between AICAR
transformylase and IMP cyclohydrolase has been shown.)""",]},
'B4476' : {'ecocyc-rxns': {"""TRANS-RXN-81""": """H+[periplasmic space] + fructuronate[periplasmic space] =H+[cytosol] + fructuronate[cytosol] """,},'ucsd-rxns' : ['GLCNt2rpp',], 'protein-comments' : ["""(GntU is one of four known transporters for gluconate in E. coli, the others
being the homologous GntT, GntP and IdnT transporters. Whole cell experiments have
shown that the cloned gntU gene was able to complement a gluconate transport
negative mutant and confers low affinity gluconate transport with a Km of approx
212 μM |CITS: [96236044]|. Transcriptional analysis has shown that gntU
forms a dicistronic operon with the gntK gene encoding a gluconate kinase.
Expression of gntU is induced by gluconate and controlled by the GntR
repressor.
GntU is a member of the Gnt family of gluconate transporters |CITS: [97212001]|.
Gluconate uptake has been reported to occur via a proton-symport mechanism in
E. coli |CITS: [74033664]|. It seems likely that GntU is a low affinity
gluconate uptake system that functions via D-gluconate/proton symport.)""",]},
'B0590' : {'ecocyc-rxns': {"""RXN0-2181""": """ferric enterobactin[extracellular space] =ferric enterobactin[cytosol] ""","""ABC-10-RXN""": """ATP + ferric enterobactin[periplasmic space] + H2O =ADP + phosphate + ferric enterobactin[cytosol] """,},'ucsd-rxns' : ['FEENTERabcpp','FE3DHBZSabcpp',], 'protein-comments' : ["""NIL""","""(FepBCDG are components of a ferric enterobactin transport complex that is a member of the ATP-binding
cassette (ABC) family of transporters. E. coli and several other species of Enterobacteriaceae
secrete the catecholate siderophore enterobactin. The enterobactin siderophore is a small organic
molecule with a high affinity for Fe 3+. FepA has been shown |CITS:[21424666]|, to be
involved in transport of ferric enterobactin across the outer membrane into the periplasm in a TonB-
dependent process which requires the transduction of energy derived from the cytoplasmic membrane
across the periplasm to FepA. Deletion studies |CITS: [92157868]| indicate that fepD and
fepG are essential for transport and sequence analysis indicates that these two proteins are highly
homologous with other integral membrane proteins involved in iron-chelating ABC uptake systems. Based
on sequence similarity, FepC is the ATP-binding component and provides the energy required for transport
across the inner membrane. FepB is not coded in the same operon but has been shown to bind ferric
enterobactin and probably functions as the periplasmic binding protein of the ferric enterobactin ABC
transporter |CITS: [96004464]|.)""","""(FepA is a 22-stranded membrane-spanning beta barrel protein in the outer membrane. FepA is a TonB dependent active transporter
that recognizes ferric enterobactin and translocates the molecule across the outer membrane into the periplasm. FepB is a
periplasmic binding protein that binds ferric enterobactin for transport across the inner membrane by the FepCDG ABC transporter.)""",]},
'B0593' : {'ecocyc-rxns': {"""ISOCHORSYN-RXN""": """chorismate -> isochorismate""",},'ucsd-rxns' : ['ICHORSi',], 'protein-comments' : ["""NIL""",]},
'B0592' : {'ecocyc-rxns': {"""RXN0-2181""": """ferric enterobactin[extracellular space] =ferric enterobactin[cytosol] ""","""ABC-10-RXN""": """ATP + ferric enterobactin[periplasmic space] + H2O =ADP + phosphate + ferric enterobactin[cytosol] """,},'ucsd-rxns' : ['FEENTERabcpp','FE3DHBZSabcpp',], 'protein-comments' : ["""NIL""","""(FepBCDG are components of a ferric enterobactin transport complex that is a member of the ATP-binding
cassette (ABC) family of transporters. E. coli and several other species of Enterobacteriaceae
secrete the catecholate siderophore enterobactin. The enterobactin siderophore is a small organic
molecule with a high affinity for Fe 3+. FepA has been shown |CITS:[21424666]|, to be
involved in transport of ferric enterobactin across the outer membrane into the periplasm in a TonB-
dependent process which requires the transduction of energy derived from the cytoplasmic membrane
across the periplasm to FepA. Deletion studies |CITS: [92157868]| indicate that fepD and
fepG are essential for transport and sequence analysis indicates that these two proteins are highly
homologous with other integral membrane proteins involved in iron-chelating ABC uptake systems. Based
on sequence similarity, FepC is the ATP-binding component and provides the energy required for transport
across the inner membrane. FepB is not coded in the same operon but has been shown to bind ferric
enterobactin and probably functions as the periplasmic binding protein of the ferric enterobactin ABC
transporter |CITS: [96004464]|.)""","""(FepA is a 22-stranded membrane-spanning beta barrel protein in the outer membrane. FepA is a TonB dependent active transporter
that recognizes ferric enterobactin and translocates the molecule across the outer membrane into the periplasm. FepB is a
periplasmic binding protein that binds ferric enterobactin for transport across the inner membrane by the FepCDG ABC transporter.)""",]},
'B0595' : {'ecocyc-rxns': {"""ENTMULTI-RXN""": """6 ATP + 3 L-serine + 3 2,3-dihydroxybenzoate = 6 diphosphate + 6 AMP + enterobactin""","""ENTG-RXN""": """3 (2,3-dihydroxybenzoyl)adenylate + 3 L-Seryl-AMP = enterobactin + 6 AMP""","""ISOCHORMAT-RXN""": """H2O + isochorismate = pyruvate + 2,3-dihydro-2,3-dihydroxybenzoate""",},'ucsd-rxns' : ['ICHORT',], 'protein-comments' : ["""(The EntB protein is bifunctional, the N-terminal domain contains the
isochorismate lyase activity and the C-terminal contains the apo-aryl carrier
protein (ArCP) domain. The apo-ArCP becomes phosphopantetheinylated in a
reaction catalyzed by the entD gene product, phosphopantetheinyl transferase.
The holo-EntB can now serve as a substrate for the DHB-AMP ligase which activates
DHB as the acyl-AMP derivative. The acyl fragment is then transferred onto
holo-EntB. The arylated holo-EntB serves as the aryl donor for the amide
bond formation in enterobactin assembly. |CITS: [97361959] [98153148]|)""","""NIL""","""(Recent gel filtration data suggest that EntB may be a trimer not a pentamer.
|CITS: [98153148]|)""","""NIL""",]},
'B0594' : {'ecocyc-rxns': {"""ENTMULTI-RXN""": """6 ATP + 3 L-serine + 3 2,3-dihydroxybenzoate = 6 diphosphate + 6 AMP + enterobactin""","""DHBAMPLIG-RXN""": """ATP + 2,3-dihydroxybenzoate = diphosphate + (2,3-dihydroxybenzoyl)adenylate""",},'ucsd-rxns' : ['DHBS',], 'protein-comments' : ["""NIL""","""(Recent gel filtration data suggest that EntE may be a monomer not a dimer.
|CITS: [98153148]|)""","""NIL""",]},
'B0596' : {'ecocyc-rxns': {"""DHBDEHYD-RXN""": """NAD+ + 2,3-dihydro-2,3-dihydroxybenzoate -> NADH + 2,3-dihydroxybenzoate""",},'ucsd-rxns' : ['DHBD',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B3791' : {'ecocyc-rxns': {"""RFFTRANS-RXN""": """dTDP-4-dehydro-6-deoxy-D-glucose + L-glutamate = dTDP-D-fucosamine + α-ketoglutarate""",},'ucsd-rxns' : ['TDPAGTA',], 'protein-comments' : ["""NIL""",]},
'B2243' : {'ecocyc-rxns': {"""GLYC3PDEHYDROG-RXN""": """sn-glycerol-3-phosphate + ubiquinone-8 = dihydroxy-acetone-phosphate + ubiquinol-8""",},'ucsd-rxns' : ['G3PD7','G3PD6','G3PD5',], 'protein-comments' : ["""NIL""","""(The GlpABC enzyme is loosely associated with the cell membrane. A functional two subunit form, GlpAC, has been
isolated, and it is assumed that the third subunit (GlpB) is responsible for membrane anchoring.
The GlpA subunit contains noncovalently bound FAD, and the GlpC subunit is thought to bind flavin mononucleotide
|CITS: [3286606]|.
The GlpB subunit contains two iron-sulfur clusters, and does not contain any transmembrane helices, so
the mechanism by which it acts as the membrane anchor for the complex is not clear
|CITS: [3286606][7576488]|.
Please note: reference |CITS: [6363389]| and reference |CITS: [3286606]| utilize different terminologies for the
members of the glpACB operons. The former names the genes A,B,C, while the later names them A,C and B,
respectively. Throughout this discussion we have used the nomenclature of the later.
This three-subunit enzyme converts glycerol-3-phosphate to dihydroxyacetone phosphate (DHAP) using
electron acceptors other than oxygen, and functions mostly under anaerobic conditions.
The anaerobic dehydrogenase protein complex is encoded by the glpACB operon,
and is regulated by glycerol and catabolite repression |CITS: [6363389]|.
The reducing equivalents are passed through a simple electron transport chain which terminates with
fumarate or nitrate as the electron acceptor |CITS:[82007833]|.
Expression of glpABC (along with other members of the glp regulon |CITS: [825019]| is repressed by
GlpR and induced by glycerol-3-phosphate. Optimal intracellular levels of glycerol-3-phosphate are maintained for
biosynthesis of phospholipids. The glpTQ operon, which encodes glycerol-3-phosphate transporter and
phosphodiesterase is adjacent to glpABC. The two operons are divergently transcribed; the operators to
which GlpR binds overlap the ,glpA promoter |CITS: [9179845]|.
)""",]},
'B2519' : {'ecocyc-rxns': {},'ucsd-rxns' : ['MPTG','MPTG2',], 'protein-comments' : ["""(The PbpC protein contains both a penicillin-binding and a transglycosylase domain. Deletion of the pbpC gene
does not cause an obvious phenotype, and overproduction of the PbpC protein does not rescue the defect of a
ponAts ponB double mutant |CITS: [10542235]|.
PbpC interacts with PBP1B, PBP3, and MltA |CITS: [10542235]|.)""",]},
'B0980' : {'ecocyc-rxns': {"""6-PHYT-RXN""": """H2O + phytate = phosphate + D-myo-inositol (1,2,3,4,5)-pentakisphosphate""","""RXN0-1021""": """GTP + H2O = GDP + phosphate""",},'ucsd-rxns' : ['PHYTSpp','NTP3pp',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B2240' : {'ecocyc-rxns': {"""TRANS-RXN-22""": """H+[periplasmic space] + sn-glycerol-3-phosphate[periplasmic space] =H+[cytosol] + sn-glycerol-3-phosphate[cytosol] """,},'ucsd-rxns' : ['GLYC3Pt6pp',], 'protein-comments' : ["""(GlpT is the major E. coli uptake system for glycerol-3-phosphate, and this transporter belongs to the
Major Facilitator Superfamily (MFS) of transporters |CITS: [93174460]|. Uptake of glycerol-3-phosphate via
the GlpT transporter leads to the simultaneous counterflow of inorganic phosphate from the cell |CITS:
[98377424]|. GlpT also catalyzes a reversible phosphate: phosphate exchange |CITS: [86250840]|. Both
glycerol-3-phosphate: phosphate and phosphate: phosphate exchange activities were observed in
GlpT-reconstituted proteoliposomes |CITS: [86250840]|. In addition, mutants that lack the GlpT system fail
to exchange internal phosphate for either external phosphate or glycerol-3-phosphate |CITS: [85130783]|.
Using phosphate-loaded proteoliposomes, the Km for the transport of glycerol-3-phosphate via
GlpT was estimated to be near 20 μM |CITS: [86250840]|. Mutation in the gene glpR derepressed
the transcription of glpT, indicating the regulatory role of the GlpR in glpT transcription
|CITS: [97323397]|. The crystal structure for GlpT has been determined at 3.3 A |CITS:[22776144]|.)""",]},
'B3374' : {'ecocyc-rxns': {"""RXN0-962""": """fructoselysine + ATP = fructoselysine-6-phosphate + ADP""",},'ucsd-rxns' : ['FRULYSK',], 'protein-comments' : ["""(FrlD is a monomeric fructoselysine 6-kinase |CITS: [12147680]|. FrlD is a member of the PfkB family of kinases and
has similarity to the glucosamine-6-phosphate synthase isomerase domain |CITS: [12147680]|.
Fructoselysine 6-kinase activity is undetectable when cells are grown on glucose; stationary phase
extract of cells grown on fructoselysine or psicoselysine have a kinase activity of 100 nmol/min per mg of protein
|CITS: [14641112]|.
FrlD: "fructoselysine" |CITS: [12147680]|.)""",]},
'B2167' : {'ecocyc-rxns': {"""TRANS-RXN-158""": """phosphoenolpyruvate + fructose[periplasmic space] =fructose-1-phosphate[cytosol] + pyruvate """,},'ucsd-rxns' : ['FRUptspp',], 'protein-comments' : ["""(contains PTS Enzyme IIB', IIB and IIC domains)""","""(FruAB, the fructose PTS permease, belongs to the functional superfamily
of the phosphoenolpyruvate (PEP)-dependent, sugar transporting
phosphotransferase system (PTS). The PTS transports and simultaneously
phosphorylates its sugar substrates in a process called group
translocation. FruAB takes up exogenous fructose, releasing the
1-phosphate ester into the cell cytoplasm in preparation for metabolism,
primarily via glycolysis |CITS: [8246840]|.
FruAB, the Enzyme IIFru complex, possesses
three domains in the FruA protein with the domain order IIB'-IIB-IIC
|CITS: [89341690]| and three domains in its FruB protein, also named diphosphoryl
transfer protein (DTP), with the domain order IIA-M-H where IIA
is the first phosphorylation site domain, M is a central domain
of unknown function, and H is an HPr-like domain called FPr (fructose-inducible
HPr) |CITS: [2546043]|. FruAB is homologous to MtlA (the mannitol-specific
PTS Enzyme II) which has been reported to possess 6 transmembrane
α-helical segments in its IIC domain.
The IIA, IIB and IIB' domains are localized to the cytoplasmic
side of the membrane. IIB' is required for high affinity binding
of FruB to FruA but does not participate in phosphoryl transfer
|CITS: [8626640]|. The overall PTS-mediated phosphoryl transfer reaction, requiring
the two general energy coupling proteins of the PTS, Enzyme I
and HPr, as well as the three domains of the Enzyme II complex
is:
PEP --> Enzyme I(his~~P)
--> HPr(his~~P)
--> IIA(his~~P) -->
IIB(cys~~P) -(IIC)-> fructose-1-P.
FruAB transports fructose with low micromolar affinity.
The fru operon is inducible in wild type E. coli K12
due to the presence of the fructose repressor, FruR, also known
as the catabolite repressor/activator (Cra) protein. Cra is a
member of the LacI-GalR family |CITS: [2203752] [8230205]|. The fru operon
is also subject to positive control by the cyclic AMP-cyclic AMP
receptor protein (CRP) complex. The fru operon contains
the fruB gene, the fruK gene (encoding fructose-1-P
kinase) and the fruA gene in that order. The fruR gene
does not map near the fru operon. FruK is a homologue
of phosphofructokinase.)""",]},
'B0386' : {'ecocyc-rxns': {"""PYRROLINECARBREDUCT-RXN""": """L-proline + NAD(P)+ = pyrroline 5-carboxylate + NAD(P)H + H+""",},'ucsd-rxns' : ['P5CR',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B3823' : {'ecocyc-rxns': {"""TRANS-RXN-244""": """H+[periplasmic space] + L-threonine[cytosol] =H+[cytosol] + L-threonine[periplasmic space] """,},'ucsd-rxns' : ['THRt2pp',], 'protein-comments' : ["""(RhtC is a probable threonine efflux transporter. Expression of the
rhtC gene conferred resistance to threonine |CITS: [99313167]|.
RhtC is related to the RhtB homoserine efflux transporter and is a
member of the Rht family of amino acid efflux proteins |CITS: [99257453]|.
It seems likely that RhtC functions as a threonine/proton antiport system.)""",]},
'B0381' : {'ecocyc-rxns': {"""DALADALALIG-RXN""": """2 D-alanine + ATP = D-alanyl-D-alanine + phosphate + ADP""",},'ucsd-rxns' : ['ALAALAr',], 'protein-comments' : ["""(The subunit structure is not known at this time. |CITS:
[91129242]|)""",]},
'B0383' : {'ecocyc-rxns': {"""ALKAPHOSPHA-RXN""": """a phosphate monoester + H2O = an alcohol + phosphate""",},'ucsd-rxns' : ['PPTHpp',], 'protein-comments' : ["""(Alkaline phosphatase is a dimer that occurs in three forms, depending upon the growth conditions of the cell. These
forms have been designated isozymes 1, 2 and 3. They differ by the presence of an NH2-terminal arginine residue on
the subunits of isozyme 1, the absence of this residue on isozyme 3 and isozyme 2 being a heterodimer
of one subunit each of isozymes 1 and 3 |CITS: [81273081]|.
The precursor polypeptide is secreted across the inner membrane to the periplasmic space concommitant with
removal of the signal sequence |CITS: [87031576]|.
Transposon mutagenesis and biochemical assays showed that the PhoA protein oxidizes phosphite to phosphate,
producing molecular H2 |CITS: [15148399]|.)""","""NIL""",]},
'B1319' : {'ecocyc-rxns': {"""RXN0-2542""": """mono-, di-, or trisaccharide < 600 Da[extracellular space] =mono-, di-, or trisaccharide < 600 Da[periplasmic space] """,},'ucsd-rxns' : ['H2Otex',], 'protein-comments' : ["""(OmpG is an efficient unspecific channel for mono-, di, and trisaccharides with size less than 600 Daltons. It has been
crystalized in two dimensions. Projection maps of OmpG at 6 Angstroms revealed a monomeric structure in contrast
to the trimeric porins, OmpF and OmpC. A multitude of other experiments have supported the hypothesis that OmpG functions as a monomer.
This monomeric porin is believed to have 14 beta strands. |CITS: [11114248]|
OmpG is able to rescue the growth of porin-deficient bacteria on media containing maltodextrins as large as maltopentose
as the sole carbon source. Liposome swelling assay demonstrated that OmpG is capable of transporting large solutes.
)""",]},
'B2162' : {'ecocyc-rxns': {"""RXN0-361""": """cytidine + H2O -> cytosine + D-ribose""","""URIDINE-NUCLEOSIDASE-RXN""": """uridine + H2O -> uracil + D-ribose""",},'ucsd-rxns' : ['URIH','CYTDH',], 'protein-comments' : ["""(The rihB gene encodes a ribonucleoside hydrolase that can utilize both cytidine and uridine, but shows a
preference for cytidine |CITS: [21125610]|. There are two other ribonucleoside hydrolases present in E. coli,
encoded by the rihA and rihC genes, with differing specificities |CITS: [21125610]|.
Regulation has been described |CITS: [11027694]|. The rihB gene is hardly expressed unless mutated, and the
rihA and rihC genes are subject to catabolite repression |CITS: [11027694]|.
A triple mutant lacking rihA, rihB and rihC grows normally |CITS: [11027694]|.
A crystal structure of RihB has been solved at 1.7 A resolution |CITS: [15130467]|.)""",]},
'B2458' : {'ecocyc-rxns': {},'ucsd-rxns' : ['PTAr',], 'protein-comments' : ["""(No information about this protein was found by a literature search conducted on January 20, 2006.)""",]},
'B0388' : {'ecocyc-rxns': {"""SHIKIMATE-KINASE-RXN""": """shikimate + ATP = shikimate-3-phosphate + ADP""",},'ucsd-rxns' : ['SHKK',], 'protein-comments' : ["""(Expression of the structural gene of one of the coli
shikimate kinase isoenzyme, the aroL gene product is regulated by the
tyrR gene product protein with tyrosine or tryptophan as co-repressor.
|CITS:[87099857]| A second gene, designated aroM, that encodes a
26-kilodalton gene product of unknown function was shown to be
cotranscribed with aroL. |CITS:[86085676]|)""",]},
'B3825' : {'ecocyc-rxns': {"""LYSOPHOSPHOLIPASE-RXN""": """a 2-acyl-sn-glycero-3-phosphocholine + H2O = a carboxylate + L-1-glycero-3-phosphocholine""",},'ucsd-rxns' : ['LPLIPAL2ATG120','LPLIPAL2G140','LPLIPAL2G141','LPLIPAL2E160','LPLIPAL2E161','LPLIPAL2G180','LPLIPAL2G181','LPLIPAL2ATG180','LPLIPAL2ATG161','LPLIPAL2ATG160','LPLIPAL2ATE180','LPLIPAL2A120','LPLIPAL2ATE181','LPLIPAL2E120','LPLIPAL2ATG141','LPLIPAL2ATG140','LPLIPAL2A140','LPLIPAL2A141','LPLIPAL2ATE140','LPLIPAL2A160','LPLIPAL2A161','LPLIPAL2ATE161','LPLIPAL2ATE160','LPLIPAL2A180','LPLIPAL2A181','LPLIPAL2G120','LPLIPAL2E180','LPLIPAL2E181','LPLIPAL2ATG181','LPLIPAL2ATE141','LPLIPAL2ATE120','LPLIPAL2G160','LPLIPAL2G161','LPLIPAL2E140','LPLIPAL2E141',], 'protein-comments' : ["""(Lysophospholipase L(2) (PldB) catalyzes the conversion of 1-lysophosphatidylcholine
to glycerophosphocholine, as well as performing a similar reaction on other substrates.
PldB hydrolyzes 2-acyl glycerophosphoethanolamine and 1-lysophosphatidylcholine
(2-acyl glycerophosphocholine)
most effectively, and hydrolyzes the 1-acyl versions of each compound somewhat
less effectively. In addition, it can transfer an acyl group from lysophospholipid
to phosphatidylglycerol to yield acyl phosphatidylglycerol |CITS: [3908447][2934380][6386795]|.)""",]},
'B2690' : {'ecocyc-rxns': {},'ucsd-rxns' : ['PGMT',], 'protein-comments' : ["""(Phosphatase activity of YqaB was discovered in a high-throughput screen of purified proteins |CITS: [15808744]|.
)""",]},
'B3821' : {'ecocyc-rxns': {"""PHOSPHOLIPASE-A1-RXN""": """H2O + a phosphatidylcholine -> a 2-acyl-sn-glycero-3-phosphocholine + a carboxylate""",},'ucsd-rxns' : ['PLIPA2A180pp','PLIPA1A181pp','PLIPA2E120pp','PLIPA2A141pp','PLIPA1G120pp','PLIPA1G160pp','PLIPA1E160pp','PLIPA1A160pp','PLIPA2E141pp','PLIPA1G161pp','PLIPA1E161pp','PLIPA1A120pp','PLIPA2A120pp','PLIPA2A161pp','PLIPA2E140pp','PLIPA2G140pp','PLIPA2A160pp','PLIPA1E120pp','PLIPA2G181pp','PLIPA2G141pp','PLIPA1A161pp','PLIPA2E160pp','PLIPA2G180pp','PLIPA2G160pp','PLIPA1E180pp','PLIPA1G140pp','PLIPA1E141pp','PLIPA2E181pp','PLIPA1G141pp','PLIPA1G181pp','PLIPA1A180pp','PLIPA1E140pp','PLIPA2G120pp','PLIPA2E180pp','PLIPA1E181pp','PLIPA1A140pp','PLIPA2G161pp','PLIPA2E161pp','PLIPA1A141pp','PLIPA2A140pp','PLIPA2A181pp','PLIPA1G180pp',], 'protein-comments' : ["""(PldA is the Phospholipase A1 precursor which is a member of EC 3.1.1.32. X-ray crystallography has determined its
structure to consist of 12 antiparallel beta strands. |CITS: [10537112]| Its major function is in the secretion of
bacteriocins. |CITS: [11080680]| The process by which PldA is belived to achieve this function is by forming a homodimeric complex and binding
substrate and calcium.The resulting complex hydrolyzes phospholipids forming lysophospholipids and fatty acids which
perturb the lipid bilayer, allowing for the semispecific secretion of bacteriocins. |CITS: [10537112]|
Colicin A is a protein secreted by strains of E. coli carrying a colicinogenic plasmid and is lethal to other related E. coli strains.
The assembly of colicin A requires a outer membrane porin such as OmpC or OmpF and OMPLA. However, OMPLA is sufficient
for secretion of colicin A. It is suspected that OMPLA and colicin Au may form a structural homologue to that of TolC.
The beta barrel of OMPLA has a 12 beta stranded topology and spans the outer membrane like TolC.
Colicin Au may form an alpha helical tunnel connecting the outer membrane to the periplasm. |CITS: [12057969]|)""",]},
'B2920' : {'ecocyc-rxns': {"""RXN0-268""": """propionyl-CoA + succinate = propionate + succinyl-CoA""",},'ucsd-rxns' : ['PPCSCT',], 'protein-comments' : ["""NIL""",]},
'B2518' : {'ecocyc-rxns': {"""NUCLEOSIDE-DIP-KIN-RXN""": """a ribonucleoside diphosphate + ATP -> a ribonucleoside triphosphate + ADP""","""UDPKIN-RXN""": """UDP + ATP = UTP + ADP""","""CDPKIN-RXN""": """CDP + ATP = CTP + ADP""","""DUDPKIN-RXN""": """dUDP + ATP = dUTP + ADP""","""DCDPKIN-RXN""": """dCDP + ATP = dCTP + ADP""","""DTDPKIN-RXN""": """dTDP + ATP = dTTP + ADP""","""DADPKIN-RXN""": """dADP + ATP = dATP + ADP""","""DGDPKIN-RXN""": """dGDP + ATP = dGTP + ADP""","""GDPKIN-RXN""": """GDP + ATP = GTP + ADP""",},'ucsd-rxns' : ['NDPK4','NDPK8','NDPK2','NDPK3','NDPK1','NDPK6','NDPK7','NDPK5',], 'protein-comments' : ["""(Nucleoside diphosphate kinase catalyzes the reaction in which the terminal phosphate of a nucleoside-triphosphate
is transferred to a nucleoside-diphosphate. The enzyme exhibits broad substrate specificity. The reaction
mechanism is an ordered bi-molecular ping-pong type |CITS: [79062418]|. The intracellular levels of ATP are
considerably higher than other nucleoside triphosphates. In addition, ATP is far more abundant than ADP or AMP,
so there is a strong thermodynamic tendency for the potential energy of ATP to be used in the synthesis of other
high-energy compounds. Therefore nucleoside diphosphate kinase is unlikely to be involved in the synthesis of ATP
|CITS: [Mathews&vanHolde]|.
The purified enzyme is tetrameric |CITS: [6089829][7730286]| and was detected in the periplasmic fraction after cold
osmotic shock |CITS: [214126]|. A periplasmic location for the enzyme appears inconsistent with its function
|CITS: [COLISALII]|.
ndk is not essential for growth, but mutants display a mutator phenotype |CITS: [7490752]|, generating high
levels of mispairs that must be corrected by the mismatch-repair system |CITS: [12242219]|.
Ndk had been reported to acts as a uracil-processing nuclease in DNA repair |CITS: [14585934]|, but this activity
was likely due to contamination of the enzyme preparation by uracil-DNA glycosylase |CITS: [15096615][15380104]|.
Review: |CITS: [11768309]|)""","""NIL""",]},
'B3824' : {'ecocyc-rxns': {"""TRANS-RXN-242A""": """H+[periplasmic space] + homoserine lactone[cytosol] =H+[cytosol] + homoserine lactone[periplasmic space] ""","""TRANS-RXN-242""": """H+[periplasmic space] + homoserine[cytosol] =H+[cytosol] + homoserine[periplasmic space] """,},'ucsd-rxns' : ['HOMt2pp',], 'protein-comments' : ["""(RhtB is a probable homoserine and homoserine lactone efflux
transporter. Expression of the rhtB gene conferred
resistance to homoserine and homoserine lactone and increased
accumulation of homoserine in the external medium |CITS: [99313167]|.
Inactivation of the rhtB gene decreased resistance to
these susbtrates and decreased accumulation of homoserine in
the external medium |CITS: [99313167]|. RhtB is the prototype
of the Rht family and is related to the LysE family of amino
acid efflux proteins |CITS: [99257453]|. It seems likely that
RhtB functions as a homoserine or homoserine lactone/proton
antiport system.)""",]},
'B2927' : {'ecocyc-rxns': {"""ERYTH4PDEHYDROG-RXN""": """D-erythrose-4-phosphate + H2O + NAD+ = erythronate-4-phosphate + NADH""",},'ucsd-rxns' : ['E4PD',], 'protein-comments' : ["""(The enzyme is composed of 4 monomers of 37.2 kDa each |CITS: [7751290]|.
An epd mutant does not exhibit the growth defect, aggregation phenotype, or lysis phenotype exhibited by a
gapA mutant |CITS: [9260967]|.)""","""NIL""",]},
'B2260' : {'ecocyc-rxns': {"""O-SUCCINYLBENZOATE-COA-LIG-RXN""": """ATP + O-succinylbenzoate + coenzyme A = AMP + diphosphate + O-succinylbenzoyl-CoA""",},'ucsd-rxns' : ['SUCBZL',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B2697' : {'ecocyc-rxns': {"""ALANINE--TRNA-LIGASE-RXN""": """tRNAala + L-alanine + ATP -> L-alanyl-tRNAala + diphosphate + AMP""",},'ucsd-rxns' : ['ALATRS',], 'protein-comments' : ["""(Alanyl-tRNA synthetase (AlaRS) is a member of the family of aminoacyl-tRNA synthetases, which interpret the
genetic code by covalently linking amino acids to their specific tRNA molecules. The reaction is driven by ATP
hydrolysis. AlaRS belongs to the Class II aminoacyl tRNA synthetases, which share three regions of homology
|CITS: [2203971][1852601]|.
AlaRS is a homotetramer in solution |CITS: [7005211]|. Later experiments determined that AlaRS exists in an
equilibrium between a homodimeric and a homodecameric state, depending on temperature
|CITS: [8645007][9343380]|. The enzyme contains one molecule of zinc per AlaS polypeptide |CITS: [1712632]|; zinc
binds cooperatively and induces a conformational change in AlaRS |CITS: [8024549][10441391]|. Zinc is important for
tRNA recognition |CITS: [1549561]|.
Specificity determinants within tRNAAla that are important for recognition by AlaRS have been
identified |CITS: [3053691][8539617][8601277][10390340][10889033][11983895][12022232]|. A single nucleotide
base pair in the acceptor helix of tRNAAla, G3-U70, is necessary and sufficient for aminoacylation of
that tRNA with alanine |CITS: [3285220][2452483][2462282][1608452][9294178][10518524]|. A mutation in alaS
which compensates for a mutant tRNAAla containing a G3-C70 base pair has been isolated
|CITS: [2001352]|. Discrimination of the G3-U70 base pair maps to a 76 amino acid region outside the catalytic
center of AlaRS |CITS: [7742303]|. The nucleotide at position 73 modulates the efficiency of the transfer step of
aminoacylation |CITS: [1692733][1704363][10601268][10871402]|.
Specificity determinants and residues within AlaRS that are important for catalytic activity have been investigated
|CITS: [2271589][9736622]|. An N-terminal 461 amino acid fragment of the AlaS polypeptide was shown to
complement a temperature-sensitive alaS allele in vivo; the C-terminal portion of the enzyme appears to
be dispensable for catalytic activity, but is required for formation of the tetramer
|CITS: [7005211][7025207][6358898][3882689]|. The C-terminal domain plays a role in activating the catalytic sites
of the N-terminal domain |CITS: [6200234]|. Mutagenesis of an N-terminal domain peptide reveals residues that
increase catalytic activity of the fragment |CITS: [3892692]|.
A central region of AlaRS is essential for interaction with alanine-specific tRNA |CITS: [2435005]|. Site-directed
mutagenesis has identified the Arg69 residue within motif 2 |CITS: [8163518][8060998]|, the Cys665 residue
|CITS: [7918446]| and the Asp232 residue |CITS: [8172905]| as important for catalysis. The Lys73 residue is
important for recognition of tRNAAla |CITS: [2543446][8239663]|.
Kinetic parameters for binding of AlaRS to tmRNA have been determined |CITS: [10704215]|.
Many aminoacyl tRNA synthetases have been shown to have editing functions. AlaRS misactivates glycine and
serine, but has a pre-transfer editing function, hydrolyzing the non-cognate amino acid before transfer to
tRNAAla, and/or a post-transfer editing function that deacetylates mischarged tRNAAla
|CITS: [6117825]|. The covalently continuous two-domain structure of the tRNA is required to enable editing
|CITS: [12949076]|.
AlaRS represses transcription of the alaS gene by binding to a region flanking the transcription start site, and
thus autoregulates its own expression. The autoregulatory effect depends on the concentration of alanine, with higher
concentrations leading to lower levels of alaS transcription. At physiological levels of AlaRS, repression of
alaS transcription is solely mediated by alanine levels |CITS: [6264314]|.
The alaS21 allele leads to increased resistance to novobiocin |CITS: [10217798]|. Mutations in ribosomal
proteins S5 and S20 partially suppresses the temperature sensitive growth defect of an alaS mutation
|CITS: [4280505]|. The mechanism of suppression is thought to be a reduction in the rate of polypeptide synthesis
|CITS: [796671]|.
Reviews: |CITS: [10966471][2669241][1379318]|
)""","""NIL""",]},
'B1264' : {'ecocyc-rxns': {"""ANTHRANSYN-RXN""": """chorismate + L-glutamine = anthranilate + pyruvate + L-glutamate""",},'ucsd-rxns' : ['ANS',], 'protein-comments' : ["""(The TrpE protein is also called Component I of the anthranilate synthase enzyme complex. In vitro in the
absence of the TrpD (Component II) protein, TrpE can use ammonia as the amino donor for the synthesis of
anthranilate from chorismate at approximately 20% efficiency |CITS: [4886289]|. As a component of the anthranilate
synthase complex, TrpD (Component II) provides the glutamine amidotransferase function that allows glutamine to
serve as the amino donor in anthranilate formation.
The TrpE subunit contains the tryptophan binding site for feedback inhibition |CITS:[90024964]|. Both the TrpE and
TrpA polypeptides in the trp operon lack tryptophan residues |CITS:[7021857][81267360]|.)""","""(The native anthranilate synthase enzyme exists as a tetrameric complex of two subunits each of the TrpE (Component I) and TrpD (Component II) proteins |CITS: [5331787] [74173403]|.
The TrpD protein is bifunctional; it also catalyzes the second reaction in the biosynthesis of tryptophan from chorismate |CITS:[81267360]|.
)""",]},
'B2957' : {'ecocyc-rxns': {"""ASPARAGHYD-RXN""": """L-asparagine + H2O = L-aspartate + ammonia""",},'ucsd-rxns' : ['GLUNpp','ASNNpp',], 'protein-comments' : ["""NIL""","""(There are two asparaginase enzymes in E. coli, I and II. The synthesis of L-asparaginase
II in E. coli is subject to regulation by cyclic AMP receptor protein (CRP) and is
also induced by anaerobiosis. The latter form of regulation involves
the fnr gene product , which also activates a number of other
anaerobically regulated genes. |CITS:[90170867]| AnsII has a higher
affinity for substrate than AnsI. In humans, AnsII causes
rapid decline of plasma and cerebrospinal fluid L-asparagine levels
when administered to patients with lymphoblastic leukemia, resulting
in selective toxicity to malignant lymphoblasts, which have a relatively
high nutritional requirement for this amino acid |CITS:[90382683]|.
A signal peptide effects secretion |CITS:[90382683]|.)""",]},
'B2925' : {'ecocyc-rxns': {"""F16ALDOLASE-RXN""": """fructose-1,6-bisphosphate = dihydroxy-acetone-phosphate + D-glyceraldehyde-3-phosphate""",},'ucsd-rxns' : ['FBA',], 'protein-comments' : ["""(The amino acid sequence of the E. coli Class II fructose-1,6-bisphosphate aldolase inferred from the DNA
sequence of the fda gene is the first primary structure of a Class II aldolase to be established. There is no
immediately apparent sequence homology with any of the Class I fructose-1,6-bisphosphate aldolases which have
beenwidely studied |CITS:[89193446]|. In relation to the Class I enzymes (primarily studied and found in eukaryotes),
comparatively little is known about the class II enzymes. The Class II aldolases of Saccharomyces cerevisiae
and E. coli are the best characterized |CITS: [89193446]|. The E. coli enzyme resembles the typical
class II aldolase from yeast in size and amino acid composition. This is a strong suggestion that they are related
|CITS:[78165651]|. These less well studied aldolases are found both in the eukaryotic green algae and fungi, and in
the prokaryotic blue-green algae and bacteria |CITS:[78165651]|.
An fda mutant exhibits a heat-sensitive defect in rRNA transcription that is elicited via altered abundance of
ppGpp and of initiating NTPs |CITS: [14526031]|.
Fda has similarity to an Edwardsiella ictaluri protein that provokes an immune response in catfish
|CITS: [12542086]|.
)""","""NIL""",]},
'B1260' : {'ecocyc-rxns': {"""TRYPSYN-RXN""": """indole-3-glycerol-phosphate + L-serine -> L-tryptophan + H2O + D-glyceraldehyde-3-phosphate""","""RXN0-2381""": """indole-3-glycerol-phosphate = indole + D-glyceraldehyde-3-phosphate""",},'ucsd-rxns' : ['TRPS2','TRPS3','TRPS1',], 'protein-comments' : ["""(The TrpA polypeptide (TSase α) functions as the α subunit of the tetrameric (α2-β2)
tryptophan synthase complex.
As a purified protein, the α subunit is a monomer. TSase α contains the
binding site for indole-3-glycerol-phosphate (InGP) and can carry out the cleavage reaction of InGP to
indole and glyceraldehyde-3-phosphate, also termed the alpha reaction. Within the physiological complex with the
β subunit, the reaction rate is increased by 1-2 orders of magnitude.
The reaction carried out by the α subunit
alone is reversible, while the overall reaction is not.
Crystal structures of the wild-type and a double mutant TrpA protein have been reported at 2.5 and 1.8 Å
resolution, respectively |CITS: [14684907][15879705]|.)""","""(The physiologically active form of tryptophan synthase is a tetrameric α2-β2 complex consisting of two
α subunits
(the protein product of the trpA gene) and a dimer of two β subunits (the protein product of the trpB gene).
This complex catalyzes the last two steps in the
biosynthesis of tryptophan.)""",]},
'B1261' : {'ecocyc-rxns': {"""TRYPSYN-RXN""": """indole-3-glycerol-phosphate + L-serine -> L-tryptophan + H2O + D-glyceraldehyde-3-phosphate""","""RXN0-2382""": """indole + L-serine = L-tryptophan + H2O""",},'ucsd-rxns' : ['TRPS2','TRPS3','TRPS1',], 'protein-comments' : ["""(The TrpB polypeptide functions as the β subunit of the tetrameric (α2-β2) tryptophan synthase
complex.
The TrpB protein forms a homodimer (TSase β2) in which each subunit contains a molecule of the
cofactor pyridoxal phosphate covalently linked to the epsilon-amino group of a lysine residue via a Schiff base
|CITS: [788781]|. This complex catalyzes the synthesis of L-tryptophan from indole and L-serine, also termed the
beta reaction. This partial reaction carried out by the beta complex is irreversible.
The TrpB subunit possesses binding sites for L-serine and PLP and can catalyze a variety of reactions involving
these compounds.)""","""NIL""","""(The physiologically active form of tryptophan synthase is a tetrameric α2-β2 complex consisting of two
α subunits
(the protein product of the trpA gene) and a dimer of two β subunits (the protein product of the trpB gene).
This complex catalyzes the last two steps in the
biosynthesis of tryptophan.)""",]},
'B2515' : {'ecocyc-rxns': {"""RXN0-882""": """1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate + H2O + a protein disulfide = 2-C-methyl-D-erythritol-2,4-cyclodiphosphate + a protein dithiol""",},'ucsd-rxns' : ['MECDPDH2',], 'protein-comments' : ["""(IspG acts in the mevalonate-independent pathway of isopentenyl diphosphate biosynthesis
|CITS: [11163766][11274098]|, catalyzing the conversion of 2C-methyl-D-erythritol 2,4-cyclodiphosphate into
1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate |CITS: [11752431]|. It was determined that some additional
components from cell extract were necessary for the activity of purified IspG in vitro |CITS: [12571359]|. IspG
is reported to contain a [4Fe-4S] cluster |CITS: [12434382]|, and coexpression of ispG with the isc
operon encoding genes involved in Fe-S cluster assembly dramatically improves activity of the purified enzyme
|CITS: [16268586]|. Mutations in cysteine residues responsible for Fe-S cluster coordination abolish enzymatic
activity of IspG |CITS: [16268586]|. Flavodoxin I appears to supply reducing equivalents for reducing the Fe-S
cluster to form the active enzyme |CITS: [15978585]|.
Possible reaction mechanisms are discussed |CITS: [11752431][12571359]|.
IspG is essential |CITS: [1521767][11274098]|. Conditional amber mutants |CITS: [15090508]| as well as mutant
strains dependent on a different biosynthetic route for isopentenyl diphosphate have been isolated |CITS: [12859972]|.
An ispG mutant shows a defect in activation of human Vgamma9/Vdelta2 T lymphocytes |CITS: [11238603]|
due to a defect in production of (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate (HMB-PP), an antigenic
compound that accumulates in an ispH mutant |CITS: [11741609]|.
IspG is predicted to be a globular TIM barrel protein |CITS: [11717301]|.)""",]},
'B2514' : {'ecocyc-rxns': {"""HISTIDINE--TRNA-LIGASE-RXN""": """tRNAhis + L-histidine + ATP -> L-histidyl-tRNAhis + diphosphate + AMP""",},'ucsd-rxns' : ['HISTRS',], 'protein-comments' : ["""(Histidyl-tRNA synthetase (HisRS) is a member of the family of aminoacyl-tRNA synthetases, which interpret the
genetic code by covalently linking amino acids to their specific tRNA molecules. The reaction is driven by ATP
hydrolysis. HisRS belongs to the Class II aminoacyl tRNA synthetases, which share three regions of homology
|CITS: [2203971][1852601]|.
HisRS is a dimer in solution |CITS: [4591623]|. The C-terminal domain of the protein is required for dimerization, while
the N-terminal domain contains most of the catalytic activity. The two domains do not complement each other in trans
|CITS: [9131996]|.
Specificity determinants within tRNAHis that are important for recognition by HisRS have been
identified; the unique G-1:C73 base pair was found to play a crucial role
|CITS: [2678006][8144499][10747795][14709061]|. Specificity determinants and residues within HisRS that are
important for catalytic activity have been investigated |CITS: [8643360][9266856][10521280][11329259][14744140]|.
The C-terminal domain of HisRS was found to be largely responsible for recognition of the tRNAHis
anticodon |CITS: [8639604]|.
Crystal structures of HisRS have been determined, and a reaction mechanism was proposed
|CITS: [7556055][9207058]|. Various types of experiments support a substrate-assisted concerted reaction
mechanism |CITS: [15751955]|.
Reviews: |CITS: [10430027][10966471]|)""","""NIL""",]},
'B4079' : {'ecocyc-rxns': {"""FHLMULTI-RXN""": """formate = CO2 + H2""","""RXN0-3281""": """formate -> CO2 + 2 H+ + 2 e-""",},'ucsd-rxns' : ['FHL','FHL',], 'protein-comments' : ["""(Formate dehydrogenase-H is one of three formate dehydrogenases in E. coli |CITS: [7747941]|. Two of these
enzymes oxidize formate under anaerobic conditions. One is the nitrate reductase-linked formate dehydrogenase-N
(FDH-N) located in the inner membrane, and the other is the hydrogenase-linked formate dehydrogenase-H
(FDH-H) located in the cytoplasm. Together with hydrogenase-3, FDH-H forms the formate-hydrogen lyase
complex |CITS: [2211698][7747941]|.
Selenocysteine is incorporated cotranslationally at the position of an in-frame UGA stop codon in the FdhF open
reading frame |CITS: [2941757]|. The requirements for cotranslational incorporation of selenocysteine into FdhF
have been studied in detail |CITS: [2141170][1396569][8483932][8226830][8918790]|. The selenium atom may be
directly involved in the oxidation of formate |CITS: [1924303]| and is coordinating the molybdenum cofactor
|CITS: [8052647]|. FDH-H contains 3.3 g atoms of iron per mol, suggesting that it may contain a [4Fe-4S] iron-sulfur
center |CITS: [2211698]|.
A crystal structure of FDH-H has been solved at 2.3 A resolution, confirming the presence of a [4Fe-4S] cluster,
coordination of the Mo cofactor by selenocysteine, and the position of the binding site for the inhibitor nitrate. A
reaction mechanism was proposed |CITS: [9036855]|.
Expression of fdhF is induced by formate and the absence of external electron acceptors, and is repressed by
nitrate, nitrite, trimethylamine N-oxide, and the presence of oxygen |CITS: [3118141][6360066][9274019]|. Inhibition of
DNA gyrase enhances expression of fdhF |CITS: [2829213]|.
)""","""(A report has described that formate oxidation in anaerobically grown E. coli is coupled to proton translocation
|CITS: [15848284]|.)""",]},
'B4177' : {'ecocyc-rxns': {"""ADENYLOSUCCINATE-SYNTHASE-RXN""": """L-aspartate + inosine-5'-phosphate + GTP = adenylo-succinate + phosphate + GDP""",},'ucsd-rxns' : ['ADSS',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B3225' : {'ecocyc-rxns': {"""ACNEULY-RXN""": """N-acetylneuraminate = N-acetylmannosamine + pyruvate""",},'ucsd-rxns' : ['ACNML',], 'protein-comments' : ["""(Regulation has been described |CITS: [12897000]|. Transcription of the nanATEK-yhcH (sialic acid catabolic operon) is repressed by a NanR homodimer |CITS: [12897000]|.)""","""NIL""",]},
'B1415' : {'ecocyc-rxns': {"""SUCCINATE-SEMIALDEHYDE-DEHYDROGENASE-RXN""": """H2O + NAD+ + succinate semialdehyde = NADH + succinate""","""GLYCOLALD-DEHYDROG-RXN""": """H2O + NAD+ + glycolaldehyde -> NADH + glycolate""","""LACTALDDEHYDROG-RXN""": """H2O + NAD+ + lactaldehyde -> NADH + lactate""",},'ucsd-rxns' : ['LCADi','GCALDD',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B3829' : {'ecocyc-rxns': {"""HOMOCYSMET-RXN""": """L-homocysteine + 5-methyltetrahydropteroyltri-L-glutamate = L-methionine + tetrahydropteroyltri-L-glutamate""",},'ucsd-rxns' : ['METS',], 'protein-comments' : ["""NIL""",]},
'B4072' : {'ecocyc-rxns': {"""1.7.7.2-RXN""": """ammonia + 6 oxidized cytochrome c552 + 2 H2O -> nitrite + 6 reduced cytochrome c552 + 7 H+""",},'ucsd-rxns' : ['NTRIR3pp','NTRIR4pp',], 'protein-comments' : ["""(The nrfC gene encodes a transmembrane Fe-S protein, part of a nitrite reductase
reaction, which may transfer electrons from the quinone pool to the c-type
cytochromes or it may be an adapter that enables formate dehydrogenase H to
transfer electrons into an electrogenic electron-transfer chain. |CITS: [94335626]|
)""","""(E. coli has two distinct nitrite reductases--NrfA and NirB. Expresssion is complementary: with low nitrate in the
environment NrfA is made; with high nitrate NirB is made almost exclusively. At intermediate concentration of nitrate,
both are made. This regulation acts through the Nar regulatory circuit. Nitrite also induces the formation of both
enzymes but it is a less effective inducer than nitrate by at least two orders of magnitude. Both enzymes reduce nitrite
to ammonia. The two nitrate reductases have different cellular locations locations and metabolic roles. NrfA is associated
with the cytoplasmic membrane with its cytochrome components facing or free in the periplasm; actiing as a terminal
electron acceptor of an electron transport chain beginning with membrane-associated formate-oxidizing enzymes it
generates a proton gradient. NirB, which is located in the cytoplasm, does not generate a proton gradient. Its probable metabolic
role is to detoxify nitrite. However when cells are growing on high concentrations of nitrate (and NirB is active) nitrite,
nevertheless is excreted into the environment |CITS: [11004182]|.
The structure and spectroscopic properties of this penta-heme periplasmic cytochrome c nitrite
reductase has been determined |CITS: [11863430]|. NrfA can also reduce and thereby detoxify nitric
oxide (NO); mutant strains lacking NrfA activity have increased sensitivity to NO.
)""",]},
'B4073' : {'ecocyc-rxns': {"""1.7.7.2-RXN""": """ammonia + 6 oxidized cytochrome c552 + 2 H2O -> nitrite + 6 reduced cytochrome c552 + 7 H+""",},'ucsd-rxns' : ['NTRIR3pp','NTRIR4pp',], 'protein-comments' : ["""(The nrfD gene encodes a transmembrane protein that is part of the nitrite reductase
reaction and it may transfer electrons from the quinone pool to the c-type
cytochromes or it may be an adapter that enables formate dehydrogenase H to
transfer electrons into an electrogenic electron-transfer chain. |CITS: [94335626]|)""","""(E. coli has two distinct nitrite reductases--NrfA and NirB. Expresssion is complementary: with low nitrate in the
environment NrfA is made; with high nitrate NirB is made almost exclusively. At intermediate concentration of nitrate,
both are made. This regulation acts through the Nar regulatory circuit. Nitrite also induces the formation of both
enzymes but it is a less effective inducer than nitrate by at least two orders of magnitude. Both enzymes reduce nitrite
to ammonia. The two nitrate reductases have different cellular locations locations and metabolic roles. NrfA is associated
with the cytoplasmic membrane with its cytochrome components facing or free in the periplasm; actiing as a terminal
electron acceptor of an electron transport chain beginning with membrane-associated formate-oxidizing enzymes it
generates a proton gradient. NirB, which is located in the cytoplasm, does not generate a proton gradient. Its probable metabolic
role is to detoxify nitrite. However when cells are growing on high concentrations of nitrate (and NirB is active) nitrite,
nevertheless is excreted into the environment |CITS: [11004182]|.
The structure and spectroscopic properties of this penta-heme periplasmic cytochrome c nitrite
reductase has been determined |CITS: [11863430]|. NrfA can also reduce and thereby detoxify nitric
oxide (NO); mutant strains lacking NrfA activity have increased sensitivity to NO.
)""",]},
'B4070' : {'ecocyc-rxns': {"""1.7.7.2-RXN""": """ammonia + 6 oxidized cytochrome c552 + 2 H2O -> nitrite + 6 reduced cytochrome c552 + 7 H+""",},'ucsd-rxns' : ['NTRIR3pp','NTRIR4pp',], 'protein-comments' : ["""(The gene nrfA is the structural gene for cytochrome C552, which functions as a
formate-dependent nitrite reductase. Cytochrome C552 covalently binds five
heme-c groups per molecule |CITS: [9593308]|. Electrons are transferred from formate through any
of the three known formate dehydrogenases to cytochrome C552. It is believed
that the cytochrome C encoded by the nrfB gene is responsible for the direct
transfer of electrons to cytochrome C552. The reduced cytochrome C552 can then
directly reduce nitrite to ammonia. In addition to formate, pyruvate, ethanol,
and D-lactate can serve as electron donors. |CITS: [95020657] [94335626]
[94014980] [94314186] [86018359] [84291318] [ColiSalII] [67173589]|
NirA is located inthe periplasm. It is presumably sescreted into the periplasm where the heme groups are added.)""","""(E. coli has two distinct nitrite reductases--NrfA and NirB. Expresssion is complementary: with low nitrate in the
environment NrfA is made; with high nitrate NirB is made almost exclusively. At intermediate concentration of nitrate,
both are made. This regulation acts through the Nar regulatory circuit. Nitrite also induces the formation of both
enzymes but it is a less effective inducer than nitrate by at least two orders of magnitude. Both enzymes reduce nitrite
to ammonia. The two nitrate reductases have different cellular locations locations and metabolic roles. NrfA is associated
with the cytoplasmic membrane with its cytochrome components facing or free in the periplasm; actiing as a terminal
electron acceptor of an electron transport chain beginning with membrane-associated formate-oxidizing enzymes it
generates a proton gradient. NirB, which is located in the cytoplasm, does not generate a proton gradient. Its probable metabolic
role is to detoxify nitrite. However when cells are growing on high concentrations of nitrate (and NirB is active) nitrite,
nevertheless is excreted into the environment |CITS: [11004182]|.
The structure and spectroscopic properties of this penta-heme periplasmic cytochrome c nitrite
reductase has been determined |CITS: [11863430]|. NrfA can also reduce and thereby detoxify nitric
oxide (NO); mutant strains lacking NrfA activity have increased sensitivity to NO.
)""",]},
'B3816' : {'ecocyc-rxns': {"""TRANS-RXN-141B""": """Ni2+[periplasmic space] =Ni2+[cytosol] ""","""TRANS-RXN-141A""": """Co2+[periplasmic space] =Co2+[cytosol] ""","""TRANS-RXN-141""": """Mg2+[periplasmic space] =Mg2+[cytosol] """,},'ucsd-rxns' : ['NI2tpp','COBALT2tpp','MG2tpp',], 'protein-comments' : ["""(CorA is a magnesium ion transporter that is a member of the Metal Ion Transporter (MIT) family |CITS: [93300795]|.
The CorA transport system is comprised of the unlinked loci corA, corB, corC, and corD.
While the corA locus is responsible for the influx of magnesium ions, the presence of the unlinked corBCD
loci allows magnesium ion efflux in addition to influx |CITS: [93300795] [92140040]|. Mutation at the corA locus
result in total abolition of CorA-mediated magnesium influx and efflux |CITS: [93300795]|, whereas mutations individually
or simultaneously at the corBCD loci result in diminished capacity for magnesium efflux with no significant effect
on influx activity |CITS: [93300795]|. However, the exact roles of CorBCD are undetermined. Cobalt ion is a competitive
inhibitor of the CorA-mediated magnesium transport activity and cobalt transport was completely abolished by a mutation
in corA |CITS: [87057057]|.)""",]},
'B4077' : {'ecocyc-rxns': {"""TRANS-RXN-122A""": """H+[periplasmic space] + L-aspartate[periplasmic space] =H+[cytosol] + L-aspartate[cytosol] ""","""TRANS-RXN-162""": """H+[periplasmic space] + L-glutamate[periplasmic space] =H+[cytosol] + L-glutamate[cytosol] """,},'ucsd-rxns' : ['ASPt2pp','GLUt2rpp',], 'protein-comments' : ["""(GltP is a proton dependent transporter for glutamate and aspartate.
E. coli K12 cannot grow on glutamate as a sole carbon and
nitrogen source, selection of mutants which can grow on glutamate
(Glt+) are typically due to mutations which overexpress either
the GltS or GltP glutamate transporters |CITS: [90218004]|. The
cloned gltP gene has been shown to confer the ability to
utilise and transport glutamate |CITS: [90264315]|. Whole cell
transport experiments have shown that GltP is a proton dependent
transporter with can transport glutamate and aspartate with Km of
approx 5 μM |CITS: [78046051]|. This has been confirmed in E. coli membrane
vesicles, where GltP was shown to function via an electrogenic symport
mechanism where L-glutamate was co-transported with at least two protons
|CITS: [96154946]|. GltP is a member of the DAACS family of proton or
sodium-dependent amino acid or dicarboxylate transporter family.)""",]},
'B3128' : {'ecocyc-rxns': {"""GALACTARDEHYDRA-RXN""": """D-galactarate -> 5-keto-4-deoxy-D-glucarate + H2O""",},'ucsd-rxns' : ['GALCTD',], 'protein-comments' : ["""(The subunit structure is unknown.)""",]},
'B2092' : {'ecocyc-rxns': {"""TRANS-RXN-161""": """phosphoenolpyruvate + galactitol[periplasmic space] =galactitol-1-phosphate[cytosol] + pyruvate """,},'ucsd-rxns' : ['GALTptspp',], 'protein-comments' : ["""(contains a PTS Enzyme IIC domain)""","""(GatABC, the galactitol PTS permease, belongs to the functional
superfamily of the phosphoenolpyruvate (PEP)-dependent, sugar
transporting phosphotransferase system (PTS). The PTS transports
and simultaneously phosphorylates its sugar substrates in a process
called group translocation. GatABC takes up exogenous galactitol,
releasing the phosphate ester into the cell cytoplasm in preparation
for oxidation and further metabolism, primarily via a modified
glycolytic pathway, the tagatose-6-P glycolytic pathway |CITS: [94066914] [97290497] [97114348]|.
GatABC, the Enzyme IIGat complex, possesses
three polypeptide chains, GatA (IIAGat), GatB
(IIBGat) and GatC (IICGat).
GatB is homologous to IIBSga and IIBSgc
and shows limited sequence similarity to the IIB proteins of the
lactose and cellobiose permeases (IIBLac and
IIBCel) |CITS:[reizergenomescitech153] [97419490]|. GatC is homologous to the
SgcC (IICSgc) protein |CITS:[reizergenomescitech153]| and shows limited
sequence similarity to IICFru. The latter
domain has been reported to possess 6 transmembrane α-helical
segments. The IIB and IIA proteins are localized to the cytoplasmic
side of the membrane. The overall PTS-mediated phosphoryl transfer
reaction, requiring the two general energy coupling proteins of
the PTS, Enzyme I and HPr, as well as the three domains of the
Enzyme II complex is:
PEP --> Enzyme I(his~~P)
--> HPr(his~~P)
--> IIA(his~~P) -->
IIB(cys~~P) -(IIC)-> galactitol-1-P.
GatABC transports galactitol with micromolar affinity.
The gat operon (gatYZABCDR) contains the gatY
gene encoding tagatose 1,6-bis-P aldolase and the gatZ
gene encoding tagatose 6-P kinase as well as gatD, the
NAD-dependent galactitol 1-P dehydrogenase |CITS: [95290497] [97113438]|. gatR
encodes the repressor of the gat operon. The gat
operon is either constitutively expressed or galactitol inducible
in wild type E. coli strains. In E. coli strains
which express the gat operon constitutively, the gatR
gene is truncated. The gat operon is subject to positive
control by the cyclic AMP-cyclic AMP receptor protein (CRP) complex.)""",]},
'B2093' : {'ecocyc-rxns': {"""TRANS-RXN-161""": """phosphoenolpyruvate + galactitol[periplasmic space] =galactitol-1-phosphate[cytosol] + pyruvate """,},'ucsd-rxns' : ['GALTptspp',], 'protein-comments' : ["""(contains a PTS Enzyme IIB domain)""","""(GatABC, the galactitol PTS permease, belongs to the functional
superfamily of the phosphoenolpyruvate (PEP)-dependent, sugar
transporting phosphotransferase system (PTS). The PTS transports
and simultaneously phosphorylates its sugar substrates in a process
called group translocation. GatABC takes up exogenous galactitol,
releasing the phosphate ester into the cell cytoplasm in preparation
for oxidation and further metabolism, primarily via a modified
glycolytic pathway, the tagatose-6-P glycolytic pathway |CITS: [94066914] [97290497] [97114348]|.
GatABC, the Enzyme IIGat complex, possesses
three polypeptide chains, GatA (IIAGat), GatB
(IIBGat) and GatC (IICGat).
GatB is homologous to IIBSga and IIBSgc
and shows limited sequence similarity to the IIB proteins of the
lactose and cellobiose permeases (IIBLac and
IIBCel) |CITS:[reizergenomescitech153] [97419490]|. GatC is homologous to the
SgcC (IICSgc) protein |CITS:[reizergenomescitech153]| and shows limited
sequence similarity to IICFru. The latter
domain has been reported to possess 6 transmembrane α-helical
segments. The IIB and IIA proteins are localized to the cytoplasmic
side of the membrane. The overall PTS-mediated phosphoryl transfer
reaction, requiring the two general energy coupling proteins of
the PTS, Enzyme I and HPr, as well as the three domains of the
Enzyme II complex is:
PEP --> Enzyme I(his~~P)
--> HPr(his~~P)
--> IIA(his~~P) -->
IIB(cys~~P) -(IIC)-> galactitol-1-P.
GatABC transports galactitol with micromolar affinity.
The gat operon (gatYZABCDR) contains the gatY
gene encoding tagatose 1,6-bis-P aldolase and the gatZ
gene encoding tagatose 6-P kinase as well as gatD, the
NAD-dependent galactitol 1-P dehydrogenase |CITS: [95290497] [97113438]|. gatR
encodes the repressor of the gat operon. The gat
operon is either constitutively expressed or galactitol inducible
in wild type E. coli strains. In E. coli strains
which express the gat operon constitutively, the gatR
gene is truncated. The gat operon is subject to positive
control by the cyclic AMP-cyclic AMP receptor protein (CRP) complex.)""",]},
'B2091' : {'ecocyc-rxns': {"""GALACTITOLPDEHYD-RXN""": """galactitol-1-phosphate + NAD+ = tagatose-6-phosphate + NADH""",},'ucsd-rxns' : ['GLTPD',], 'protein-comments' : ["""NIL""",]},
'B2096' : {'ecocyc-rxns': {"""TAGAALDOL-RXN""": """tagatose-1,6-bisphosphate = dihydroxy-acetone-phosphate + D-glyceraldehyde-3-phosphate""",},'ucsd-rxns' : ['TGBPA',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B2036' : {'ecocyc-rxns': {"""GALPMUT-RXN""": """UDP-galactose = UDP-D-galacto-1,4-furanose""",},'ucsd-rxns' : ['UDPGALM',], 'protein-comments' : ["""NIL""",]},
'B2094' : {'ecocyc-rxns': {"""TRANS-RXN-161""": """phosphoenolpyruvate + galactitol[periplasmic space] =galactitol-1-phosphate[cytosol] + pyruvate """,},'ucsd-rxns' : ['GALTptspp',], 'protein-comments' : ["""(contains a PTS Enzyme IIA domain)""","""(GatABC, the galactitol PTS permease, belongs to the functional
superfamily of the phosphoenolpyruvate (PEP)-dependent, sugar
transporting phosphotransferase system (PTS). The PTS transports
and simultaneously phosphorylates its sugar substrates in a process
called group translocation. GatABC takes up exogenous galactitol,
releasing the phosphate ester into the cell cytoplasm in preparation
for oxidation and further metabolism, primarily via a modified
glycolytic pathway, the tagatose-6-P glycolytic pathway |CITS: [94066914] [97290497] [97114348]|.
GatABC, the Enzyme IIGat complex, possesses
three polypeptide chains, GatA (IIAGat), GatB
(IIBGat) and GatC (IICGat).
GatB is homologous to IIBSga and IIBSgc
and shows limited sequence similarity to the IIB proteins of the
lactose and cellobiose permeases (IIBLac and
IIBCel) |CITS:[reizergenomescitech153] [97419490]|. GatC is homologous to the
SgcC (IICSgc) protein |CITS:[reizergenomescitech153]| and shows limited
sequence similarity to IICFru. The latter
domain has been reported to possess 6 transmembrane α-helical
segments. The IIB and IIA proteins are localized to the cytoplasmic
side of the membrane. The overall PTS-mediated phosphoryl transfer
reaction, requiring the two general energy coupling proteins of
the PTS, Enzyme I and HPr, as well as the three domains of the
Enzyme II complex is:
PEP --> Enzyme I(his~~P)
--> HPr(his~~P)
--> IIA(his~~P) -->
IIB(cys~~P) -(IIC)-> galactitol-1-P.
GatABC transports galactitol with micromolar affinity.
The gat operon (gatYZABCDR) contains the gatY
gene encoding tagatose 1,6-bis-P aldolase and the gatZ
gene encoding tagatose 6-P kinase as well as gatD, the
NAD-dependent galactitol 1-P dehydrogenase |CITS: [95290497] [97113438]|. gatR
encodes the repressor of the gat operon. The gat
operon is either constitutively expressed or galactitol inducible
in wild type E. coli strains. In E. coli strains
which express the gat operon constitutively, the gatR
gene is truncated. The gat operon is subject to positive
control by the cyclic AMP-cyclic AMP receptor protein (CRP) complex.)""",]},
'B2095' : {'ecocyc-rxns': {"""TAGAALDOL-RXN""": """tagatose-1,6-bisphosphate = dihydroxy-acetone-phosphate + D-glyceraldehyde-3-phosphate""",},'ucsd-rxns' : ['TGBPA',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B3736' : {'ecocyc-rxns': {"""ATPSYN-RXN""": """H+[cytosol] + H2O + ATP =H+[periplasmic space] + phosphate + ADP """,},'ucsd-rxns' : ['ATPS4rpp','ATPS4rpp',], 'protein-comments' : ["""NIL""","""(The b subunit complex is involved in binding the F-1 complex to the F-O complex
and is necessary for the assembly of the F-O complex. Most of the subunit
complex is exposed to the cytoplasm with only the short hydrophobic amino
terminus embedded in the membrane. |CITS: [85234519] [93147708]|)""","""(The F-O complex of ATP synthase functions as the proton channel and consists of
three subunits. All are required for a functional F-O complex. The F-O complex
is membrane-bound. |CITS: [90303438] [93147708]|)""","""(The enzyme is made up of two subcomplexes, the F-1 complex and the F-O complex.
There are eight total subunits all required for activity. The F-1 complex is
the catalytic unit. The F-O complex anchors the F-1 complex to the membrane
and also forms the proton channel. |CITS: [89123355] [90303438] [93252965]|)""",]},
'B3588' : {'ecocyc-rxns': {"""RXN0-3962""": """acetaldehyde + NADP+ + H2O -> acetate + NADPH + H+""",},'ucsd-rxns' : ['ALDD3y','ALDD2y',], 'protein-comments' : ["""NIL""","""(AldB has NADP-dependent acetaldehyde dehydrogenase activity |CITS: [15659684]|, which may be identical to the
activity detected by Heim and Strehler in crude cell extracts |CITS: [1840553]|. The enzyme is a homotetramer.
Similar to the human liver mitochondrial aldehyde dehydrogenase, MgCl2 increases the enzymatic
activity of AldB on a variety of substrates |CITS: [15659684]|.
AldB expression is induced by ethanol and at the beginning of stationary phase and may play a role in detoxifying
alcohols and aldehydes present during stationary phase |CITS: [95286498]|.
Based on sequence similarity, AldB was also predicted to be an aminobutyraldehyde dehydrogenase
|CITS: [12952533]|.
A transposon insertion in the intergenic region between yiaW and aldB causes increased sensitivity to
various antimicrobial drugs, but an aldB deletion mutant shows no such effect |CITS: [15668009]|.)""",]},
'B3460' : {'ecocyc-rxns': {"""ABC-35-RXN""": """ATP + L-leucine[periplasmic space] + H2O =ADP + phosphate + L-leucine[cytosol] ""","""ABC-36-RXN""": """ATP + L-valine[periplasmic space] + H2O =ADP + phosphate + L-valine[cytosol] ""","""ABC-15-RXN""": """ATP + L-isoleucine[periplasmic space] + H2O =ADP + phosphate + L-isoleucine[cytosol] """,},'ucsd-rxns' : ['VALabcpp','THRabcpp','ALAabcpp','ILEabcpp','LEUabcpp',], 'protein-comments' : ["""NIL""","""(LivFGHMJ and LivFGHMK are two ATP-dependent high-affinity branched-chain amino acid transport
system and are members of the ATP Binding Cassette (ABC) Superfamily of transporters |CITS: [20053876]|.
The two systems are responsible for the high affinity transport of branched-chain amino acids in E. coli.
They have shared membrane and ATP-binding components but have distinctive periplasmic binding proteins.
Due to the different periplasmic binding components, the two complexes differ in their binding specificity:
LivFGHMK is specific for the transport of leucine, while LivFGHMJ is a transporter for leucine, isoleucine,
and valine |CITS: [85288998]|. Based on sequence similarity and hydrophobicity analysis, LivJ and LivK
are the two periplasmic animo acid-binding proteins, LivH and LivM are the membrane components, and
LivG and LivF are the ATP-binding component of the ABC transport complexes |CITS: [90307651]|.
Deletions each of the liv genes resulted in the inability to transport leucine |CITS: [90307651]|. In
addition, a deletion strain that does not express any of the liv genes was unable to carry out high-
affinity transport of leucine unless one of the binding protein genes and all of the membrane complex genes
were provided on a plasmid |CITS: [90307651]|. In a separate experiment, liv gene mutants were
found to be resistant to a toxic analog of leucine, azaleucine, due to its inability in branched-chain amino
acid transport |CITS: [85288998]|. This system has also been shown |CITS:[14702302]| to serve as a third (along
with the AroP and PheP systems) complex for transport of phenylanine across the inner membrane.)""",]},
'B0932' : {'ecocyc-rxns': {"""3.4.11.2-RXN""": """EC# 3.4.11.2""",},'ucsd-rxns' : ['AMPTASEPG','AMPTASECG',], 'protein-comments' : ["""(Aminopeptidase N is an aminoendopeptidase, capable of breaking down small peptides as well
as whole, native proteins |CITS: [1271][12482750]|.
Some results suggest that aminopeptidase N synthesis is independent of growth conditions,
though other experiments have demonstrated increased synthesis of this protein during
phosphate starvation, anaerobiosis and growth on glycerol and succinate |CITS: [6752120][6129564][2863254]|.)""",]},
'B0931' : {'ecocyc-rxns': {"""NICOTINATEPRIBOSYLTRANS-RXN""": """nicotinate nucleotide + diphosphate = nicotinate + 5-phosphoribosyl 1-pyrophosphate""",},'ucsd-rxns' : ['NAMNPP',], 'protein-comments' : ["""(Nicotinate phosphoribosyltransferase (NAPRTase) mediates the formation of nicotinate mononucleotide from
exogenous nicotinate and PRPP. The product is then converted intracellularly into NAD. The enzyme also
participates in resynthesizing NAD by recycling intracellular nicotinate resulting from NAD degradation
|CITS: [78150776]|.
NAPRTase was reported to localize to the periplasm |CITS: [346557]|. However, the enzyme does not have a
recognizable signal sequence, and N-terminal sequencing of the partially purified protein gives no indication of
N-terminal processing of the enzyme |CITS: [2211655]|. Additional unpublished evidence for localization to the
periplasm or cytoplasmic membrane is mentioned |CITS: [2211655]|.)""",]},
'B0930' : {'ecocyc-rxns': {"""ASPARAGINE--TRNA-LIGASE-RXN""": """tRNAasn + L-asparagine + ATP -> L-asparaginyl-tRNAasn + diphosphate + AMP""",},'ucsd-rxns' : ['ASNTRS',], 'protein-comments' : ["""(Asparaginyl-tRNA synthetase (AsnRS) is a member of the family of aminoacyl-tRNA synthetases, which interpret the
genetic code by covalently linking amino acids to their specific tRNA molecules. The reaction is driven by ATP
hydrolysis. AsnRS belongs to the Class II aminoacyl tRNA synthetases, which share three regions of homology
|CITS: [2203971]|.
AsnRS is a dimer in solution |CITS: [2693216][1425658]|. Analysis of mutants suggests that the Y426 residue is
involved in ATP binding |CITS: [2009959]|; a P231L mutation, which is located in the conserved motif 2 of class II
aminoacyl-tRNA synthetases, leads to increases in the Km for asparagine and ATP |CITS: [1544480]|.
Review: |CITS: [10966471]|)""","""NIL""",]},
'B0937' : {'ecocyc-rxns': {"""FMNREDUCT-RXN""": """FMNH2 + NAD(P)+ = FMN + NAD(P)H + H+""",},'ucsd-rxns' : ['FMNRx2','FMNRx',], 'protein-comments' : ["""(The SsuE protein is a NAD(P)H-dependent FMN reductase that provides FMNH2 for SsuD, an
FMNH2-dependent monooxygenase |CITS: [10480865]|. FMN is the preferred flavin substrate of SsuE,
but the enzyme is also active with FAD and riboflavin |CITS: [10480865]|.
Analysis of the kinetics of the enzyme both in the presence and absence of SsuD showed that the presence of both
SsuD and its alkanesulfonate substrate are required for the SsuE-catalyzed FMN reductase reaction to proceed from
the ternary complex |CITS: [15882995]|.
A preliminary analysis of the crystal structure of SsuE has been published |CITS: [16511173]|.
Expression of SsuE appears to be induced by sulfate or cysteine starvation |CITS: [8774726]|. Transcription of
ssuE is repressed by sulfate or cysteine, and the effect requires the transcriptional regulator Cbl
|CITS: [10506196]|. APS may serve as the signaling molecule to regulate activity of Cbl |CITS: [11918818]|.
Review: |CITS: [11479697]|)""","""NIL""",]},
'B0936' : {'ecocyc-rxns': {},'ucsd-rxns' : ['ETHSO3abcpp','SULFACabcpp','BUTSO3abcpp','ISETACabcpp','MSO3abcpp',], 'protein-comments' : ["""NIL""","""(Deletion mutation studies |CITS:[10506196]| indicate that the ssuEADCB gene cluster codes for proteins that enable Escherichia coli
to utilize sulfonates other than taurine as a sulfur source. Based on sequence similarity SsuABC is the ABC type transport system with
SsuA being the periplasmic substrate-binding subunit, SsuB the ATP-binding subunit and SsuC the permease. ssuD and
ssuE encode an FMNH2-dependent monooxygenase and an NAD(P)H-dependent FMN reductase, respectively.)""",]},
'B0935' : {'ecocyc-rxns': {"""RXN0-280""": """an alkanesulfonate + O2 + FMNH2 = an aldehyde + sulfite + H2O + FMN""",},'ucsd-rxns' : ['FDMO3','FDMO2','FDMO6','FDMO4','FDMO',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B0934' : {'ecocyc-rxns': {},'ucsd-rxns' : ['ETHSO3abcpp','SULFACabcpp','BUTSO3abcpp','ISETACabcpp','MSO3abcpp',], 'protein-comments' : ["""(membrane component of ABC transporter
Protein topology in the inner membrane has been determined |CITS: [11867724]|.)""","""(Deletion mutation studies |CITS:[10506196]| indicate that the ssuEADCB gene cluster codes for proteins that enable Escherichia coli
to utilize sulfonates other than taurine as a sulfur source. Based on sequence similarity SsuABC is the ABC type transport system with
SsuA being the periplasmic substrate-binding subunit, SsuB the ATP-binding subunit and SsuC the permease. ssuD and
ssuE encode an FMNH2-dependent monooxygenase and an NAD(P)H-dependent FMN reductase, respectively.)""",]},
'B3469' : {'ecocyc-rxns': {},'ucsd-rxns' : ['COBALT2abcpp','CD2abcpp','HG2abcpp','CU2abcpp','ZN2abcpp','NI2abcpp',], 'protein-comments' : ["""(The gene product of the yhhO gene, also referred to as zntA, is
a P-type ATPase involved in the efflux of Pb(II), Cd(II), and Zn(II) |CITS:[98070750] [20263730]|.
ZntA displays a Km of approximately 20 μM for Cd(II) and
100 μM for Zn(II) |CITS:[20127859]|. The transporter appears to be inhibited
by vanadate, a common inhibitor of P-type ATPase. The ATPase activity of the
transporter was found to follow the order Pb(II), Cd(II), Zn(II), and Hg(II) |CITS:[20127859]|.
A zntA mutant showed hypersensitivity to Cd(II) and Zn(II) |CITS:[98070750]|.
The zntA gene was found to be under the control of the transcriptional
regulator ZntR. zntA expression is activated by an increased concentration
of Cd(II) and Zn(II) within the cell, showing greater induction by Cd(II) than by
Zn(II) |CITS:[20127859]|.)""",]},
'B1002' : {'ecocyc-rxns': {"""RXN0-1001""": """phytate + H2O -> D-myo-inositol (1,2,4,5,6)-pentakisphosphate + phosphate""","""GLUCOSE-1-PHOSPHAT-RXN""": """H2O + α-D-glucose 1-phosphate -> phosphate + β-D-glucose""",},'ucsd-rxns' : ['G1PPpp','GAL1PPpp',], 'protein-comments' : ["""(Glucose-1-phosphatase, encoded by the agp gene, is a dimeric periplasmic enzyme that shows optimum
glucose-1-phosphate hydrolysis activity at pH 4 |CITS: [90130318][91297199]|. Glucose-1-phosphatase is a
3-phosphatase |CITS: [12455612]|. Glucose-1-phosphatase shows activity toward glucose-1-phosphate
(Km of 0.39 mM), p-nitrophenyl phosphate (Km of 13 mM), myo-inositol hexakisphosphate (InsP6; Km of 0.54 mM),
D-Ins(1,2,3,4,5)P5, Ins(1,3,4,5,6)P5, and Ins(1,2,3,4,6)P5 |CITS: [12455612]|. The enzyme also acts on
D-galactose-1-phosphate, more slowly than on glucose-1-phosphate. The enzyme is stable at a wide range of pH
conditions, and pH optima for hydrolysis of various substrates are discussed |CITS: [12455612]|.)""","""NIL""",]},
'B1263' : {'ecocyc-rxns': {"""PRTRANS-RXN""": """N-(5'-phosphoribosyl)-anthranilate + diphosphate = anthranilate + 5-phosphoribosyl 1-pyrophosphate""","""ANTHRANSYN-RXN""": """chorismate + L-glutamine = anthranilate + pyruvate + L-glutamate""",},'ucsd-rxns' : ['ANPRT','ANS',], 'protein-comments' : ["""(The trpD gene encodes a bifunctional protein that participates in both of the two first steps of tryptophan biosynthesis
from chorismate: it contains a glutamine amidotransferase (GATase) activity which, along with the TrpE protein, forms
the anthranilate synthase complex that catalyzes the first step of the pathway, and an anthranilate phosphoribosyl
transferase (PRTase) activity which catalyzes the second step. The two activities are encoded as separate
polypeptides (TrpD and TrpG) in other organisms |CITS:[84183611]|; in them, the gene encoding GATase is
designated trpD and the one encoding anthranilate PRTase is designated trpG. For this reason, the domain of the
E. coli TrpD protein with anthranilate PRTase activity is sometimes termed the TrpG domain.
The TrpD protein is also called Component II of the anthranilate synthase enzyme complex, where its TrpD domain
provides the glutamine amidotransferase function that allows glutamine to serve as the amino donor in anthranilate
formation, channelling the nitrogen from glutamine to the active site of the anthranilate synthase enzyme complex.
|CITS: [ColiSalII]|
The TrpG domain of the TrpD protein catalyzes the second step in the tryptophan biosynthesis pathway, converting
anthranilate + PRPP to phosphoribosylanthranilate |CITS:[82150258]|. This activity can be carried out by the purified
TrpD protein and is thus independent of TrpE, the second component of the anthranilate synthase complex.
Genetic and biochemical studies have shown that the glutamine amidotransferase function resides in the
amino-terminal third of the TrpD protein. The carboxyl-terminal two thirds of the polypeptide is sufficient to perform
the phosphoribosyltransferase reaction, since deletion mutants lacking the first 1/3 of the trpD gene retain
phosphoribosyltransferase activity |CITS:[368647]|.
The protein is unusual in having only one tryptophan residue. This should be advantageous, since translation of
message coding for an enzyme required for tryptophan biosynthesis would be impeded in cases of severe tryptophan
starvation if it contained a significant number of tryptophan codons |CITS:[82216842]|.
)""","""(The native anthranilate synthase enzyme exists as a tetrameric complex of two subunits each of the TrpE (Component I) and TrpD (Component II) proteins |CITS: [5331787] [74173403]|.
The TrpD protein is bifunctional; it also catalyzes the second reaction in the biosynthesis of tryptophan from chorismate |CITS:[81267360]|.
)""","""(Component II of anthranilate synthase also provides PRTase
activity. The amino terminal 1/3 provides the glutamine amidotransferase
function. The carboxyl terminal 2/3 of the polypeptide carries out
the PRTase reaction |CITS:[74173403]| Anthranilate synthase is a
tetramer composed of 2 component I polypeptides and 2 component II polypeptides. In E. coli
component II is larger and its C-terminal 2/3 has the 2.4.2.18
activity |CITS:[82216842]|.)""",]},
'B1006' : {'ecocyc-rxns': {},'ucsd-rxns' : ['URAt2rpp',], 'protein-comments' : ["""(E. coli K-12 contains a previously undescribed pathway for pyrimidine degradation. The enzymes of the
pathway are encoded by the rutABCDEFG operon. The rutG gene product is an uncharacterized
member of the NCS2 family of nucleobase transporters. Based on sequence similarity, RutG may function as a
proton-driven uracil uptake system.
RutG contains 11 predicted transmembrane helices; the C terminus of the protein is located on the cytoplasmic side
of the inner membrane |CITS: [15919996]|.
The rutG gene is the last gene in an operon together with genes involved in the utilization of
pyrimidines as nitrogen sources. Expression of the rutABCDEFG operon is under the control of nitrogen
regulatory protein C (NtrC) |CITS: [11121068]|.
RutG: "pyrimidine utilization" |CITS: [16540542]|
)""",]},
'B3266' : {'ecocyc-rxns': {"""TRANS-RXN-92""": """H+[periplasmic space] + multidrug[cytosol] =H+[cytosol] + multidrug[periplasmic space] """,},'ucsd-rxns' : ['INDOLEt2pp',], 'protein-comments' : ["""NIL""","""(AcrEF is a multidrug efflux system in Escherichia coli that is highly homologous to the AcrAB multidrug efflux system |CITS:[1720861]|.
Plasmid overexpression of acrEF suppress the hyper-drug sensitivity of acrAB deletion mutants |CITS:[10518736]| however
the AcrEF system is not thought to play a large role in drug resistance as acrEF deletion mutants do not display a drug sensitive
phenotype. The level of expression of acrEF is thought to be low under laboratory conditions |CITS:[8830678]|.
Complementation studies have shown that plasmid-expressed acrF is able to complement an acrB deletion mutation.
AcrEF plasmid complementation is dependent on TolC, strongly suggesting that AcrEF, like AcrAB, forms a complex with the outer
membrane protein |CITS:[11274125]|.)""",]},
'B1778' : {'ecocyc-rxns': {"""PROTEIN-METHIONINE-S-OXIDE-REDUCTASE-RXN""": """a protein-L-methionine + oxidized thioredoxin = a protein-L-methionine-S-oxide + reduced thioredoxin""","""METHIONINE-S-OXIDE-REDUCTASE-RXN""": """a thioredoxin disulfide + L-methionine + H2O = a reduced thioredoxin + L-methionine sulfoxide""",},'ucsd-rxns' : ['METSOXR2','METSOXR2',], 'protein-comments' : ["""(MsrB exhibits methionine sulfoxide reductase activity (Km of 6.7 mM) and dimethylsulfoxide reductase activity in vitro |CITS: [11677230]|. MsrB exhibits 1000-fold lower catalytic efficiency than MsrA toward free methionine sulfoxide |CITS: [11677230]|. MsrA and MsrB exhibit similar activity (quantitatively) toward an oxidized peptide substrate, though they appear to exhibit some differences in specificity for substrate sites within the peptide |CITS: [11677230]|. MsrB exhibits weak activity toward the met-R-(o) enantiomer of free (non-peptide) methionine sulfoxide |CITS: [12504094]|.
An msrB mutant shows increased cadmium sensitivity, compared to wild type, but does not exhibit an apparent growth defect on rich medium, consistent with a role for MsrB in resistance to oxidative stress |CITS: [11677230]|.
Some organisms produce a methionine sulfoxide reductase composed of two domains with similarity to MsrA and MsrB, respectively, whereas E. coli produces these two distinct polypeptides |CITS: [11677230]|. The E. coli MsrA and MsrB polypeptides do not interact with each other in vitro or in a yeast two-hybrid test |CITS: [11677230]|.
The protein has similarity to Neisseria gonorrhea PilB protein |CITS: [12096194]|.
MsrB was overproduced and purified |CITS: [11677230]|.
Additional methionine sulfoxide reductase activities have been observed in a msrA msrB double mutant, including a soluble activity toward the met-R-(o) enantiomer of free (non-peptide) methionine sulfoxide (fRMsr activity) |CITS: [12504094]|, a soluble activity toward the met-S-(o) enantiomer of free (non-peptide) methionine sulfoxide (fSMsr activity) |CITS: [12504094]|, a soluble NADPH-dependent activity toward the met-S-(o) enantiomer of peptide-linked methionine sulfoxide (MsrA1 activity) |CITS: [12504094], [12604343]|, and a membrane-associated NADPH-dependent activity toward both met-S-(o) and met-R-(o) enantiomers of peptide-linked and free methionine sulfoxide |CITS: [12504094], [12604343]|.)""",]},
'B0508' : {'ecocyc-rxns': {"""RXN0-305""": """hydroxypyruvate = tartronate semialdehyde""",},'ucsd-rxns' : ['HPYRI',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B3265' : {'ecocyc-rxns': {"""TRANS-RXN-92""": """H+[periplasmic space] + multidrug[cytosol] =H+[cytosol] + multidrug[periplasmic space] """,},'ucsd-rxns' : ['INDOLEt2pp',], 'protein-comments' : ["""NIL""","""(AcrEF is a multidrug efflux system in Escherichia coli that is highly homologous to the AcrAB multidrug efflux system |CITS:[1720861]|.
Plasmid overexpression of acrEF suppress the hyper-drug sensitivity of acrAB deletion mutants |CITS:[10518736]| however
the AcrEF system is not thought to play a large role in drug resistance as acrEF deletion mutants do not display a drug sensitive
phenotype. The level of expression of acrEF is thought to be low under laboratory conditions |CITS:[8830678]|.
Complementation studies have shown that plasmid-expressed acrF is able to complement an acrB deletion mutation.
AcrEF plasmid complementation is dependent on TolC, strongly suggesting that AcrEF, like AcrAB, forms a complex with the outer
membrane protein |CITS:[11274125]|.)""",]},
'B2393' : {'ecocyc-rxns': {"""TRANS-RXN-108I""": """H+[periplasmic space] + uridine[periplasmic space] =H+[cytosol] + uridine[cytosol] ""","""TRANS-RXN-108H""": """H+[periplasmic space] + thymidine[periplasmic space] =H+[cytosol] + thymidine[cytosol] ""","""TRANS-RXN-108G""": """H+[periplasmic space] + inosine[periplasmic space] =H+[cytosol] + inosine[cytosol] ""","""TRANS-RXN-108F""": """H+[periplasmic space] + deoxyuridine[periplasmic space] =H+[cytosol] + deoxyuridine[cytosol] ""","""TRANS-RXN-108E""": """H+[periplasmic space] + deoxyinosine[periplasmic space] =H+[cytosol] + deoxyinosine[cytosol] ""","""TRANS-RXN-108D""": """H+[periplasmic space] + deoxycytidine[periplasmic space] =H+[cytosol] + deoxycytidine[cytosol] ""","""TRANS-RXN-108C""": """H+[periplasmic space] + deoxyadenosine[periplasmic space] =H+[cytosol] + deoxyadenosine[cytosol] ""","""TRANS-RXN-108B""": """H+[periplasmic space] + cytidine[periplasmic space] =H+[cytosol] + cytidine[cytosol] ""","""TRANS-RXN-108A""": """H+[periplasmic space] + adenosine[periplasmic space] =H+[cytosol] + adenosine[cytosol] """,},'ucsd-rxns' : ['ADNt2pp','THMDt2pp','DADNt2pp','URIt2pp','CYTDt2pp','DCYTt2pp','DURIt2pp',], 'protein-comments' : ["""(NupC is one of two high-affinity nucleoside transporters in E. coli.
Studies of chromosomal mutants using membrane vesicles have shown that
NupC differs from NupG by mediating transport of nucleosides except for
guanosine or deoxyguanosine, whereas NupG transports all nucleosides
|CITS: [73250126] [79173073]|. Studies with inhibitors have indicated that
NupC transport is dependent on the proton motive force, and NupC
presumably functions as a nucleoside/proton symporter |CITS: [79173073]|.
The cloned nupC gene has been demonstrated to complement nupC
chromosomal mutations |CITS: [94293784]|. NupC is a member of the NUP
family of nucleoside transporters |CITS: [99184734]|.
nupC is located in a monocistronic operon and its expression is
repressed by the CytR repressor.
Imported nucleosides serve as precursors of DNA and RNA, as well as
of histidine and various co-factors.)""",]},
'B2392' : {'ecocyc-rxns': {"""RXN0-2421""": """Fe2+[periplasmic space] + H+[periplasmic space] =Fe2+[cytosol] + H+[cytosol] ""","""TRANS-RXN-241""": """Mn2+[periplasmic space] + H+[periplasmic space] =Mn2+[cytosol] + H+[cytosol] """,},'ucsd-rxns' : ['MNt2pp','FE2t2pp',], 'protein-comments' : ["""(The MntH protein is a member of the natural resistance-associated macrophage proteins
(NRAMP) family of metal ion transporters. The protein has 11 putative membrane spanning alpha helices.
This permease is involved in the uptake of Metal 2+. Uptake of Mn2+ is mediated by a high affinity proton
symport reaction. The permease also transports Fe2+ at a lower affinity. Mutation of five of the six acidic
residues in MntH, Asp-34, Glu-102, Asp-109, Glu-112, and Asp-238, shows they are important for
function of the protein. The lack of function of the protein upon mutation of the residues in the DPGN
signature sequence of the Nramp family suggests that these helix-breaking residues form a binding pocket
for Mn2+ transport |CITS:[15630547]|.)""",]},
'B0507' : {'ecocyc-rxns': {"""GLYOCARBOLIG-RXN""": """2 glyoxylate = CO2 + tartronate semialdehyde""",},'ucsd-rxns' : ['GLXCL',], 'protein-comments' : ["""NIL""","""(The protein contains quinone, thiamine pyrophosphate and FAD
binding sites. |CITS: [93179387]|)""",]},
'B0365' : {'ecocyc-rxns': {"""ABC-64-RXN""": """taurine[periplasmic space] + ATP + H2O =taurine[cytosol] + ADP + phosphate """,},'ucsd-rxns' : ['BUTSO3abcpp','ISETACabcpp','TAURabcpp',], 'protein-comments' : ["""(substrate-binding component of ABC transporter)""","""(The TauABC transporter belongs to the ATP Binding Cassette (ABC)
superfamily |CITS: [96381453]|, and is believed to be responsible for taurine uptake
in E. coli |CITS: [96404792]|. E. coli rely on organosulfur compounds
such as taurine as sources of sulfur when the level of inorganic sulfate
available in the invironment is low |CITS: [96404792]|. Disruption of the tauABC
genes resulted in the loss of the ability to utilize taurine
(2-aminoethanesulfonate) as a source of sulfur but did not affect the
utilization of a range of other aliphatic sulfonates as sulfur sources.
Taurine utilization was restored when the tauABC mutants
were complemented with a clone of the tauABC locus |CITS: [96404792]|. TauA
contains a N-terminal signal sequence, indicating that it is probably
located in the periplasm, and therefore may function as the substrate
binding component of the ABC transporter |CITS: [96404792]|. TauC is the membrane
component of the TauABC taurine ABC transporter |CITS:[8808933]|. Membrane topology
predictions using experimentally determined C terminus locations indicate that TauC has
6 transmembrane helices and the C-terminus is located in the cytoplasm |CITS:[15044727]|
TauB and TauC show strong sequence similarities to ATP-binding components and
membrane components, respectively, of other members of the ABC
superfamily |CITS: [96404792]|. Expression of tauABC is induced by sulfate
starvation, and analysis of LacZ fusions showed that the tauABC
operon is repressed by the presence of sulfur containing compounds, such as sulfate,
cysteine, cystine, ethanesulfonate, and lanthionine |CITS: [96404792]|.)""",]},
'B2997' : {'ecocyc-rxns': {"""RXN0-4141""": """H2 + an acceptor = 2 H+ + a reduced acceptor""",},'ucsd-rxns' : ['HYD1pp','HYD2pp','HYD3pp',], 'protein-comments' : ["""(HybO is the small subunit of hydrogenase 2, and it contains three Fe-S centers |CITS: [98409297]|. Hydrogenase 2
is associated with the periplasmic side of the cytoplasmic membrane |CITS: [3516690][8772179]|. HybO contains a
twin-arginine signal sequence which is required for membrane targeting by the Tat system |CITS: [9738917]|.
HybC and HybO are coordinately assembled and processed; the presence of both subunits, nickel acquisition and
the subsequent processing of HybC are required for export of both subunits by the Tat system |CITS: [8772179]
[10224080]|.
Review: |CITS: [15119826]|
)""","""(Trypsin treatment of membranes releases an active, soluble fragment of hydrogenase 2 which consists of the large
and small subunits |CITS: [3516690]|. The complete enzyme complex is thought to consist of the HybA, HybB, HybC,
and HybO subunits |CITS: [DUBINI02]|.
The substrate specificity of hydrogenase 2 for various quinones is unknown |CITS: [11506918]|.)""",]},
'B0077' : {'ecocyc-rxns': {"""ACETOLACTSYN-RXN""": """2 pyruvate = 2-acetolactate + CO2""","""ACETOOHBUTSYN-RXN""": """pyruvate + 2-oxobutanoate = 2-aceto-2-hydroxy-butyrate + CO2""",},'ucsd-rxns' : ['ACLS','ACHBS',], 'protein-comments' : ["""(IlvI is the catalytic (large) subunit of acetolactate synthase III |CITS: [8756689]|.
)""","""(Acetohydroxy acid synthase III (AHAS III) is one of two functional isozymes catalyzing the decarboxylation of
pyruvate and transfer of the resulting acetaldehyde group to either pyruvate or α-ketobutyrate, producing
α-acetolactate for the valine pathway and α-aceto-α-hydroxybutyrate for the isoleucine pathway.
This is the first common step in the biosynthesis of the branched-chain amino acids isoleucine, leucine, and valine.
A third isozyme, AHAS II, is not functional in E. coli K-12 due to the presence of a frame shift mutation in the
gene encoding the large subunit, ilvG. |CITS: [colisalII]|
In the presence of both pyruvate and α-ketobutyrate, AHAS III produces approximately 40-fold more
acetohydroxybutyrate than acetolactate, while AHAS I shows no product preference |CITS: [3301814][2675968]|.
The differential regulation of enzymatic activity and
expression of the isozymes has direct physiological consequences and has been under intense study. The end
products of the branched-chain amino acid biosynthesis pathways all inhibit AHAS III activity, although inhibition by
valine is most significant |CITS: [2675968]|. Both AHAS I and III are inhibited by valine |CITS: [Defelice78]|. Activity
of AHAS III is only partially inhibited by leucine, while AHAS I activity can be almost completely inhibited
|CITS: [6351926]|.)""",]},
'B0074' : {'ecocyc-rxns': {"""2-ISOPROPYLMALATESYN-RXN""": """2-keto-isovalerate + acetyl-CoA + H2O = 2-isopropylmalate + coenzyme A""",},'ucsd-rxns' : ['IPPS',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B2994' : {'ecocyc-rxns': {"""RXN0-4141""": """H2 + an acceptor = 2 H+ + a reduced acceptor""",},'ucsd-rxns' : ['HYD1pp','HYD2pp','HYD3pp',], 'protein-comments' : ["""(HybC is the large subunit of hydrogenase 2. Hydrogenase 2 is associated with the periplasmic side of the
cytoplasmic membrane |CITS: [3516690][8772179]|. HybC is processed; N-terminal sequencing of the mature
protein confirmed that processing does not occur at the N terminus |CITS: [9738917]|, while alteration of the C
terminus of HybC interferes with processing |CITS: [12829374]|.
HybC and HybO are coordinately assembled and processed; the presence of both subunits, nickel acquisition and
the subsequent processing of HybC, and the N-terminal signal sequence of HybO are required for export of both
subunits by the Tat system |CITS: [8772179][10224080]|.
Expression of the hyb operon is induced under anaerobic conditions and repressed by nitrate
|CITS: [10537212]|.
Review: |CITS: [15119826]|
)""","""(Trypsin treatment of membranes releases an active, soluble fragment of hydrogenase 2 which consists of the large
and small subunits |CITS: [3516690]|. The complete enzyme complex is thought to consist of the HybA, HybB, HybC,
and HybO subunits |CITS: [DUBINI02]|.
The substrate specificity of hydrogenase 2 for various quinones is unknown |CITS: [11506918]|.)""",]},
'B0072' : {'ecocyc-rxns': {"""3-ISOPROPYLMALISOM-RXN""": """2-isopropylmalate = 3-isopropylmalate""",},'ucsd-rxns' : ['IPPMIb','IPPMIa',], 'protein-comments' : ["""NIL""","""(The complex consists of two different subunits: LEUC and
LEUD. |CITS: [SwissProt]|)""",]},
'B3919' : {'ecocyc-rxns': {"""TRIOSEPISOMERIZATION-RXN""": """D-glyceraldehyde-3-phosphate = dihydroxy-acetone-phosphate""",},'ucsd-rxns' : ['TPI',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B0070' : {'ecocyc-rxns': {"""TRANS-RXN-82""": """lactose[cytosol] + H+[periplasmic space] =lactose[periplasmic space] + H+[cytosol] """,},'ucsd-rxns' : ['LCTSt3ipp',], 'protein-comments' : ["""(YabM is a probable efflux transporter for sugars such as lactose and IPTG.
Cells overexpressing yabM show decreased accumulation of lactose and IPTG |CITS: [99226230]|.
Everted membrane vesicles prepared from cells overexpressing yabM exhibit
lactose transport activity which is abolished by uncouplers |CITS: [99226230]|. YabM is a member
of the major facilitator superfamily (MFS) of transporters, and it probably
functions as a proton/sugar antiporter. The physiological significance and
regulation of yabM remain unclear. The yabM gene probably constitutes a
monocistronic operon.)""",]},
'B0071' : {'ecocyc-rxns': {"""3-ISOPROPYLMALISOM-RXN""": """2-isopropylmalate = 3-isopropylmalate""",},'ucsd-rxns' : ['IPPMIb','IPPMIa',], 'protein-comments' : ["""NIL""","""(The complex consists of two different subunits: LEUC and
LEUD. |CITS: [SwissProt]|)""",]},
'B3735' : {'ecocyc-rxns': {"""ATPSYN-RXN""": """H+[cytosol] + H2O + ATP =H+[periplasmic space] + phosphate + ADP """,},'ucsd-rxns' : ['ATPS4rpp','ATPS4rpp',], 'protein-comments' : ["""(The delta subunit is required for binding the F-1 complex to the F-O complex.
It may also block proton conduction through the F-O complex. |CITS: [90148989] [94308197]|)""","""(The F-1 complex of ATP synthase contains the catalytic sites. The complex
consists of five subunits, each of which is required for activity.
|CITS: [90303438] [89372792]|)""","""(The enzyme is made up of two subcomplexes, the F-1 complex and the F-O complex.
There are eight total subunits all required for activity. The F-1 complex is
the catalytic unit. The F-O complex anchors the F-1 complex to the membrane
and also forms the proton channel. |CITS: [89123355] [90303438] [93252965]|)""",]},
'B3915' : {'ecocyc-rxns': {"""RXN0-6""": """Fe2+[cytoplasm] + H+[periplasmic space] =Fe2+[periplasmic space] + H+[cytoplasm] ""","""TRANS-RXN-200""": """Zn2+[cytosol] + H+[periplasmic space] =Zn2+[periplasmic space] + H+[cytosol] """,},'ucsd-rxns' : ['NI2t3pp','HG2t3pp','COBALT2t3pp','MN2t3pp','CD2t3pp','FE2t3pp','ZN2t3pp',], 'protein-comments' : ["""(The FieF protein is a member of the cation diffusion facilitator (CDF) family of metal cation
transporters |CITS: [97232493]|. Based on sequence similarity, FieF functions as a divalent metal cation
transporter. Metal binding properties of the purified protein have been described |CITS: [14960568]|. FieF
has been shown to form dimers in detergent-lipid micelles by size-exclusion chromatography and laser
light-scattering photometry, and in reconstituted membranes by electron microscopic analysis of FieF
crystals |CITS:[15258151]|.
The fieF gene probably constitutes a monocistronic operon. Transcription of fieF has been
shown to correlate with iron concentration independent of the ferrous iron uptake regulator Fur. Double
fieF and fur led to growth deficiency in complex growth medium, which was partially
alleviated by in trans expression of fieF. E.coli cells overexpressing fieF
exhibited reduced isotopic Fe accumulation, and Zn(II) efflux was shown to be catalyzed through a proton
antiport mechanism in membrane eversion studies. Transmembrane flux of iron cations was measured
using fluorescence quenching in conjunction with purified and reconstituted FieF. The results suggest that
FieF is an iron and zinc efflux system which functions in detoxification. |CITS:[15549269]|.)""",]},
'B3916' : {'ecocyc-rxns': {"""6PFRUCTPHOS-RXN""": """D-fructose-6-phosphate + ATP = ADP + fructose-1,6-bisphosphate""","""NAD-KIN-RXN""": """NAD+ + ATP = NADP+ + ADP""",},'ucsd-rxns' : ['PFK_2','PFK',], 'protein-comments' : ["""NIL""","""(This enzyme is an isozyme with phosphofructokinase-2. The
nucleotide sequences of the genes are not similar |CITS: [85203917]|. The
tetrameric species is the only one which can bind both substrates and
effectors, and thus have both catalytic and regulatory properties. The
C terminal end of the peptide is required for allosteric
properties.|CITS: [90276415]| Crystal structures have been solved
with and without activators and inhibitors. |CITS: [89342465], [89125622]|)""",]},
'B0888' : {'ecocyc-rxns': {"""THIOREDOXIN-REDUCT-NADPH-RXN""": """a reduced thioredoxin + NADP+ = oxidized thioredoxin + NADPH + H+""",},'ucsd-rxns' : ['TRDR','TRDR',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B0078' : {'ecocyc-rxns': {"""ACETOLACTSYN-RXN""": """2 pyruvate = 2-acetolactate + CO2""","""ACETOOHBUTSYN-RXN""": """pyruvate + 2-oxobutanoate = 2-aceto-2-hydroxy-butyrate + CO2""",},'ucsd-rxns' : ['ACLS','ACHBS',], 'protein-comments' : ["""(IlvH is the regulatory (small) subunit of acetolactate synthase III; it confers sensitivity to inhibition by valine and is
required for full catalytic activity of acetolactate synthase III holoenzyme |CITS: [8756689]|.
The crystal structure of IlvH has been determined at 1.75 Å resolution. It forms a dimer with two ferredoxin
domains in each monomer. The valine binding sites can be tentatively assigned to the interface between the two
N-terminal domains |CITS: [16458324]|.)""","""(Acetohydroxy acid synthase III (AHAS III) is one of two functional isozymes catalyzing the decarboxylation of
pyruvate and transfer of the resulting acetaldehyde group to either pyruvate or α-ketobutyrate, producing
α-acetolactate for the valine pathway and α-aceto-α-hydroxybutyrate for the isoleucine pathway.
This is the first common step in the biosynthesis of the branched-chain amino acids isoleucine, leucine, and valine.
A third isozyme, AHAS II, is not functional in E. coli K-12 due to the presence of a frame shift mutation in the
gene encoding the large subunit, ilvG. |CITS: [colisalII]|
In the presence of both pyruvate and α-ketobutyrate, AHAS III produces approximately 40-fold more
acetohydroxybutyrate than acetolactate, while AHAS I shows no product preference |CITS: [3301814][2675968]|.
The differential regulation of enzymatic activity and
expression of the isozymes has direct physiological consequences and has been under intense study. The end
products of the branched-chain amino acid biosynthesis pathways all inhibit AHAS III activity, although inhibition by
valine is most significant |CITS: [2675968]|. Both AHAS I and III are inhibited by valine |CITS: [Defelice78]|. Activity
of AHAS III is only partially inhibited by leucine, while AHAS I activity can be almost completely inhibited
|CITS: [6351926]|.)""",]},
'B3575' : {'ecocyc-rxns': {"""RXN0-703""": """2,3-diketo-L-gulonate + NADH -> 3-keto-L-gulonate + NAD+""",},'ucsd-rxns' : ['DOGULNR',], 'protein-comments' : ["""(The yiaK gene encodes a 2,3-diketo-L-gulonate reductase |CITS: [11741871], [14718529]|. The enzyme is homodimeric |CITS: [14718529]|.
A YiaK crystal structure is presented at 2.0 A resolution |CITS: [14718529]|, and a structure with NAD and tartrate is presented at 2.2 A resolution |CITS: [14718529]|. The His44 residue is predicted to be catalytic |CITS: [14718529]|. YiaK shows an atypical interaction with the NAD |CITS: [14718529]|.
A mutation causing consitutive yiaKLMNOPQRS operon expression results in
induction of L-lyxose metabolic capability |CITS: [9525947]|.
Regulation has been described |CITS: [9525947], [10913096]|.
)""","""NIL""",]},
'B3236' : {'ecocyc-rxns': {"""MALATE-DEH-RXN""": """malate + NAD+ = oxaloacetate + NADH""",},'ucsd-rxns' : ['MDH',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B2027' : {'ecocyc-rxns': {},'ucsd-rxns' : ['O16AP1pp','O16AP2pp','O16AP3pp',], 'protein-comments' : ["""(In E. coli strains O8 and O9, the orthologous Wzz protein was shown to control the length of the O-antigen
component of lipopolysaccharide |CITS: [8606163][9383197]|. Regulation of O-antigen chain length is required
for virulence of Salmonella typhimurium |CITS: [12603743]|. E. coli K12 does not produce O-antigen.
WzzB appears to be present as a dimer in the membrane |CITS: [16079137]|.
rol: "regulator of O length" |CITS: [1715860]|
cld: "chain length determinant" |CITS: [7682279]|)""",]},
'B2026' : {'ecocyc-rxns': {"""HISTCYCLOHYD-RXN""": """phosphoribosyl-AMP + H2O -> phosphoribosylformiminoAICAR-phosphate""","""HISTPRATPHYD-RXN""": """phosphoribosyl-ATP + H2O -> phosphoribosyl-AMP + diphosphate""",},'ucsd-rxns' : ['PRATPP','PRAMPC',], 'protein-comments' : ["""(This is a bifunctional enzyme: the carboxyl terminal domain
carries out EC 3.6.1.31(phosphoribosyl-ATP pyrophosphatase), the N-terminal
domain carries out EC 3.5.4.19(phosphoribosyl-AMP cyclohydrolase).
The protein posseses two independent domains, one proximal for hisI
activity (EC 3.5.4.19, third step) and one distal for hisE activity (EC
3.6.1.31, second step). |CITS:86310273| The hisIE gene undergoes intragenic
complementation.)""",]},
'B2025' : {'ecocyc-rxns': {"""GLUTAMIDOTRANS-RXN""": """phosphoribulosylformimino-AICAR-P + L-glutamine -> D-erythro-imidazole-glycerol-phosphate + AICAR + L-glutamate""",},'ucsd-rxns' : ['IG3PS',], 'protein-comments' : ["""(The hisF protein alone can catalyze a multistep, ammonia-dependent reaction converting PRFAR to
AICAR and IGP. These activities include an ammonia-dependent carbon-nitrogen
ligase, a carbon-nitrogen lyase and a carbon-nitrogen cycloligase. However,
when complexed in a 1:1 dimer with the hisH protein, the holoenzyme IGP synthase
is formed. IGP synthase catalyzes the conversion of PRFAR to AICAR and IGP in
the presence of glutamine as the nitrogen donor without the release of any free
metabolic intermediate. Glutamine is the preferred donor for IGP biosynthesis.
|CITS: [93264432] [97005596]|)""","""(Imidazole glycerol phosphate synthase is a dimer made up of
one chain each of the polypeptides of the hisH and hisF genes. A
complex reaction is catalyzed involving an enzyme-bound intermediate.
The holoenzyme uses glutamine as a donor of a nitrogen atom for the
imidazole ring, retains the intermediate bound to the enzyme,cyclizes
to form the imidazole ring and releases the products IGP and
AICAR.(IGP of the histidine pathway is imidazole glycerol phosphate,
whereas in the tryptophan pathway IGP means indoleglycerol phosphate.)
|CITS: [93264432]|)""",]},
'B2024' : {'ecocyc-rxns': {"""PRIBFAICARPISOM-RXN""": """phosphoribosylformiminoAICAR-phosphate -> phosphoribulosylformimino-AICAR-P""",},'ucsd-rxns' : ['PRMICI',], 'protein-comments' : ["""NIL""",]},
'B2023' : {'ecocyc-rxns': {"""GLUTAMIDOTRANS-RXN""": """phosphoribulosylformimino-AICAR-P + L-glutamine -> D-erythro-imidazole-glycerol-phosphate + AICAR + L-glutamate""",},'ucsd-rxns' : ['IG3PS',], 'protein-comments' : ["""(The product of the hisH subunit has no detectable catalytic activity alone.
However, when combined with the hisF subunit in a stable 1:1 dimeric complex
the two proteins constitute the IGP synthase holoenzyme. The synthase reaction
is carried out in the presence of glutamine as the nitrogen donor. Any
intermediates of the reaction remain enzyme bound. |CITS: [97005596]
[93264432]|)""","""(Imidazole glycerol phosphate synthase is a dimer made up of
one chain each of the polypeptides of the hisH and hisF genes. A
complex reaction is catalyzed involving an enzyme-bound intermediate.
The holoenzyme uses glutamine as a donor of a nitrogen atom for the
imidazole ring, retains the intermediate bound to the enzyme,cyclizes
to form the imidazole ring and releases the products IGP and
AICAR.(IGP of the histidine pathway is imidazole glycerol phosphate,
whereas in the tryptophan pathway IGP means indoleglycerol phosphate.)
|CITS: [93264432]|)""",]},
'B2022' : {'ecocyc-rxns': {"""IMIDPHOSDEHYD-RXN""": """D-erythro-imidazole-glycerol-phosphate -> imidazole acetol-phosphate + H2O""","""HISTIDPHOS-RXN""": """L-histidinol-phosphate + H2O -> histidinol + phosphate""",},'ucsd-rxns' : ['HISTP','IGPDH',], 'protein-comments' : ["""NIL""","""(The hisB gene encodes a bifunctional enzyme that catalyzes the seventh and ninth steps of histidine
biosynthesis, encompassing two enzyme activities: histidinol-P phosphatase and
imidazoleglycerol-phosphate dehydratase. In view of the strong tendency of the enzyme to aggregate, the most
likely configuration of the catalytically active form is that of a dimer, similar to other
bifunctional enzymes |CITS:[86174354]|.
The hisB gene is characterized by four complementation
groups, Ba, Bb, Bc, and Bd, each of which is distributed throughout the gene |CITS:[73160452]|.
While only the dehydratase activity is lost when mutations occur in the Ba, Bb, or
Bd complementation groups, both enzyme activities are lost if mutations
occur in the Bc complementation group |CITS: [86174354]|.
A model for the evolution of the bifunctional hisB gene has been proposed |CITS: [15042344]|.)""",]},
'B2788' : {'ecocyc-rxns': {},'ucsd-rxns' : ['GLCRD',], 'protein-comments' : ["""(No information about this protein was found by a literature search conducted on January 9, 2006.)""",]},
'B2789' : {'ecocyc-rxns': {},'ucsd-rxns' : ['GALCTt2rpp','GLCRt2rpp','GLYCAt2rpp',], 'protein-comments' : ["""(The YgcZ protein may function as a glucarate transporter. The
ygcZ gene is encoded in a probable operon with genes
encoding two subunits of a putative glucarate dehydratase. YgcZ
is a member of the major facilitator superfamily (MFS) of
transporters |CITS: [98190790]| and shares a high level of sequence
similarity with probable glucarate transporters from various
organisms. YgcZ probably functions as a glucarate/proton transporter.)""",]},
'B1677' : {'ecocyc-rxns': {},'ucsd-rxns' : ['ALPATG160pp','ALPATE160pp',], 'protein-comments' : ["""(Lpp, the major lipoprotein, is one of the most abundant proteins in Escherichia coli |CITS:[4610570]| and is
necessary for the stabilization and integrity of the bacterial cell envelope |CITS:[11790745]|. The three-dimensional crystal structure of Lpp has been determined to 1.9 A resolution |CITS:[10843861]|. Cells lacking Lpp or with mutations affecting the attachment of Lpp to the murein (peptidoglycan) layer exhibit outer membrane blebs, are hypersensitive to toxic compounds, and release periplasmic proteins to the extracellular medium |CITS:[105245]|. Lpp exists in two forms, a free form and a covalently linked bound form attached to the peptidoglycan. Both forms are localized to the outer membrane |CITS:[4245367]|, |CITS:[4565677]|. Lpp is expressed as a prolipoprotein, having 20 amino acid residues extending from the amino terminus |CITS:[322142]| During translocation across the cytoplasmic membrane, the prolipoprotein undergoes modifications of the amino terminus cysteine residue followed by cleavage of the signal peptide extension |CITS:[8051048]|. The mature lipoprotein is then translocated to the outer membrane where it is covalently bound to the peptidoglycan layer |CITS:[6369111]|, |CITS:[6363408]|. Globomycin was found to inhibit the cleavage by signal peptidase II through noncompetitive binding to the enzyme |CITS:[3888977]|. Studies using inhibitors of the proton motive force (pmf) and ATP-depleted cells indicated that both the pmf and ATP are required for translocation of an OmpF-Lpp chimeric protein |CITS:[3029075]|. Translocation across the inner membrane was found to involve the Sec export apparatus |CITS:[2842297]|. Immunoelectron microscopy revealed that free lipoprotein is inserted equally over the entire cell wall, that lipoprotein synthesis increases with cell length, and that cell shape depends on total lipoprotein content of the cell in that low total lipoprotein corresponds to a spherical shape and a higher lipoprotein content corresponds with a rod shape |CITS:[3316185]|. Pulse-chase labeling followed by cell fractionation found that Lpp utilizes the LolA-LolB system to facilitate its release from the inner membrane and localization to the outer membrane |CITS:[10521496]|. Chemical cross-linking has revealed that Lpp organizes into trimers and interacts with OmpA, a major outer membrane lipoprotein |CITS:[3013869]|.)""",]},
'B2787' : {'ecocyc-rxns': {"""GLUCARDEHYDRA-RXN""": """D-glucarate -> 5-keto-4-deoxy-D-glucarate + H2O""",},'ucsd-rxns' : ['GLCRD',], 'protein-comments' : ["""(The subunit structure is unknown.)""",]},
'B2784' : {'ecocyc-rxns': {"""GDPPYPHOSKIN-RXN""": """ATP + GDP = AMP + guanosine 5'-diphosphate,3'-diphosphate""","""GTPPYPHOSKIN-RXN""": """GTP + ATP = guanosine 3'-diphosphate 5'-triphosphate + AMP""",},'ucsd-rxns' : ['GDPDPK','GTPDPK',], 'protein-comments' : ["""NIL""",]},
'B4478' : {'ecocyc-rxns': {"""GALACTONDEHYDRAT-RXN""": """D-galactonate = H2O + 2-dehydro-3-deoxy-D-galactonate""",},'ucsd-rxns' : ['GALCTND',], 'protein-comments' : ["""(The subunit structure is unknown.)""",]},
'B2780' : {'ecocyc-rxns': {"""CTPSYN-RXN""": """ATP + UTP + ammonia -> ADP + phosphate + CTP""",},'ucsd-rxns' : ['CTPS2',], 'protein-comments' : ["""(CTP synthetase exists as a dimer, but undergoes aggregation
to form a tetramer. ATP or UTP alone can induce conformational
changes and tetrameric formation, however, the combination of both
substrates is even more effective. |CITS: [Koshland&LevitzkiEnzymes10,539,1974]|
Site-directed mutagenesis and limited proteolysis of CTP synthetase have allowed identification of residues critical
for enzymatic activity and activation |CITS: [12383057][12752439]|.
A crystal structure has been solved at 2.3 A resolution. The structure suggests that the active form of the enzyme
is a tetramer, and that the dimer-tetramer equilibrium contributes to positive cooperativity |CITS: [15157079]|.)""","""NIL""",]},
'B2781' : {'ecocyc-rxns': {"""RXN0-1041""": """a nucleoside triphosphate + H2O -> a nucleoside monophosphate + diphosphate""",},'ucsd-rxns' : ['NTPP8','NTPP7','NTPP6','NTPP5','NTPP4','NTPP3','NTPP2','NTPP1',], 'protein-comments' : ["""(MazG limits the deleterious effect of the MazF toxin under nutritional stress conditions |CITS: [16390452]|.
MazG exhibits pyrophosphohydrolase activity toward all four dNTPs and also exhibits (somewhat less) activity toward
all four rNTPs |CITS: [12218018]|. Hydrolysis of GTP is more efficient that hydrolysis of ATP |CITS: [16390452]|.
Addition of purified MazEF proteins causes inhibition of MazG enzymatic activity |CITS: [16390452]|.
Overexpression of mazG inhibits cell growth and negatively affects accumulation of (p)ppGpp, while
overexpression of the entire mazEFG operon has no effect on cell growth or (p)ppGpp accumulation. A
mazG deletion mutant is less able to survive under nutritional stress conditions |CITS: [16390452]|.
MazG and Era associate in vitro and by yeast two-hybrid test. Nucleotide influences the association; binding
is weaker with GTPγS than with GDP added |CITS: [12218018]|.
)""",]},
'B3415' : {'ecocyc-rxns': {"""TRANS-RXN-81""": """H+[periplasmic space] + fructuronate[periplasmic space] =H+[cytosol] + fructuronate[cytosol] """,},'ucsd-rxns' : ['GLCNt2rpp',], 'protein-comments' : ["""(GntT is one of four known transporters for gluconate in E. coli, the others
being the homologous GntU, GntP and IdnT transporters. Whole cell experiments have
shown that the cloned gntT gene was able to complement a gluconate transport
negative mutant and confers high affinity gluconate transport with a Km of approx
6 μM |CITS: [97197521]|. Transcriptional analysis has shown that gntT
constitutes a monocistronic operon. Analysis of gntT-lacZ fusions
has indicated that gntT expression is induced at low levels of gluconate,
partially repressed by glucose, and increased in early logarithmic phase
|CITS: [97197521]|. Expression of both gntT and gntU is controlled
by the GntR repressor and by cyclic AMP-CRP |CITS: [98196721]|.
GntT is a member of the Gnt family of gluconate transporters |CITS: [97212001]|.
Gluconate uptake has been reported to occur via a proton-symport mechanism in
E. coli |CITS: [74033664]|. It seems likely that GntT is a high affinity
gluconate uptake system that functions via D-gluconate/proton symport.
Imported gluconate is metabolised primarily via the Entner-Douderoff pathway and
secondarily via the pentose phosphate pathway.)""",]},
'B4094' : {'ecocyc-rxns': {"""RXN0-1401""": """ribose-1,5-bisphosphate + ATP = 5-phosphoribosyl 1-pyrophosphate + ADP""",},'ucsd-rxns' : ['R15BPK',], 'protein-comments' : ["""(The phnN gene encodes ribose 1,5-bisphosphokinase, which catalyzes the final step in a pathway of 5-phospho-D-ribosyl alpha-1-diphosphate (PRPP) biosynthesis |CITS: [12700258]|.
The phnN gene is part of an operon involved in utilization of alkylphosphonates as a source of phosphorus |CITS: [2155230]|. PhnN has been suggested to be a subunit of a C-P lyase |CITS: [1368181]|, possibly some accessory factor, as C-P lyase activity does not exhibit a strict requirement for the PhnN protein |CITS: [8388873]|.
The substrate specificity of ribose 1,5-bisphosphokinase has been characterized |CITS: [12700258]|. GTP does not substitute for ATP in the reaction, and the enzyme does not exhibit activity toward ribose, ribose 1-phosphate, or ribose 5-phosphate |CITS: [12700258]|.
Purification of 6-His tagged PhnN is described |CITS: [12700258]|.
Regulation has been described |CITS: [2155230], [1335942]|.)""",]},
'B3417' : {'ecocyc-rxns': {"""MALDEXPHOSPHORYL-RXN""": """maltodextrin + phosphate = maltotetraose + α-D-glucose 1-phosphate""",},'ucsd-rxns' : ['MLTP1','MLTP2','MLTP3','GLCP2','GLCP',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B4071' : {'ecocyc-rxns': {"""1.7.7.2-RXN""": """ammonia + 6 oxidized cytochrome c552 + 2 H2O -> nitrite + 6 reduced cytochrome c552 + 7 H+""",},'ucsd-rxns' : ['NTRIR3pp','NTRIR4pp',], 'protein-comments' : ["""(The nrfB gene encodes a cytochrome C that is believed to be the direct electron
donor for cytochrome C552 in the formate-dependent reduction of nitrite to
ammonia. |CITS: [94335626]|
There are five heme-c groups per monomer.)""","""(E. coli has two distinct nitrite reductases--NrfA and NirB. Expresssion is complementary: with low nitrate in the
environment NrfA is made; with high nitrate NirB is made almost exclusively. At intermediate concentration of nitrate,
both are made. This regulation acts through the Nar regulatory circuit. Nitrite also induces the formation of both
enzymes but it is a less effective inducer than nitrate by at least two orders of magnitude. Both enzymes reduce nitrite
to ammonia. The two nitrate reductases have different cellular locations locations and metabolic roles. NrfA is associated
with the cytoplasmic membrane with its cytochrome components facing or free in the periplasm; actiing as a terminal
electron acceptor of an electron transport chain beginning with membrane-associated formate-oxidizing enzymes it
generates a proton gradient. NirB, which is located in the cytoplasm, does not generate a proton gradient. Its probable metabolic
role is to detoxify nitrite. However when cells are growing on high concentrations of nitrate (and NirB is active) nitrite,
nevertheless is excreted into the environment |CITS: [11004182]|.
The structure and spectroscopic properties of this penta-heme periplasmic cytochrome c nitrite
reductase has been determined |CITS: [11863430]|. NrfA can also reduce and thereby detoxify nitric
oxide (NO); mutant strains lacking NrfA activity have increased sensitivity to NO.
)""",]},
'B2148' : {'ecocyc-rxns': {"""ABC-18-RXN""": """ATP + β-D-galactose[periplasmic space] + H2O =ADP + phosphate + β-D-galactose[cytosol] """,},'ucsd-rxns' : ['GALabcpp','GLCabcpp',], 'protein-comments' : ["""NIL""","""(MglABC is a beta-methylgalactoside transport system that is a member of the ATP-Binding Cassette (ABC) Superfamily
of transporters |CITS: [96381453]|. Based on sequence similarity, mglB encodes the galactose-binding component,
mglC encodes the integral membrane component, and mglA encodes the ATP-binding component of the ABC
transporter. Insertional mutations in each gene indicate that all three components are necessary for beta-methylgalactoside
transport function |CITS: [83082637]|. Complementation experiments show that mlg genes cloned into a plasmid
vector are able to complement the transport functions of the mglA, mglB, and mglC mutants
|CITS: [82239395]|. MglB, but not MglA or MglC, was found to also serve as the galactose chemoreceptor in E. coli
|CITS: [83082637]|. mglB mutants eliminate the chemotactic function in E. coli; however, mglA and
MglC mutants exhibit normal galactose taxis but defective galactoside uptake activities |CITS: [87286407] [83082637]|.)""",]},
'B2149' : {'ecocyc-rxns': {"""ABC-18-RXN""": """ATP + β-D-galactose[periplasmic space] + H2O =ADP + phosphate + β-D-galactose[cytosol] """,},'ucsd-rxns' : ['GALabcpp','GLCabcpp',], 'protein-comments' : ["""NIL""","""(MglABC is a beta-methylgalactoside transport system that is a member of the ATP-Binding Cassette (ABC) Superfamily
of transporters |CITS: [96381453]|. Based on sequence similarity, mglB encodes the galactose-binding component,
mglC encodes the integral membrane component, and mglA encodes the ATP-binding component of the ABC
transporter. Insertional mutations in each gene indicate that all three components are necessary for beta-methylgalactoside
transport function |CITS: [83082637]|. Complementation experiments show that mlg genes cloned into a plasmid
vector are able to complement the transport functions of the mglA, mglB, and mglC mutants
|CITS: [82239395]|. MglB, but not MglA or MglC, was found to also serve as the galactose chemoreceptor in E. coli
|CITS: [83082637]|. mglB mutants eliminate the chemotactic function in E. coli; however, mglA and
MglC mutants exhibit normal galactose taxis but defective galactoside uptake activities |CITS: [87286407] [83082637]|.)""",]},
'B0430' : {'ecocyc-rxns': {"""CYT-UBIQUINOL-OXID-RXN""": """ubiquinol-8 + O2 = ubiquinone-8 + 2 H2O""",},'ucsd-rxns' : ['CYTBO3_4pp',], 'protein-comments' : ["""(CyoC is subunit III of the cytochrome bo terminal oxidase complex encoded by cyoABCDE.
The CyoC polypeptide contains five transmembrane helices |CITS: [2165491]|.
A crystal structure of the entire cytochrome bo terminal oxidase complex
containing CyoC has been determined at 3.5 A resolution |CITS: [11017202]|.)""","""NIL""",]},
'B0431' : {'ecocyc-rxns': {"""CYT-UBIQUINOL-OXID-RXN""": """ubiquinol-8 + O2 = ubiquinone-8 + 2 H2O""",},'ucsd-rxns' : ['CYTBO3_4pp',], 'protein-comments' : ["""(CyoB is subunit I of the cytochrome bo terminal oxidase complex encoded by cyoABCDE.
CyoB contains the binding sites for the cytochrome b562 and b555 prosthetic groups and the Cu cofactor
|CITS: [92112945]|. The CyoB polypeptide contains 15 transmembrane helices |CITS: [2165491]|.
The crystal structure of the entire cytochrome bo terminal oxidase complex suggests that a potential
ubiquinone binding site is located in the membrane domain of subunit I |CITS: [11017202]|.
)""","""NIL""",]},
'B1245' : {'ecocyc-rxns': {"""ABC-22-RXN""": """ATP + a peptide[periplasmic space] + H2O =ADP + phosphate + a peptide[cytosol] """,},'ucsd-rxns' : ['4PEPTabcpp','3PEPTabcpp',], 'protein-comments' : ["""(membrane component of ABC transporter)""","""(OppABCDF is an ATP-dependent oligopeptide transporter that is a
member of the ATP-Binding Cassette (ABC) Superfamily of transporters |CITS:[1738314]|.
OppABCDF has not been investigated in detail in E. coli,
but the orthologous system in Salmonella typhimurium has been
extensively characterized. Binding affinity and competition assays have
shown that OppABCDF will transport oligopeptides up to five amino acids
in length, but has no affinity for free amino acids |CITS:[3536860],[8801122]|.
The system has been observed to function in oligopeptide uptake, as
well as recycling of cell wall peptides |CITS:[2821267]|. Based on
sequence similarity, OppB and OppC are the membrane components
of the ABC transporter, and OppD and OppF are the ATP-binding
components of the ABC transporter |CITS:[8801122],[1738314]|.
OppA is the periplasmic substrate-binding component, however MppA
can replace OppA as a periplasmic-binding component of the transporter
when it binds murein tripeptides |CITS:[9495761]|. MppA was shown to be
required for murein tripeptide transport in a diaminoimelic acid-requiring
strain |CITS:[9495761]|. Insertion mutation of the oppF gene has
shown that OppF is required for Opp transporter function |CITS:[2821267]|.
In addition, Insertional mutants of each of the opp genes were
constructed, and the opp-minus strains were unable to utilize the
peptide Pro-Gly-Gly, normally transported by the wild-type transporter |CITS:[2821267]|.
Expression of oppABCD increased after long-term adaptation
to growth in complex medium with acetate or propionate |CITS:[12620868]|.
Expression of mppA decreased after long-term adaptation to growth
in complex medium with acetate or propionate |CITS:[12620868]|.
Expression of mppA was shown to be activated by cyclic AMP
receptor protein |CITS:[15520470]|.
)""","""(OppABCDF is an ATP-dependent oligopeptide transporter that is a member of the ATP-Binding Cassette
(ABC) Superfamily of transporters |CITS: [92149312]|. OppABCDF has not been investigated in detail in
E. coli, but the orthologous system in Salmonella typhimurium has been extensively
characterized. Binding affinity and competition assays have shown that OppABCDF will transport
oligopeptides up to five amino acids in length, but has no affinity for free amino acids |CITS: [87056967]
[8801122]|. The system has been observed to function in oligopeptide uptake, as well as recycling of cell
wall peptides |CITS: [88011222]|. Based on sequence similarity, OppB and OppC are the membrane
components of the ABC transporter, and OppD and OppF are the ATP-binding components of the ABC
transporter |CITS: [8801122][92149312]|. OppA is the periplasmic substrate-binding component that binds
oligopeptides with a Kd of approximately 1E-6 |CITS: [94261830]|. Insertion mutant of the
oppF gene has shown that OppF is required for Opp transporter function |CITS: [88011222]|. In
addition, Insertional mutants of each of the opp genes were constructed, and the opp-minus
strains were unable to utilize the peptide Pro-Gly-Gly, normally transported by the wild-type transporter
|CITS: [88011222]|.
OppA has been crystallized and its structure resolved to 2.3 A resolution showing OppA to be a bilobal,
principally beta-stranded, three-domain protein |CITS:[15299334]|.
Targeting of OppA to the Sec-translocase for transport across the inner membrane
is SecB-dependent |CITS:[16352602]|.)""",]},
'B0207' : {'ecocyc-rxns': {"""RXN0-4281""": """methylglyoxal + NADPH -> acetol + NADP+""","""1.1.1.274-RXN""": """NADPH + 2,5-didehydro-D-gluconate = 2-dehydro-D-gluconate + NADP+""",},'ucsd-rxns' : ['ALR2','DKGLCNR1',], 'protein-comments' : ["""(DkgB was shown to have methylglyoxal reductase activity. Growth of a dkgB gloA double mutant is inhibited by
0.3 mM methylglyoxal |CITS: [16077126]|.
The dkgB gene was reported to encode 2,5-diketo-D-gluconate reductase (25DKGR) B, one of two 25DKG
reductases in E. coli. The enzyme uses NADPH as the preferred electron donor. It is thought to be involved in
ketogluconate metabolism |CITS: [99357626]|. The specific activity of the enzyme towards 2,5-diketo-D-gluconate
was reported to be almost 1000-fold lower than its activity towards methylglyoxal |CITS: [16077126]|.
Expression of dkgB is not increased in response to methylglyoxal |CITS: [16077126]|.)""",]},
'B2103' : {'ecocyc-rxns': {"""OHMETPYRKIN-RXN""": """ATP + hydroxymethylpyrimidine = ADP + hydroxymethylpyrimidine phosphate""","""PYRIMSYN3-RXN""": """hydroxymethylpyrimidine phosphate + ATP = 4-amino-5-hydroxymethyl-2-methylpyrimidine-pyrophosphate + ADP""",},'ucsd-rxns' : ['HMPK1','PMPK',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B0200' : {'ecocyc-rxns': {"""RXN0-4361""": """D-β-D-heptose-1,7-bisphosphate = D-β-D-heptose-1-phosphate + phosphate""",},'ucsd-rxns' : ['GMHEPPA',], 'protein-comments' : ["""(gmhB encodes the D,D-heptose 1.7-bisphosphate phosphatase of the ADP-heptose biosynthesis pathway.
A gmhB deletion strain has a partial defect in LPS core synthesis, but is not completely heptoseless
|CITS: [11751812]|.
It has been proposed that the gmhB gene and the HOL-P phosphatase moiety of hisB evolved via a
paralogous duplication event of an ancestral DDDD phosphatase-encoding gene |CITS: [15042344]|.)""",]},
'B1584' : {'ecocyc-rxns': {"""DIAMACTRANS-RXN""": """an aliphatic α,ω-diamine + acetyl-CoA = an aliphatic N-acetyl-diamine + coenzyme A""","""SPERMACTRAN-RXN""": """acetyl-CoA + spermidine = coenzyme A + an N-acetylspermidine""",},'ucsd-rxns' : ['SPMDAT1','SPMDAT2',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B2104' : {'ecocyc-rxns': {"""THIAZOLSYN3-RXN""": """ATP + 4-methyl-5-(β-hydroxyethyl)thiazole = ADP + 4-methyl-5-(β-hydroxyethyl)thiazole phosphate""",},'ucsd-rxns' : ['HETZK',], 'protein-comments' : ["""(The subunit structure is unknown.)""",]},
'B1064' : {'ecocyc-rxns': {},'ucsd-rxns' : ['RNDR2b','RNDR3b','RNDR1b','GRXR','PAPSR2','RNDR4b','ASR',], 'protein-comments' : ["""(Glutaredoxins are ubiquitous proteins that catalyze the reduction of disulfides via reduced glutathione (GSH).
Escherichia coli has three glutaredoxins (Grx1, Grx2, and Grx3) containing the classic dithiol active site
CPYC, and a fourth one which contains a monothiol (CGFS) potential active site |CITS: [15833738]|.
The glutaredoxins do not act as enzymes, but rather as a cofactor, enabling intracellular redox reactions through
a disulfide/dithiol enzymatic mechanism involving the active site cysteines.
There is almost no similarity between the amino acid sequence of Grx2 (an approximately 27 kDa protein) and Grx1
or Grx3 (both 9-kDa proteins), with the exception of the active site which is identical in all three glutaredoxins.
In contrast to glutaredoxin 1 and 3, Grx 2 is not a hydrogen donor for ribonucleotide reductase.
On the other hand, Grx2 is the primary hydrogen donor to ArsC-catalyzed arsenate reduction (|FRAME: RXN-982|)
|CITS: [10593884]|. It is also the most abundant glutaredoxin in the cell, with an intracellular concentration
of 5 µM, compared with 0.2 µM and 2.4 µM for Grx1 and 3, respectively |CITS: [10593884]|.)""","""(Glutaredoxins are ubiquitous proteins that catalyze the reduction of disulfides via reduced glutathione (GSH).
Escherichia coli has three glutaredoxins (Grx1, Grx2, and Grx3) containing the classic dithiol active site
CPYC, and a fourth one which contains a monothiol (CGFS) potential active site |CITS: [15833738]|.
The glutaredoxins do not act as enzymes, but rather as a cofactor, enabling intracellular redox reactions through
a disulfide/dithiol enzymatic mechanism involving the active site cysteines.
There is almost no similarity between the amino acid sequence of Grx2 (an approximately 27 kDa protein) and Grx1
or Grx3 (both 9-kDa proteins), with the exception of the active site which is identical in all three glutaredoxins.
In contrast to glutaredoxin 1 and 3, Grx 2 is not a hydrogen donor for ribonucleotide reductase.
On the other hand, Grx2 is the primary hydrogen donor to ArsC-catalyzed arsenate reduction (|FRAME: RXN-982|)
|CITS: [10593884]|. It is also the most abundant glutaredoxin in the cell, with an intracellular concentration
of 5 µM, compared with 0.2 µM and 2.4 µM for Grx1 and 3, respectively |CITS: [10593884]|.)""",]},
'B0121' : {'ecocyc-rxns': {"""SPERMIDINESYN-RXN""": """putrescine + S-adenosyl-L-methioninamine = spermidine + 5'-methylthioadenosine""",},'ucsd-rxns' : ['SPMS',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B4289' : {'ecocyc-rxns': {"""RXN0-2261""": """ferric dicitrate[extracellular space] =ferric dicitrate[cytosol] ""","""ABC-9-RXN""": """ATP + ferric dicitrate[periplasmic space] + H2O =ADP + phosphate + ferric dicitrate[cytosol] """,},'ucsd-rxns' : ['FE3DCITabcpp',], 'protein-comments' : ["""(FecC is one of two (along with FecD) integral membrane protein components of the iron dicitrate ABC transporter.)""","""(FecBCDE is an ATP Binding Cassette (ABC) citrate-dependent iron (III) transport system. Sequence
homology and hydropathy analyses indicate that FecB is the periplasmic binding protein, FecC and FecD
are integral membrane proteins and FecE is the ATP-binding protein |CITS: [88227855]|. Mutation and
induction studies indicate that exogenous ferric citrate induces the expression of fec transport genes
through a signaling mechanism which does not require ferric citrate to enter the cytoplasm |CITS: [82004187]|.
|CITS:[81116964]|, or to cross the outer membrane into the periplasmic space |CITS: [95246736]|. Rather,
induction of fec transport genes is a function of FecA-ferric citrate binding and is coupled through
the TonB, ExbB and ExbD proteins independent of their role in uptake |CITS:[95246736]|.)""","""NIL""",]},
'B3001' : {'ecocyc-rxns': {"""RXN0-4281""": """methylglyoxal + NADPH -> acetol + NADP+""",},'ucsd-rxns' : ['ALR2',], 'protein-comments' : ["""(YghZ is an aldo-keto reductase that detoxifies methylglyoxal |CITS: [12583903]|. YghZ defines the AKR14
(aldo-keto reductase 14) protein family |CITS: [12583903]|.
YghZ overproduction results in decreased sensitivity to methylglyoxal, compared to wild type |CITS: [12583903]|.
Growth of a yghZ gloA double mutant is inhibited by 0.3 mM methylglyoxal |CITS: [16077126]|.
YghZ has similarity to potassium channel beta-subunits and to aflatoxin dialdehyde reductases of the aldo-keto
reductase AKR6 and AKR7 families, respectively |CITS: [12583903]|.
Expression of yghZ is not increased in response to methylglyoxal |CITS: [16077126]|.)""",]},
'B3006' : {'ecocyc-rxns': {"""RXN0-2121""": """cob(I)alamin[extracellular space] =cob(I)alamin[cytosol] ""","""RXN0-1565""": """cob(I)alamin[extracellular space] =cob(I)alamin[periplasmic space] ""","""RXN0-2181""": """ferric enterobactin[extracellular space] =ferric enterobactin[cytosol] ""","""RXN0-1682""": """ferric enterobactin[extracellular space] =ferric enterobactin[periplasmic space] ""","""RXN0-2241""": """iron (III) hydroxamate complex[extracellular space] =iron (III) hydroxamate complex[cytosol] ""","""RXN0-1701""": """iron (III) hydroxamate complex[extracellular space] =iron (III) hydroxamate complex[periplasmic space] ""","""RXN0-2261""": """ferric dicitrate[extracellular space] =ferric dicitrate[cytosol] ""","""RXN0-1684""": """ferric dicitrate[extracellular space] =ferric dicitrate[periplasmic space] """,},'ucsd-rxns' : ['FEENTERtonex','CPGNtonex','CBItonex','FE3DHBZStonex','FE3DHBZStonex','FEOXAMtonex','CBL1tonex','FECRMtonex','FE3HOXtonex','ADOCBLtonex','FE3DCITtonex',], 'protein-comments' : ["""(ExbB and ExbD proteins function as part of the TonB-dependent energy transduction system
for the import of iron-siderophore complexes and vitamin B12 across the outer membrane.
ExbB and ExbD are encoded by the exb operon in Escherichia coli |CITS:[12193634]|.)""","""(TonB is a cytoplasmic membrane protein which transduces the proton motive force (pmf) of the cytoplasmic
membrane to the outer membrane active transporters thus providing the energy source required for the import
of iron-siderophore complexes and vitamin B12 across the outer membrane |CITS:[9159515]|.
The amino-terminal signal sequence of TonB is thought to span the cytoplasmic membrane, with the rest
of the protein residing within the periplasmic space |CITS:[8316087]|. TonB has been shown to come into
close contact with proteins located in both membranes |CITS:[8344918]|. Sucrose density gradient
centrifugation studies found that TonB is distributed approximately equally in the inner and outer
membrane fractions |CITS:[9159515]|. In conjunction with cytoplasmic membrane proteins ExbB
and ExbD, TonB forms an energy transduction complex which interacts with a variety of outer membrane
active transporter proteins |CITS:[11934617]|. When complexed with ExbB and ExbD, TonB is
thought to adopt an energized conformation which is subsequently released from the cytoplasmic
membrane to the outer membrane whereupon it interacts with an array of outer membrane
proteins |CITS:[11872715]|. TonB is then thought to respond to the conformational changes
induced in the active transport proteins upon substrate binding |CITS:[9353297]|, releasing its
stored energy to the active transporters and reassociating with ExbB and ExbD at the cytoplasmic
membrane to be re-energized |CITS:[12823822]|.)""","""(The Outer Membrane Ferric Citrate Transport System is responsible for the transport of ferric
citrate across the outer membrane by FecA energized by the TonB energy transducing system.)""","""NIL""","""NIL""","""NIL""","""NIL""","""(FepA is a 22-stranded membrane-spanning beta barrel protein in the outer membrane. FepA is a TonB dependent active transporter
that recognizes ferric enterobactin and translocates the molecule across the outer membrane into the periplasm. FepB is a
periplasmic binding protein that binds ferric enterobactin for transport across the inner membrane by the FepCDG ABC transporter.)""","""NIL""","""NIL""",]},
'B0809' : {'ecocyc-rxns': {"""ABC-12-RXN""": """ATP + L-glutamine[periplasmic space] + H2O =ADP + phosphate + L-glutamine[cytosol] """,},'ucsd-rxns' : ['GLNabcpp',], 'protein-comments' : ["""NIL""","""(The GlnHPQ high-affinity glutamine transport system is a member of the ATP-Binding Cassette (ABC)
Superfamily of transporters |CITS: [96381453]|. Based on sequence similarity, GlnH is the periplasmic
glutamine-binding protein, GlnQ is the ATP-binding component, and GlnP is the membrane component
of the ABC transporter. Mutation of glnP results in the impaired ability to transport glutamine as well
as the inability to utilized glutamine as a sole source of carbon |CITS: [82007680] [87115160]|. Expression
of the cloned glnHPQ genes on a plasmid vector restored the glnH, glnP, and
glnQ mutants' abilities to transport glutamine and utilize glutamine as a sole carbon source
|CITS: [87115160]|.)""",]},
'B3005' : {'ecocyc-rxns': {"""RXN0-2121""": """cob(I)alamin[extracellular space] =cob(I)alamin[cytosol] ""","""RXN0-1565""": """cob(I)alamin[extracellular space] =cob(I)alamin[periplasmic space] ""","""RXN0-2181""": """ferric enterobactin[extracellular space] =ferric enterobactin[cytosol] ""","""RXN0-1682""": """ferric enterobactin[extracellular space] =ferric enterobactin[periplasmic space] ""","""RXN0-2241""": """iron (III) hydroxamate complex[extracellular space] =iron (III) hydroxamate complex[cytosol] ""","""RXN0-1701""": """iron (III) hydroxamate complex[extracellular space] =iron (III) hydroxamate complex[periplasmic space] ""","""RXN0-2261""": """ferric dicitrate[extracellular space] =ferric dicitrate[cytosol] ""","""RXN0-1684""": """ferric dicitrate[extracellular space] =ferric dicitrate[periplasmic space] """,},'ucsd-rxns' : ['FEENTERtonex','CPGNtonex','CBItonex','FE3DHBZStonex','FE3DHBZStonex','FEOXAMtonex','CBL1tonex','FECRMtonex','FE3HOXtonex','ADOCBLtonex','FE3DCITtonex',], 'protein-comments' : ["""(ExbB and ExbD proteins function as part of the TonB-dependent energy transduction system for the import of iron-siderophore complexes
and vitamin B12 across the outer membrane. ExbB and ExbD are encoded by the exb operon in Escherichia coli |CITS:[12193634]|.)""","""(TonB is a cytoplasmic membrane protein which transduces the proton motive force (pmf) of the cytoplasmic
membrane to the outer membrane active transporters thus providing the energy source required for the import
of iron-siderophore complexes and vitamin B12 across the outer membrane |CITS:[9159515]|.
The amino-terminal signal sequence of TonB is thought to span the cytoplasmic membrane, with the rest
of the protein residing within the periplasmic space |CITS:[8316087]|. TonB has been shown to come into
close contact with proteins located in both membranes |CITS:[8344918]|. Sucrose density gradient
centrifugation studies found that TonB is distributed approximately equally in the inner and outer
membrane fractions |CITS:[9159515]|. In conjunction with cytoplasmic membrane proteins ExbB
and ExbD, TonB forms an energy transduction complex which interacts with a variety of outer membrane
active transporter proteins |CITS:[11934617]|. When complexed with ExbB and ExbD, TonB is
thought to adopt an energized conformation which is subsequently released from the cytoplasmic
membrane to the outer membrane whereupon it interacts with an array of outer membrane
proteins |CITS:[11872715]|. TonB is then thought to respond to the conformational changes
induced in the active transport proteins upon substrate binding |CITS:[9353297]|, releasing its
stored energy to the active transporters and reassociating with ExbB and ExbD at the cytoplasmic
membrane to be re-energized |CITS:[12823822]|.)""","""(The Outer Membrane Ferric Citrate Transport System is responsible for the transport of ferric
citrate across the outer membrane by FecA energized by the TonB energy transducing system.)""","""NIL""","""NIL""","""NIL""","""NIL""","""(FepA is a 22-stranded membrane-spanning beta barrel protein in the outer membrane. FepA is a TonB dependent active transporter
that recognizes ferric enterobactin and translocates the molecule across the outer membrane into the periplasm. FepB is a
periplasmic binding protein that binds ferric enterobactin for transport across the inner membrane by the FepCDG ABC transporter.)""","""NIL""","""NIL""",]},
'B4219' : {'ecocyc-rxns': {"""PROTEIN-METHIONINE-S-OXIDE-REDUCTASE-RXN""": """a protein-L-methionine + oxidized thioredoxin = a protein-L-methionine-S-oxide + reduced thioredoxin""","""METHIONINE-S-OXIDE-REDUCTASE-RXN""": """a thioredoxin disulfide + L-methionine + H2O = a reduced thioredoxin + L-methionine sulfoxide""",},'ucsd-rxns' : ['METSOXR1','METSOXR1',], 'protein-comments' : ["""(MsrA exhibits methionine sulfoxide reductase activity in vitro (Km of 120 micromolar) |CITS: [11677230]|. The reaction probably uses thioredoxin in vivo, as it does in vitro |CITS: [11604533]|. Cys51, Cys198, and Cys206 are involved in catalysis |CITS: [10964927]|. A detailed description of the reaction mechanism is presented |CITS: [10964927]|. Overproduced protein is soluble and exhibits peptide methionine sulfoxide reductase activity |CITS: [1386361]|. The N and C termini are not essential for reductase activity (with DTT), though the C terminus is required for thioredoxin-dependent reduction, and a mutant protein lacking both termini displays kinetic defects |CITS: [11604533]|.
MsrB exhibits 1000-fold lower catalytic efficiency than MsrA toward free methionine sulfoxide |CITS: [11677230]|. MsrA and MsrB exhibit similar activity (quantitatively) toward an oxidized peptide substrate, though they appear to exhibit some differences in specificity for substrate sites within the peptide |CITS: [11677230]|. The E. coli MsrA and MsrB polypeptides do not interact with each other in vitro or in a yeast two-hybrid test |CITS: [11677230]|.
An msrA mutant shows increased sensitivity to oxidative stress, compared to wild type |CITS: [7836279]|. An msrA mutant in E. coli MC1061 strain background exhibits increased sensitivity to nitrite and S-nitrosoglutathione, which are released by activated macrophages during infection, and the mutant also shows increased sensitivity to hydrogen peroxide, compared to wild type |CITS: [11481433]|. Streptococcus pneumoniae, Neisseria gonorrhoeae, and E. coli (strain MC1061) MsrA proteins are involved in host cell adhesion |CITS: [8755589]|. MsrA has 61% identity over a 199 residue region with bovine MsrA protein |CITS: [8700890]| and has 40% identity to Mycobacterium tuberculosis MsrA |CITS: [11481433]|. MsrA also has similarity to Neisseria gonorrhoeae PilB protein |CITS: [12096194]|, human CBS-1 protein |CITS: [10375640]|, and Saccharomyces cerevisiae MsrA protein |CITS: [9275166]|. The MsrA protein of the plant pathogen Erwinia chrysanthemi is involved in virulence |CITS: [9927663]|.
Some organisms produce a methionine sulfoxide reductase composed of two domains with similarity to MsrA and MsrB, respectively, whereas E. coli produces these two distinct polypeptides |CITS: [11677230]|.
Production of MsrA protein is regulated by growth phase |CITS: [7836279]|.
A crystal structure is presented at 1.9 angstrom resolution |CITS: [11080639]|. Crystallization is described |CITS: [10957644]|. His-tagged MsrA was overproduced and purified |CITS: [11677230]|.
Additional methionine sulfoxide reductase activities have been observed in a msrA msrB double mutant, including a soluble activity toward the met-R-(o) enantiomer of free (non-peptide) methionine sulfoxide (fRMsr activity) |CITS: [12504094]|, a soluble activity toward the met-S-(o) enantiomer of free (non-peptide) methionine sulfoxide (fSMsr activity) |CITS: [12504094]|, a soluble NADPH-dependent activity toward the met-S-(o) enantiomer of peptide-linked methionine sulfoxide (MsrA1 activity) |CITS: [12504094], [12604343]|, and a membrane-associated NADPH-dependent activity toward both met-S-(o) and met-R-(o) enantiomers of peptide-linked and free methionine sulfoxide |CITS: [12504094], [12604343]|.)""",]},
'B3008' : {'ecocyc-rxns': {"""LCYSDESULF-RXN""": """L-cysteine + H2O = pyruvate + ammonia + hydrogen sulfide""","""CYSTATHIONINE-BETA-LYASE-RXN""": """cystathionine + H2O = pyruvate + ammonia + L-homocysteine""",},'ucsd-rxns' : ['CYSDS','CYSTL',], 'protein-comments' : ["""(Several distinct proteins exhibit cysteine desulfhydrase activity, which is involved in cysteine degradation |CITS: [12883870]|. The tnaA and metC genes each encode a cysteine desulfhydrase, as does an additional, as-yet unidentified gene |CITS: [12883870]|.
)""","""NIL""",]},
'B0123' : {'ecocyc-rxns': {"""RXN0-2945""": """4 Cu+ + 4 H+ + O2 -> 4 Cu2+ + 2 H2O""","""RXN0-2943""": """2,3-dihydroxybenzoate + O2 -> 2-carboxymuconate""","""RXN0-1483""": """4 Fe2+ + 4 H+ + O2 -> 4 Fe3+ + 2 H2O""",},'ucsd-rxns' : ['FEROpp','CU1Opp',], 'protein-comments' : ["""(CueO multicopper oxidase is a copper-stimulated phenoloxidase and ferroxidase |CITS: [11466290]| that plays a role
in copper homeostasis |CITS: [11222619]| during aerobiosis |CITS: [11399769]|. CueO has been observed to offer
protective effects from copper-mediated damage |CITS: [11527384]|. In the presence of copper, CueO can oxidize
and thus inactivate the iron siderophores 2,3-dihydroxybenzoate and enterobactin in vitro |CITS: [11466290]
[15317788]|. A mixture of enterobactin and copper is toxic, and ferric enterobactin may be the natural substrate of
CueO in vivo; thus, CueO may play a central role as an interface between copper detoxification and iron
homeostasis |CITS: [15317788]|. The purified protein was also shown to have cuprous oxidase activity in vitro
|CITS: [15516598]|.
CueO is translocated to the periplasm via the Tat pathway |CITS: [11527384][14702305]|. Published reports disagree
as to whether CueO exhibits four |CITS: [11527384]| or six |CITS: [11466290]| atoms of copper per monomer. The
enzyme exhibits characteristics of blue copper oxidases |CITS: [11527384]|. Copper is incorporated sequentially to
the three types of binding sites in CueO |CITS: [14648285]|. Crystal structures of the enzyme are presented at 1.4 A
|CITS: [11867755]| and 1.7 A |CITS: [12794077]| resolution.
Phenoloxidase activity of CueO was demonstrated against substrates including p-phenylenediamine
|CITS: [11527384]|, 2,6-dimethoxyphenol |CITS: [11527384], [11682198]|, and iron siderophores including
2,3-dihydroxybenzoate, enterobactin, and 3-hydroxyanthranilate |CITS: [11466290]|. Optimal reaction conditions are
described |CITS: [11867755]| and details of the reaction mechanism are discussed |CITS: [11867755], [12794077]|.
PcoA and CueO exhibit functional redundancy |CITS: [12099683]|. CueO has similarity to Bacillus subtilis
CotA |CITS: [12198312], [12637519]| and to Salmonella enterica serovar Typhimurium CuiD |CITS: [12442888]|.
Regulation has been described |CITS: [10915804]|.
Review: |CITS: [12829268]|.)""",]},
'B3671' : {'ecocyc-rxns': {"""ACETOOHBUTSYN-RXN""": """pyruvate + 2-oxobutanoate = 2-aceto-2-hydroxy-butyrate + CO2""","""ACETOLACTSYN-RXN""": """2 pyruvate = 2-acetolactate + CO2""","""HYDGLUTSYN-RXN""": """propionyl-CoA + H2O + glyoxylate = 2-hydroxyglutarate + coenzyme A""",},'ucsd-rxns' : ['ACLS','ACHBS',], 'protein-comments' : ["""(IlvB is the catalytic subunit of Acetohydroxybutanoate synthase I / Acetolactate synthase I |CITS: [92380929]|.)""","""NIL""",]},
'B3670' : {'ecocyc-rxns': {"""ACETOOHBUTSYN-RXN""": """pyruvate + 2-oxobutanoate = 2-aceto-2-hydroxy-butyrate + CO2""","""ACETOLACTSYN-RXN""": """2 pyruvate = 2-acetolactate + CO2""",},'ucsd-rxns' : ['ACLS','ACHBS',], 'protein-comments' : ["""(regulatory subunit)""","""NIL""",]},
'B0616' : {'ecocyc-rxns': {"""CITLY-RXN""": """citrate = acetate + oxaloacetate""","""CITTRANS-RXN""": """acetyl-ACP + citrate = citryl-ACP + acetate""","""CITRYLY-RXN""": """citryl-ACP = acetyl-ACP + oxaloacetate""",},'ucsd-rxns' : ['CITL',], 'protein-comments' : ["""NIL""","""NIL""","""NIL""","""NIL""",]},
'B0617' : {'ecocyc-rxns': {"""CITLY-RXN""": """citrate = acetate + oxaloacetate""","""CITTRANS-RXN""": """acetyl-ACP + citrate = citryl-ACP + acetate""","""CITRYLY-RXN""": """citryl-ACP = acetyl-ACP + oxaloacetate""",},'ucsd-rxns' : ['CITL',], 'protein-comments' : ["""NIL""","""NIL""","""(In the original purification of the enzyme, this subunit was
purified with a contaminant. It was thought that the enzyme existed
in an α-6 β-6 γ-1 structure. |CITS: [84024606]| Subsequent
work identified the contaminant, and the structure was recognized as
α-6 β-6 γ-6. |CITS: [87214225]|.
The prosthetic group, 2'-(5"-phosphoribosyl)-3'-dephospho-CoA, is covalently bound to the
CitD acyl carrier protein (citrate lyase gamma subunit) |CITS: [11042274][10924139]| .
The prosthetic group is synthesized from the precursor, 2'-(5"-triphosphoribosyl)-3'-dephospho-CoA,
which is transferred to the apo-citrate lyase
forming holo-citrate lyase and pyrophosphate |CITS: [11042274][10924139]| .
The prosthetic group precursor is synthesized from ATP and
dephospho-CoA |CITS: [11042274][10924139]| .
)""","""NIL""",]},
'B0614' : {'ecocyc-rxns': {"""2.7.7.61-RXN""": """2'-(5''-triphosphoribosyl)-3'-dephospho-CoA + an apo-citrate-lyase = a holo-citrate-lyase + diphosphate""","""RXN0-263""": """2'-(5''-triphosphoribosyl)-3'-dephospho-CoA + CitD apo-ACP = diphosphate + holo-citrate lyase""",},'ucsd-rxns' : ['CITL',], 'protein-comments' : ["""NIL""",]},
'B0615' : {'ecocyc-rxns': {"""CITLY-RXN""": """citrate = acetate + oxaloacetate""","""CITTRANS-RXN""": """acetyl-ACP + citrate = citryl-ACP + acetate""","""CITRYLY-RXN""": """citryl-ACP = acetyl-ACP + oxaloacetate""",},'ucsd-rxns' : ['CITL',], 'protein-comments' : ["""NIL""","""NIL""","""NIL""","""NIL""",]},
'B3770' : {'ecocyc-rxns': {"""BRANCHED-CHAINAMINOTRANSFERVAL-RXN""": """L-valine + α-ketoglutarate = 2-keto-isovalerate + L-glutamate""","""BRANCHED-CHAINAMINOTRANSFERILEU-RXN""": """L-isoleucine + α-ketoglutarate = 2-keto-3-methyl-valerate + L-glutamate""","""BRANCHED-CHAINAMINOTRANSFERLEU-RXN""": """L-leucine + α-ketoglutarate = 2-ketoisocaproate + L-glutamate""",},'ucsd-rxns' : ['LEUTAi','VALTA','PHETA1','ILETA',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B3771' : {'ecocyc-rxns': {"""DIHYDROXYISOVALDEHYDRAT-RXN""": """2,3-dihydroxy-isovalerate = 2-keto-isovalerate + H2O""","""DIHYDROXYMETVALDEHYDRAT-RXN""": """2,3-dihydroxy-3-methylvalerate = 2-keto-3-methyl-valerate + H2O""",},'ucsd-rxns' : ['DHAD1','DHAD2',], 'protein-comments' : ["""NIL""","""(The enzyme carries out reactions in in the pathways of both the biosynthesis of isoleucine and of valine. Dihydroxy-acid dehydratase contains a [4Fe-4S] cluster
which is essential for catalysis and unstable in the presence of O2
and O(-)2. |CITS: [93315441]|)""",]},
'B3772' : {'ecocyc-rxns': {"""THREDEHYD-RXN""": """L-threonine -> 2-oxobutanoate + ammonia""",},'ucsd-rxns' : ['THRD_L',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B3774' : {'ecocyc-rxns': {"""ACETOLACTREDUCTOISOM-RXN""": """2,3-dihydroxy-isovalerate + NADP+ = 2-acetolactate + NADPH + H+""","""ACETOOHBUTREDUCTOISOM-RXN""": """2-aceto-2-hydroxy-butyrate + NADPH = 2,3-dihydroxy-3-methylvalerate + NADP+""",},'ucsd-rxns' : ['DPR','KARA1','KARA2',], 'protein-comments' : ["""(One enzyme catalyzes two reactions by using alternate
substrates. The reactions appear in two pathways, one reaction in the
biosynthesis of valine (and leucine) and the other for isoleucine.
Expression of the ilvC gene is not regulated by
the pathway end-products, but is induced in the presence of either
substrate of acetohydroxy acid isomeroreductase, acetohydroxybutyrate or
acetolactate. |CITS: [89094833]|)""",]},
'B3057' : {'ecocyc-rxns': {"""UNDECAPRENYL-DIPHOSPHATASE-RXN""": """undecaprenyl diphosphate + H2O -> undecaprenyl phosphate + phosphate""",},'ucsd-rxns' : ['UDCPDP','UDCPDPpp',], 'protein-comments' : ["""(The purified BacA protein exhibits undecaprenyl pyrophosphate phosphatase activity, but not undecaprenol
phosphokinase activity |CITS: [15138271]|. The bacA gene product is not essential for growth, but the product
of the reaction, undecaprenyl phosphate, is essential for the synthesis of peptidoglycan and other cell wall
components. At least three additional gene products, YbjG, PgpB, and YeiU, are thought to have undecaprenyl
pyrophosphate phosphatase activity in E. coli |CITS: [15778224]|. Simultaneous inactivation of bacA,
ybjG, and pgpB is lethal. Depletion of BacA in the triple mutant strain causes changes in cell
morphology and lysis. Overexpression of bacA, yeiU, ybjG, and pgpB leads to increased
undecaprenyl pyrophosphate (C55PP) phosphatase activity in crude membrane extracts. Expression
of C55PP phosphatase activity from any one of the three genes bacA, ybjG, and
pgpB appears to be sufficient for synthesis of undecaprenyl phosphate and survival |CITS: [15778224]|.
When supplied on a multicopy plasmid, bacA confers resistance to bacitracin |CITS: [8389741]|.
The bacA gene belongs to the sigmaE regulon, which is responsive to extracytoplasmic stress
|CITS: [12900013]|.)""",]},
'B2097' : {'ecocyc-rxns': {"""F16ALDOLASE-RXN""": """fructose-1,6-bisphosphate = dihydroxy-acetone-phosphate + D-glyceraldehyde-3-phosphate""",},'ucsd-rxns' : ['FBA',], 'protein-comments' : ["""NIL""","""(The typical class I aldolases of plants and animals have been
throroughly studied |CITS: [78165651]| Fructose-1,6-bisphosphate
aldolases can be divided into two
classes on the basis of their catalytic and structural properties.
|CITS: [78165651]| Class I fructose 1,6 bisphosphate aldolases were
once thought
to be confined to eukaryotic organisms but have since been detected in
several bacterial species. |CITS: [78165652]| The occurence of such
an aldolase in bacteria was unexpected in light of the
phylogenetic distribution of aldolases. |CITS: [73229139]| The
enzymes of eukaryotes generally fall into Class I and are tetramers of
identical polypeptide chains. |CITS: [89193446]|
In earlier studies |CITS: [73229139]| it was thought that the class I E. coli
aldolase was typical in that it was tetrameric with a mol. wt.
of approx. 140K. In 1978 new purification techniques were used.The true aldolase 1
activity could be measured by using Fru-1,6-P2 that had been purified
by chromatography on DEAE-cellulose to remove the
fructose-6-phosphate. Using these methods the enzyme appeared to be
larger than was previously supposed and may be a decamer with a mol. wt.
of approx. 340,000. The size of aldolase 1 and the effect of cross-linking reagents
on it, indicate that its structure must differ significantly from that
of the typical tetrameric class-I enzymes from eukaryotes. |CITS: [78165652]
[73229139]|
)""",]},
'B4213' : {'ecocyc-rxns': {"""CYCPHOSDIESTER-RXN""": """a nucleoside 2',3'-cyclic phosphate + H2O = a nucleoside 3'-phosphate""","""3-NUCLEOTID-RXN""": """a nucleoside 3'-phosphate + H2O = a ribonucleoside + phosphate""",},'ucsd-rxns' : ['23PDE9pp','3NTD9pp','23PDE2pp','3NTD7pp','3NTD4pp','23PDE4pp','23PDE7pp','3NTD2pp',], 'protein-comments' : ["""NIL""",]},
'B0759' : {'ecocyc-rxns': {"""UDPGLUCEPIM-RXN""": """UDP-D-glucose = UDP-galactose""",},'ucsd-rxns' : ['UDPG4E',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B0758' : {'ecocyc-rxns': {"""GALACTURIDYLYLTRANS-RXN""": """UDP-D-glucose + α-D-galactose 1-phosphate = α-D-glucose 1-phosphate + UDP-galactose""","""UTPHEXPURIDYLYLTRANS-RXN""": """α-D-galactose 1-phosphate + UTP = UDP-galactose + diphosphate""",},'ucsd-rxns' : ['UGLT',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B3062' : {'ecocyc-rxns': {"""LTARTDEHYDRA-RXN""": """tartrate = oxaloacetate + H2O""",},'ucsd-rxns' : ['TARTD',], 'protein-comments' : ["""(The ttdB gene encodes the beta subunit of L-tartrate dehydratase |CITS: [8371115]| and is expressed in exponentially
growing cells |CITS: [3297921]|. Expression may be translationally coupled to TtdA |CITS: [8371115]|.)""","""NIL""","""(E.coli is capable of degrading tartrate under aerobic or anaerobic conditions. L-tartrate dehydratase is induced
during anaerobic growth on glycerol plus L- and meso-tartrates |CITS: [8371115]|.)""",]},
'B3578' : {'ecocyc-rxns': {},'ucsd-rxns' : ['XYLUt2pp',], 'protein-comments' : ["""(Based on sequence similarity, YiaN is a membrane-spanning component of the YiaMNO Binding protein-dependent Secondary (TRAP) Transporter |CITS:[11524131]|.)""","""(Based on sequence similarity, the yiaMNO genes encode the only tri-partite
ATP-independent periplasmic (TRAP) transporter in Escherichia coli. The TRAP
transporters share characteristics of both the ATP-binding cassette (ABC) and secondary
families of transporters |CITS:[11524131]|. Like the ABC transporters TRAP
transporters use an extracytoplasmic solute-binding protein but rather than ATP hydrolysis
the driving force is provided by either proton-(pmf) and/or sodium ion motive
force (smf) |CITS:[11524131]|. Based on sequence similarity, YiaO is the periplasmic
solute-binding protein and YiaM and YiaN are membrane-spanning proteins.
Deletion mutation experiments |CITS:[14668138]| showed that deletion of the yiaMNO
genes affected the ability of E.coli to utilize L-xylulose when
growth was measured using various carbon substrates. Solute transport studies
|CITS:[14668138]| determined that the yiaMNO deletion strain was capable
of utilizing L-xylulose but at a lower rate, indicating that the YiaMNO transporter is
involved in, but not essential for L-xylulose utilization. Purification and binding
studies |CITS:[14668138]| using YiaO showed that YiaO was able to bind L-xylulose.
Furthermore, spheroblasts expressing the YiaMN membrane domains were
stimulated to increase uptake of L-xylulose when incubated with the periplasmic
substrate-binding YiaO while those spheroblasts not expressing YiaMN showed no
such stimulation. Deletion of yiaMNO resulted in a delay of entry into stationary phase of cells
grown in LB with glucose, or minimal medium with glucose or other compounds. These cultures obtained a
higher stationary phase OD660 and higher c.f.u. numbers. Deletion of yiaMNO also
resulted in an increased lag time in cultures with high NaCl concentrations, and a reduction in biofilm
formation in minimal medium with glucose |CITS:[15870475]|.)""",]},
'B0697' : {'ecocyc-rxns': {"""TRANS-RXN-2""": """K+[periplasmic space] + ATP + H2O =K+[cytosol] + ADP + phosphate """,},'ucsd-rxns' : ['Kabcpp',], 'protein-comments' : ["""NIL""","""(The kdpFABC genes encode an ATP-dependent high affinity P-Type ATPase potassium ion
transporter |CITS: [89078396] [89174642]|. The transporter has a high affinity and substrate specificity for
potassium ion (Km= 10 μM). It is activated by magnesium ion with an affinity constant of
80 μM |CITS: [89078396]|. ATP-driven potassium ion transport has been observed when the Kdp
complex is reconstituted in vesicles |CITS: [95204461]|. Kdp is unusual among P- type ATPases in
having three subunits: one for energy coupling (KdpB), one for substrate binding and transport (KdpA),
and one for associating the first two subunits together (KdpC) |CITS: [95204461]|. The largest subunit,
KdpB, is the homologue of other P-type ATPases. Neither of the other two subunits, KdpA or KdpC, has
homologues in other P-type ATPases. Mutation experiments have shown that all three subunits are
required for normal Kdp activity |CITS: [95204461]|. KdpA is highly hydrophobic with many predicted
membrane-spanning segments |CITS:[95204461]|. The fact that most mutants displaying lower affinity for
potassium ion had mutations that altered KdpA implies that KdpA has a major role in determining affinity for
potassium ion |CITS: [95204461]|. A truncated version of KdpA with only the N-terminal 135 amino acids
(which contains two transmembrane segments) is able to rescue a K+ transporter mutant in
media with low K+ concentration even without KdpA and KdpB. This is predicted to occur in
response to the membrane potential |CITS:[11344160]|. KdpC is predicted to have only a single
membrane-spanning segment |CITS:[95204461]|. Complementation experiments with complete and
truncated KdpC proteins and hybrids as well as sequence analysis of KdpC proteins have identified 4
major parts to the protein. There are two highly conserved regions (regions 2 and 4) and two highly
variable regions (1 and 3). Region 1, the N-terminal region, is predicted to be the membrane spanning
segment |CITS:[11248697]|. Mutational analysis also showed that KdpC is involved in linking KdpA and
KdpB together, serving to assemble and stabilize the KdpFABC complex |CITS: [99077600]|. A fourth gene
on the same operon, kdpF, encodes a small non-essential polypeptide, which was shown by
SDS-polyacrylamide gel analysis of the transporter complex to be associated with and stabilize the
KdpFABC complex in vivo |CITS: [99005984] [20076462]|. The kdp genes are expressed
when growth is limited by the availability of potassium ion |CITS:[89078396]|. Two other important
potassium ion uptake systems in E. coli include Trk and Kup |CITS: [95204461]|.)""",]},
'B0752' : {'ecocyc-rxns': {"""TRANS-RXN-200""": """Zn2+[cytosol] + H+[periplasmic space] =Zn2+[periplasmic space] + H+[cytosol] """,},'ucsd-rxns' : ['NI2t3pp','COBALT2t3pp','MN2t3pp','CD2t3pp','ZN2t3pp',], 'protein-comments' : ["""(ZitB (formerly known as YbgR) is a probable Zn2+ transporter.
It is a member of the cation diffusion facilitator family of metal ion efflux proteins |CITS: [97232493]|.
Studies have shown that disruption of zntA and zitB results in a greater
degree of Zn2+ sensitivity than disruption of zntA alone |CITS: [21336524]|.
Furthermore, overexpression of zitB results in a significant increase in Zn2+
resistance and a decrease in Zn2+ accumulation. Thus, ZitB probably functions as a
Zn2+ efflux system possibly playing a role in zinc homeostasis at low Zn2+ levels.
Transcription is Zn2+ inducible, based on zitB-lacZ gene fusion studies |CITS: [21336524]|.
Membrane topology predictions using experimentally determined C terminus
locations indicate that ZitB has 6 transmembrane helices and the C-terminus is
located in the cytoplasm |CITS:[15044727]|.)""",]},
'B0751' : {'ecocyc-rxns': {"""TRANS-RXN-9""": """nicotinamide mononucleotide[periplasmic space] =nicotinamide mononucleotide[cytosol] """,},'ucsd-rxns' : ['NMNPtpp',], 'protein-comments' : ["""(The pnuC gene encodes a component of the Nicotinamide Mononucleotide (NMN)
transport system. It is a member of the NMN uptake permease (PnuC) family. The mechanism and
energy source for NMN uptake by PnuC in E. coli are not well defined, however, based on its sequence
homology to the PnuC of Salmonella typhimurium, PnuC is believed to function cooperatively
with NadR, a bufunctional protein serving in both transcriptional regulatory and NMN transport capacities
|CITS:[90330519]|. In Salmonella typhimurium, PnuC is shown to be an integral membrane protein
due to its hydrophobic nature, and is essential for the transport of NMN across the cytoplasmic membrane.
Mutant alleles of the pnuC gene permit NMN transport in the absence of NadR function |CITS:[91123208]|.)""",]},
'B0750' : {'ecocyc-rxns': {"""QUINOLINATE-SYNTHE-MULTI-RXN""": """L-aspartate + O2 + dihydroxy-acetone-phosphate -> quinolinate + phosphate + H2O2 + 2 H2O""","""QUINOLINATE-SYNTHA-RXN""": """iminoaspartate + dihydroxy-acetone-phosphate -> quinolinate + 2 H2O + phosphate""",},'ucsd-rxns' : ['QULNS',], 'protein-comments' : ["""(The quinolinate synthase A protein (NadA) is a component of the quinolinate synthase complex, which catalyzes
the formation of quinolinate from aspartate |CITS: [82098106][88296484]|.
The nadA gene has been cloned |CITS: [2841129]|, and the protein was initially overexpressed and purified
from inclusion bodies |CITS: [10648170]|. NadA was later shown to contains an oxygen-sensitive [4Fe-4S] cluster
that is required for its activity |CITS: [15898769][15967443]|, explaining the NAD auxotrophy of an iscS mutant.
Reaction mechanisms involving the [4Fe-4S] cluster have been proposed |CITS: [15898769]|.)""","""(A complex of two enzymes that carry out adjacent reactions. The intermediate iminoaspartate is captive in the multi-complex.)""",]},
'B3572' : {'ecocyc-rxns': {"""VALINE-PYRUVATE-AMINOTRANSFER-RXN""": """pyruvate + L-valine = L-alanine + 2-keto-isovalerate""",},'ucsd-rxns' : ['VPAMT',], 'protein-comments' : ["""NIL""",]},
'B0698' : {'ecocyc-rxns': {"""TRANS-RXN-2""": """K+[periplasmic space] + ATP + H2O =K+[cytosol] + ADP + phosphate """,},'ucsd-rxns' : ['Kabcpp',], 'protein-comments' : ["""NIL""","""(The kdpFABC genes encode an ATP-dependent high affinity P-Type ATPase potassium ion
transporter |CITS: [89078396] [89174642]|. The transporter has a high affinity and substrate specificity for
potassium ion (Km= 10 μM). It is activated by magnesium ion with an affinity constant of
80 μM |CITS: [89078396]|. ATP-driven potassium ion transport has been observed when the Kdp
complex is reconstituted in vesicles |CITS: [95204461]|. Kdp is unusual among P- type ATPases in
having three subunits: one for energy coupling (KdpB), one for substrate binding and transport (KdpA),
and one for associating the first two subunits together (KdpC) |CITS: [95204461]|. The largest subunit,
KdpB, is the homologue of other P-type ATPases. Neither of the other two subunits, KdpA or KdpC, has
homologues in other P-type ATPases. Mutation experiments have shown that all three subunits are
required for normal Kdp activity |CITS: [95204461]|. KdpA is highly hydrophobic with many predicted
membrane-spanning segments |CITS:[95204461]|. The fact that most mutants displaying lower affinity for
potassium ion had mutations that altered KdpA implies that KdpA has a major role in determining affinity for
potassium ion |CITS: [95204461]|. A truncated version of KdpA with only the N-terminal 135 amino acids
(which contains two transmembrane segments) is able to rescue a K+ transporter mutant in
media with low K+ concentration even without KdpA and KdpB. This is predicted to occur in
response to the membrane potential |CITS:[11344160]|. KdpC is predicted to have only a single
membrane-spanning segment |CITS:[95204461]|. Complementation experiments with complete and
truncated KdpC proteins and hybrids as well as sequence analysis of KdpC proteins have identified 4
major parts to the protein. There are two highly conserved regions (regions 2 and 4) and two highly
variable regions (1 and 3). Region 1, the N-terminal region, is predicted to be the membrane spanning
segment |CITS:[11248697]|. Mutational analysis also showed that KdpC is involved in linking KdpA and
KdpB together, serving to assemble and stabilize the KdpFABC complex |CITS: [99077600]|. A fourth gene
on the same operon, kdpF, encodes a small non-essential polypeptide, which was shown by
SDS-polyacrylamide gel analysis of the transporter complex to be associated with and stabilize the
KdpFABC complex in vivo |CITS: [99005984] [20076462]|. The kdp genes are expressed
when growth is limited by the availability of potassium ion |CITS:[89078396]|. Two other important
potassium ion uptake systems in E. coli include Trk and Kup |CITS: [95204461]|.)""",]},
'B0755' : {'ecocyc-rxns': {"""3PGAREARR-RXN""": """3-phosphoglycerate = 2-phosphoglycerate""",},'ucsd-rxns' : ['PGM',], 'protein-comments' : ["""(Regulation has been described |CITS: [11101675]|. Transcription is regulated by Fur |CITS: [11101675]|.)""","""NIL""",]},
'B0754' : {'ecocyc-rxns': {"""DAHPSYN-RXN""": """phosphoenolpyruvate + D-erythrose-4-phosphate + H2O = 3-deoxy-D-arabino-heptulosonate-7-phosphate + phosphate""",},'ucsd-rxns' : ['DDPA',], 'protein-comments' : ["""(Expression of aroF and aroG is repressed by the tyrR protein
with tyrosine or phenylalanine plus tryptophan, respectively as corepressors
The three genes (aroF, aroG and aroH) are widely separated on the coli chromosome. In
wild-type cells grown in minimal mediuim, the AroG enzyme makes up
about 80% of the total DAHPS activity, the AroF isoenzyme makes up
20%, and the AroH isoenzyme makes up about 1% |CITS:[89053867]|.)""","""NIL""",]},
'B1189' : {'ecocyc-rxns': {"""DAADEHYDROG-RXN""": """an acceptor + H2O + a D amino acid = a reduced acceptor + ammonia + a 2-oxo acid""","""DALADEHYDROG-RXN""": """D-alanine + H2O = pyruvate + ammonia""",},'ucsd-rxns' : ['DAAD',], 'protein-comments' : ["""NIL""","""(The enzyme is composed of two non-identical subunits, the gene dadA codes for
the smaller unit and an unidentified gene for the larger. |CITS: [80182101]
[82118098] [94156858]|)""",]},
'B4358' : {'ecocyc-rxns': {},'ucsd-rxns' : ['GALCTLO',], 'protein-comments' : ["""(YjjN did not show dehydrogenase activity in a high-throughput screen of purified proteins |CITS: [15808744]|.
)""",]},
'B0678' : {'ecocyc-rxns': {"""GLUCOSAMINE-6-P-DEAMIN-RXN""": """H2O + D-glucosamine-6-phosphate = D-fructose-6-phosphate + ammonia""",},'ucsd-rxns' : ['G6PDA',], 'protein-comments' : ["""(The structure is a trimer of dimers |CITS: [93352397]|.
Based on sequence similarity, NagB has been predicted to be a 6-phosphogluconolactonase |CITS: [12952533]|.)""","""NIL""",]},
'B4291' : {'ecocyc-rxns': {"""RXN0-2261""": """ferric dicitrate[extracellular space] =ferric dicitrate[cytosol] ""","""RXN0-1684""": """ferric dicitrate[extracellular space] =ferric dicitrate[periplasmic space] """,},'ucsd-rxns' : ['FE3DCITtonex',], 'protein-comments' : ["""(FecA is the TonB energy transducing system-dependent ferric citrate uptake receptor.
The structure of the periplasmic signaling domain of the FecA protein has been solved
by multidimensional NMR spectroscopy |CITS:[16313612]|. The crystallographic structures
of FecA with and without bound ferric citrate have been determined to resolutions of 2.5
and 2.0 angstroms |CITS:[11872840]|. Bipartite gating of the protein is described |CITS:[12196171]|.)""","""(FecARI are responsible for ferric citrate dependent induction of the ferric citrate
uptake system. When the inducer, ferric citrate, binds FecA, which is also
responsible for transport of ferric citrate across the outer membrane, a signal is
transmitted across the outer membrane to the cytoplasmic membrane protein FecR.
FecR transmits the signal across the cytoplasmic membrane and activates the
σ70 family protein FecI in the cytoplasm. FecI directs RNA
polymerase to express fecABCDE, which encodes the ferric citrate outer
membrane receptor and the ferric citrate ABC transporter, as well as fecIR
|CITS:[7729419],[10633096]|. Expression of fecIR is repressed by
Fe2+ bound to Fur |CITS:[16333751]|.
Review: |CITS:[12354617]|
)""","""(The Outer Membrane Ferric Citrate Transport System is responsible for the transport of ferric
citrate across the outer membrane by FecA energized by the TonB energy transducing system.)""","""NIL""",]},
'B0828' : {'ecocyc-rxns': {"""ASPARAGHYD-RXN""": """L-asparagine + H2O = L-aspartate + ammonia""",},'ucsd-rxns' : ['ASNN',], 'protein-comments' : ["""(Asparaginase III is first synthesized as a proenzyme which is
autocatalytically cleaved post-translationally into two smaller polypeptides.
|CITS: [20508248]|)""","""NIL""","""NIL""","""NIL""","""(A crystal structure has been determined at 1.9 Å resolution |CITS: [15946951]|.)""","""NIL""","""(A crystal structure has been determined at 1.9 Å resolution |CITS: [15946951]|.)""",]},
'B0212' : {'ecocyc-rxns': {"""GLYOXII-RXN""": """S-lactoyl-glutathione + H2O = glutathione + D-lactate""",},'ucsd-rxns' : ['GLYOX',], 'protein-comments' : ["""(The enzyme
is most likely a monomer. |CITS: [90328953]|)""",]},
'B0767' : {'ecocyc-rxns': {"""6PGLUCONOLACT-RXN""": """D-glucono-δ-lactone-6-phosphate + H2O -> 6-phospho-D-gluconate""",},'ucsd-rxns' : ['PGL',], 'protein-comments' : ["""(A pgl mutant strain has the Blu- phenotype, which is diagnostic for 6-phosphogluconolactonase
mutants |CITS: [15576773]|. The phenotype of a pgl deletion strain can be complemented by expression of the
pgl gene from Pseudomonas putida, although there is no detectable similarity between the two genes
|CITS: [15766779]|.)""",]},
'B1185' : {'ecocyc-rxns': {"""DSBBPROT-RXN""": """DSBBPROT-RXN""",},'ucsd-rxns' : ['DSBAO2','DSBAO1',], 'protein-comments' : ["""(The dsbB gene codes for a transmembrane protein that is
responsible for reoxidizing the dsbA-encoded disulfide oxidoreductase.
It is believed that the dsbB protein acts by transferring disulfide
bonds directly to the oxidoreductase. DsbB is then oxidized by
either ubiquinone, aerobic conditions, or menaquinone, anaerobic
conditions. |CITS: [95045404] [93348217]
[93157338] [95131742] [95340482] [20461465]|)""",]},
'B4356' : {'ecocyc-rxns': {},'ucsd-rxns' : ['GALCTNLt2pp',], 'protein-comments' : ["""(The YjiZ protein is an uncharacterised member of the
major facilitator superfamily (MFS) of transporters |CITS: [98190790]|.
Based on sequence similarity, YjiZ may function as a proton-driven
metabolite uptake system.)""",]},
'B2480' : {'ecocyc-rxns': {"""PEROXID-RXN""": """a reduced acceptor + H2O2 = an acceptor + 2 H2O""","""RXN0-267""": """a reduced thioredoxin + H2O2 = a thioredoxin disulfide + H2O""",},'ucsd-rxns' : ['THIORDXi','THIORDXi',], 'protein-comments' : ["""NIL""",]},
'B2328' : {'ecocyc-rxns': {"""RXN0-3461""": """EC# 3.4.99.-""",},'ucsd-rxns' : ['MDDEP3pp','MDDEP2pp','MDDEP4pp','MDDEP1pp',], 'protein-comments' : ["""NIL""","""(MepA is a penicillin-insensitive D-alanyl-D-alanine endopeptidase responsible for
hydrolyzing cell wall peptidoglycan |CITS: [365181]|.
MepA is similar to
proteins in the LAS metallopeptidase family. Mutations in putative Zinc-coordinating
residues histidine-113, aspartate-120 and histidine-211 inactive MepA, as do metal
chelators |CITS: [15292190]|.
MepA is a dimer that is localized in the periplasm by its amino-terminal signal peptide |CITS: [15292190][6343788][2187143]|.
MepA has motifs suggesting it is a LAS metallopeptidase. It is sensitive to metal chelators
in vitro and mutation sin predicted Zn coordination residues H113, D120 and H211 inactive it.
Crystal structure shown. It's a dimer. H110 is the fourth thing coordinating Zn, whereas in
other LAS peptidases this is a water |CITS: [15292190]|.)""",]},
'B2329' : {'ecocyc-rxns': {"""CHORISMATE-SYNTHASE-RXN""": """5-enolpyruvyl-shikimate-3-phosphate -> phosphate + chorismate""",},'ucsd-rxns' : ['CHORS',], 'protein-comments' : ["""(Chorismate synthase acts in the shikimate pathway. It catalyses the conversion of
5-enolpyruvylshikimate 3-phosphate into chorismate, the key
branch-point intermediate in aromatic biosynthesis.
Chorismate synthase is an AroC tetramer |CITS: [2969724]|.
The enzymatic mechanism has been studied in detail |CITS: [2407239], [7978236], [7848266], [7559411], [8634296],
[8703965], [8824216], [10956653], [11034781], [11784161]|. The enzyme catalyzes phosphate elimination by a
1,4-elimination mechanism that proceeds with anti-stereochemistry |CITS: [4550759]|. The E. coli enzyme is
unable to generate reduced flavin via
the oxidation of reduced nicotinamide nucleotides; it can synthesize
chorismate only when supplied directly with either FMNH2 or FADH2, and the preferred
flavin is FMNH2 |CITS:[88293429]|. The reaction is oxygen sensitive and the enzyme
is inactive under aerobic conditions |CITS:[67082484]|. The enzyme remains tetrameric and undergoes significant
conformational changes during catalysis |CITS: [9761730]|.
A 36-residue C-terminal truncation does not eliminate enzyme activity |CITS: [2182772]|.
Chorismate synthase exhibits low abundance in wild-type
strains |CITS:[biosoctrans(87)15-144]|. Overproduction and purification has been described |CITS: [2969724]|.
Chorismate synthase has been studied in many different organisms. Phenotypes of an E. coli aroC mutant are
functionally complemented by production of Synechocystis PCC 6803 AroC |CITS: [7505271]|,
Vibrio anguillarum AroC |CITS: [8021209]|, or Brucella suis AroC |CITS: [11119550]|.
The shikimate pathway is of great interest as a drug target |CITS: [11865437]|. Salmonella typhimurium AroC
is required for wild-type virulence |CITS: [3058818]|, as is Brucella suis AroC |CITS: [11119550]|.
S. typhimurium |CITS: [3058818], [2187747], [1311488], [7483768], [12065485], [12531654]| and S. typhi
|CITS: [9916080], [11982332], [12065485], [12531654], [12555559]| aroC mutations have been used in vaccine
strains.
Reviews: |CITS: [8674765], [9951731], [11476485], [12521268]|.)""","""NIL""",]},
'B3115' : {'ecocyc-rxns': {"""PROPKIN-RXN""": """ATP + propionate = ADP + propionyl-P""","""ACETATEKIN-RXN""": """acetate + ATP = acetylphosphate + ADP""",},'ucsd-rxns' : ['PPAKr','ACKr',], 'protein-comments' : ["""NIL""",]},
'B3458' : {'ecocyc-rxns': {"""ABC-35-RXN""": """ATP + L-leucine[periplasmic space] + H2O =ADP + phosphate + L-leucine[cytosol] """,},'ucsd-rxns' : ['LEUabcpp',], 'protein-comments' : ["""(The crystal structure of LivK in both the apo- and ligand-bound form has been determined at 1.5 and 1.8 A
resolution |CITS: [2649683][14672931]|.)""","""(LivFGHMJ and LivFGHMK are two ATP-dependent high-affinity branched-chain amino acid transport
system and are members of the ATP Binding Cassette (ABC) Superfamily of transporters |CITS: [20053876]|.
The two systems are responsible for the high affinity transport of branched-chain amino acids in
E. coli. They have shared membrane and ATP-binding components but have distinctive periplasmic
binding proteins. Due to the different periplasmic binding components, the two complexes differ in their
binding specificity: LivFGHMK is specific for the transport of leucine, while LivFGHMJ is a transporter for
leucine, isoleucine, and valine |CITS: [85288998]|. Based on sequence similarity and hydrophobicity
analysis, LivJ and LivK are the two periplasmic animo acid-binding proteins, LivH and LivM are the
membrane components, and LivG and LivF are the ATP-binding component of the ABC transport
complexes |CITS: [90307651]|. Deletions each of the liv genes resulted in the inability to transport
leucine |CITS: [90307651]|. In addition, a deletion strain that does not express any of the liv genes
was unable to carry out high-affinity transport of leucine unless one of the binding protein genes and all of
the membrane complex genes were provided on a plasmid |CITS: [90307651]|. In a separate experiment,
liv gene mutants were found to be resistant to a toxic analog of leucine, azaleucine, due to its
inability in branched-chain amino acid transport |CITS: [85288998]|.)""",]},
'B2320' : {'ecocyc-rxns': {"""ERYTHRON4PDEHYDROG-RXN""": """erythronate-4-phosphate + NAD+ = 3-hydroxy-4-phospho-hydroxy-α-ketobutyrate + NADH""",},'ucsd-rxns' : ['PERD',], 'protein-comments' : ["""(The subunit structure is not yet known.)""",]},
'B2323' : {'ecocyc-rxns': {"""RXN0-2141""": """cis-Δ3-decenoyl-ACP + malonyl-ACP = β-keto-cis-Δ5-dodecenoyl-ACP + acyl carrier protein + CO2""","""3-OXOACYL-ACP-SYNTH-BASE-RXN""": """acetyl-ACP + malonyl-ACP -> an acyl carrier protein + an acetoacetyl-ACP + CO2""","""3-OXOACYL-ACP-SYNTH-RXN""": """an acyl-ACP + malonyl-ACP -> acyl carrier protein + a β-ketoacyl-ACP + CO2""","""MALONYL-ACPDECARBOX-RXN""": """malonyl-ACP = acetyl-ACP + CO2""",},'ucsd-rxns' : ['KAS14','3OAS100','3OAS120','3OAS121','3OAS80','3OAS180','3OAS60','MACPD','3OAS161','3OAS140','3OAS141','3OAS160',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B0348' : {'ecocyc-rxns': {"""1.13.11.16-RXN""": """3-(2,3-dihydroxyphenyl)propionate + O2 = 2-hydroxy-6-oxonona-2,4-diene-1,9-dioate""",},'ucsd-rxns' : ['HPPPNDO','DHCINDO',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B3571' : {'ecocyc-rxns': {"""ALPHA-AMYL-RXN""": """a 1,4-α-D-glucan = maltodextrin""",},'ucsd-rxns' : ['AAMYLpp',], 'protein-comments' : ["""NIL""",]},
'B4321' : {'ecocyc-rxns': {"""TRANS-RXN-81""": """H+[periplasmic space] + fructuronate[periplasmic space] =H+[cytosol] + fructuronate[cytosol] """,},'ucsd-rxns' : ['GLCNt2rpp','FRUURt2rpp',], 'protein-comments' : ["""(GntP is a member of the GntP family transporters |CITS: [97212001]| and is homologous to the E. coli GntT and GntU gluconate transporters. GntP transport D-fructuronate/D-gluconate |CITS: [8550444] [15516583]|. Whole cell experiments have shown that the cloned gntP gene confers gluconate transport with a Km of approx 25 μM, but its expression is not induced by gluconate |CITS: [8550444]|. gntP gene is induced by fructuronate, the first intermediate of the glucuronate metabolism pathway. It is a member of UxuR regulon which is composed of genes induced by glucuronate via its conversion to fructuronate and these genes are repressed by UxuR |CITS:[7007313]|. gntP mutants were unable to grow using fructuronate as their sole carbon source. Taken together, these results indicate
that GntP is the primary fructuronate transporter |CITS:[15516583]|.
)""",]},
'B0893' : {'ecocyc-rxns': {"""RXN0-2161""": """tRNAsec + L-serine + ATP -> L-seryl-tRNAsec + diphosphate + AMP""","""SERINE--TRNA-LIGASE-RXN""": """tRNAser + L-serine + ATP -> L-seryl-tRNAser + diphosphate + AMP""",},'ucsd-rxns' : ['SERTRS2','SERTRS',], 'protein-comments' : ["""(Seryl-tRNA synthetase (SerRS) is a member of the family of aminoacyl-tRNA synthetases, which interpret the
genetic code by covalently linking amino acids to their specific tRNA molecules. The reaction is driven by ATP
hydrolysis. SerRS belongs to the Class II aminoacyl tRNA synthetases, which share three regions of homology
|CITS: [2203971][1852601]|.
SerRS is a dimer in solution |CITS: [4906848]|.
Specificity determinants within tRNASer that are important for recognition by SerRS have been identified
|CITS: [3045821][2068094][7504246][8233780][8114091][8654382]|. SerRS also aminoacylates a special tRNA,
tRNASec, with serine |CITS: [2963963]|. The charging efficiency for tRNASec is
approximately 1% of that for tRNASer |CITS: [1939093]|. The serine residue of
Ser-tRNASec is subsequently converted to selenocysteine by |FRAME: CPLX0-1141|.
tRNASec recognizes the stop codon UGA.
The reaction mechanism of SerRS includes the formation of an aminoacyl adenylate intermediate, which then serves
as the animo acid donor in the aminoacyl-tRNA synthetase reaction |CITS: [320199]|. The N-terminal coiled coil
domain of SerRS is required for its aminoacylation activity, but is not required for amino acid activation
|CITS: [8065908]|. This domain is an autonomously folding unit |CITS: [9054560]|.
Crystal structures of SerRS in various conformations have been solved |CITS: [2205803][8508916]|; however, they
have not been deposited in PDB.
Reviews: |CITS: [10966471][1859832][9889265]|
)""","""NIL""",]},
'B1224' : {'ecocyc-rxns': {"""RXN0-3501""": """menaquinol + NO3- -> menaquinone-8 + nitrite + H2O""",},'ucsd-rxns' : ['NO3R2pp','NO3R1pp',], 'protein-comments' : ["""(The α subunit of nitrate reductase A is the actual site of nitrate reduction and also contains the molybdenum
cofactor |CITS: [92186712]|. In addition, a novel [4Fe-4S] cluster with unusual coordination and a high-spin ground
state was detected in the crystal structure |CITS: [12910261][14725769][15122898]|.
)""","""(If it is coexpressed with the private chaperone NarJ, the NarGH complex alone is soluble and active with artificial
electron donors such as benzyl viologen. NarGH becomes localized to the cytoplasmic side of the inner membrane
by interaction with NarI |CITS: [1545706]|.
A crystal structure of the catalytic and electron transfer subunits (NarG and NarH) has been solved at 2.0 A
resolution |CITS: [14725769]|.)""","""(E. coli contains three nitrate reductases. Two of them, nitrate reductase A (NRA) and nitrate reductase Z
(NRZ), are membrane bound and biochemically similar. The third nitrate reductase, Nap, is located in the periplasm.
Nitrate reductase A is expressed when levels of nitrate in the environment are high, Nap is expressed when they are
low, while NRZ expression is not dependent on nitrate levels or anaerobiosis, but induced during stationary phase.
Nitrate reductase A functions anaerobically as a terminal electron acceptor |CITS: [10464201]|. It accepts electrons
from the quinone pool and in so doing expels two protons from the cell, thereby adding to the proton motive force
|CITS: [12910261]|. Formate dehydrogenase N and nitrate reductase A form a respiratory chain, where a redox loop
of quinone molecules couples electron transfer from formate in the periplasm to nitrate in the cytoplasm.
Nitrate reductase A is a heterotrimer composed of the α-, β- and γ chains. A fourth polypeptide,
encoded by the narJ gene, is required for the incorporation of the molybdenum cofactor into NarG, the α
subunit |CITS: [92121125] [92186712] [9632249]|.
A crystal structure of the catalytic and electron transfer subunits (NarG and NarH) has been solved at 2.0 A
resolution |CITS: [14725769]|, and structures of the NarGHI complex both alone and in complex with the Q-site
inhibitor pentachlorophenol have been solved at 1.9 and 2 A resolution |CITS: [12910261][15122898][15615728]|.
)""",]},
'B1225' : {'ecocyc-rxns': {"""RXN0-3501""": """menaquinol + NO3- -> menaquinone-8 + nitrite + H2O""",},'ucsd-rxns' : ['NO3R2pp','NO3R1pp',], 'protein-comments' : ["""(The β subunit is the electron transfer subunit containing the iron-sulfur clusters, one [3Fe-4S] cluster and three
[4Fe-4S] clusters |CITS: [92186712] [99435749]|.
)""","""(If it is coexpressed with the private chaperone NarJ, the NarGH complex alone is soluble and active with artificial
electron donors such as benzyl viologen. NarGH becomes localized to the cytoplasmic side of the inner membrane
by interaction with NarI |CITS: [1545706]|.
A crystal structure of the catalytic and electron transfer subunits (NarG and NarH) has been solved at 2.0 A
resolution |CITS: [14725769]|.)""","""(E. coli contains three nitrate reductases. Two of them, nitrate reductase A (NRA) and nitrate reductase Z
(NRZ), are membrane bound and biochemically similar. The third nitrate reductase, Nap, is located in the periplasm.
Nitrate reductase A is expressed when levels of nitrate in the environment are high, Nap is expressed when they are
low, while NRZ expression is not dependent on nitrate levels or anaerobiosis, but induced during stationary phase.
Nitrate reductase A functions anaerobically as a terminal electron acceptor |CITS: [10464201]|. It accepts electrons
from the quinone pool and in so doing expels two protons from the cell, thereby adding to the proton motive force
|CITS: [12910261]|. Formate dehydrogenase N and nitrate reductase A form a respiratory chain, where a redox loop
of quinone molecules couples electron transfer from formate in the periplasm to nitrate in the cytoplasm.
Nitrate reductase A is a heterotrimer composed of the α-, β- and γ chains. A fourth polypeptide,
encoded by the narJ gene, is required for the incorporation of the molybdenum cofactor into NarG, the α
subunit |CITS: [92121125] [92186712] [9632249]|.
A crystal structure of the catalytic and electron transfer subunits (NarG and NarH) has been solved at 2.0 A
resolution |CITS: [14725769]|, and structures of the NarGHI complex both alone and in complex with the Q-site
inhibitor pentachlorophenol have been solved at 1.9 and 2 A resolution |CITS: [12910261][15122898][15615728]|.
)""",]},
'B1226' : {'ecocyc-rxns': {},'ucsd-rxns' : ['NO3R2pp','NO3R1pp',], 'protein-comments' : ["""(NarJ is parto of the redox enzyme maturation protein (REMP) family of chaperones |CITS: [15213747]|. NarJ acts as
a private chaperone during the incorporation of the molybdenum cofactor into NarG, the α subunit of nitrate
reductase A |CITS: [8793883][9305880][9632249][15247236]|.
NarJ, encoded by the third gene in the narGHJI operon, is not part of the final nitrate reductase A enzyme, but
is essential for nitrate reductase activity |CITS: [3053688][92186712][1732220]|. NarJ interacts with the NarG subunit
of the apoenzyme complex at two distinct sites. One site is located at the N terminus of NarG and interferes with
membrane anchoring of the complex |CITS: [16286471][16540088]|, while the second site is involved in the insertion
of the molybdenum cofactor, which precedes membrane anchoring |CITS: [16286471]|. Thus, NarJ appears to
coordinate the final assembly and cofactor acquisition of nitrate reductase A.
Review: |CITS: [15213747]|)""",]},
'B1227' : {'ecocyc-rxns': {"""RXN0-3501""": """menaquinol + NO3- -> menaquinone-8 + nitrite + H2O""",},'ucsd-rxns' : ['NO3R2pp','NO3R1pp',], 'protein-comments' : ["""(The γ subunit of nitrate reductase A is a membrane-embedded heme-iron subunit resembling cytochrome b,
which transfers electrons from the quinone pool to the β subunit. There are two hemes present, a low-potential
heme bL and a high-potential heme bH |CITS: [92121125] [99435749]|.
Electrons are thought to transfer from the quinol binding site (Q-site) via heme bL and heme
bH to the [3Fe-4S] cluster of NarH |CITS: [11318649]|. The Q-site of NarI has been
characterized and is periplasmically oriented |CITS: [15615728]|.)""","""(E. coli contains three nitrate reductases. Two of them, nitrate reductase A (NRA) and nitrate reductase Z
(NRZ), are membrane bound and biochemically similar. The third nitrate reductase, Nap, is located in the periplasm.
Nitrate reductase A is expressed when levels of nitrate in the environment are high, Nap is expressed when they are
low, while NRZ expression is not dependent on nitrate levels or anaerobiosis, but induced during stationary phase.
Nitrate reductase A functions anaerobically as a terminal electron acceptor |CITS: [10464201]|. It accepts electrons
from the quinone pool and in so doing expels two protons from the cell, thereby adding to the proton motive force
|CITS: [12910261]|. Formate dehydrogenase N and nitrate reductase A form a respiratory chain, where a redox loop
of quinone molecules couples electron transfer from formate in the periplasm to nitrate in the cytoplasm.
Nitrate reductase A is a heterotrimer composed of the α-, β- and γ chains. A fourth polypeptide,
encoded by the narJ gene, is required for the incorporation of the molybdenum cofactor into NarG, the α
subunit |CITS: [92121125] [92186712] [9632249]|.
A crystal structure of the catalytic and electron transfer subunits (NarG and NarH) has been solved at 2.0 A
resolution |CITS: [14725769]|, and structures of the NarGHI complex both alone and in complex with the Q-site
inhibitor pentachlorophenol have been solved at 1.9 and 2 A resolution |CITS: [12910261][15122898][15615728]|.
)""",]},
'B2557' : {'ecocyc-rxns': {"""FGAMSYN-RXN""": """ATP + 5'-phosphoribosyl-N-formylglycineamide + L-glutamine + H2O -> ADP + phosphate + 5-phosphoribosyl-N-formylglycineamidine + L-glutamate""",},'ucsd-rxns' : ['PRFGS',], 'protein-comments' : ["""(Genetic complementation tests showed that the coli purL gene
was divided into three domains. The possible functions of domains I,
II, and III were assigned to be potential ATPase, triosephosphate
isomerase-like isomerase, and glutaminase, respectively. This argues
that the E. coli purL gene is a fused gene being composed of at least
three functionally different gene families. Domain III which resides
in the C-terminal region, is similar in amino acid sequence to several
glutamine amidotransferases and exerts the transfer of the amide
nitrogen of glutamine. Domain I resides in the N-terminal region and
contains a potential ATP binding motif. Domain II locates between
domains I and III and is composed of an alternating structure of at
least eight predicted beta-strand and alpha-helix elements, as has
been observed in the family of triosephosphate isomerases.|CITS:[90078226]|)""",]},
'B3137' : {'ecocyc-rxns': {"""TAGAALDOL-RXN""": """tagatose-1,6-bisphosphate = dihydroxy-acetone-phosphate + D-glyceraldehyde-3-phosphate""",},'ucsd-rxns' : ['TGBPA',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B3073' : {'ecocyc-rxns': {"""PUTTRANSAM-RXN""": """putrescine + α-ketoglutarate = 4-amino-butyraldehyde + L-glutamate""","""DIAMTRANSAM-RXN""": """an aliphatic α,ω-diamine + α-ketoglutarate = an aliphatic ω-aminoaldehyde + L-glutamate""",},'ucsd-rxns' : ['PTRCTA',], 'protein-comments' : ["""(Putrescine transaminase catalyzes the first step in the putrescine degradative pathway, whereby putrescine is
converted into 4-aminobutyrate via 4-aminobutyraldehyde |CITS: [86104419]|. The enzyme was originally purified
from E. coli B |CITS: [14154456]|.
Nitrogen limitation results in a 3- to 5-fold increase in ygjG levels |CITS: [11121068][12617754]|.
)""",]},
'B1380' : {'ecocyc-rxns': {"""DLACTDEHYDROGNAD-RXN""": """NAD+ + D-lactate = NADH + pyruvate""",},'ucsd-rxns' : ['LDH_D',], 'protein-comments' : ["""(D-lactate dehydrogenase, fermentative, is coded for by the
ldhA gene. A second gene, ldhB, is mentioned in the literature.
|CITS: [90198524]|)""",]},
'B3132' : {'ecocyc-rxns': {"""TAGAALDOL-RXN""": """tagatose-1,6-bisphosphate = dihydroxy-acetone-phosphate + D-glyceraldehyde-3-phosphate""",},'ucsd-rxns' : ['TGBPA',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B1386' : {'ecocyc-rxns': {"""AMINEPHEN-RXN""": """H2O + O2 + phenylethylamine = H2O2 + ammonia + phenylacetaldehyde""","""AMACETOXID-RXN""": """aminoacetone + H2O + O2 = methylglyoxal + ammonia + H2O2""","""AMINEOXID-RXN""": """an aliphatic amine + H2O + O2 = an aldehyde + ammonia + H2O2""",},'ucsd-rxns' : ['42A12BOOXpp','PEAMNOpp','TYROXDApp',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B2551' : {'ecocyc-rxns': {"""GLYOHMETRANS-RXN""": """5,10-methylene-THF + glycine + H2O = L-serine + tetrahydrofolate""",},'ucsd-rxns' : ['ALATA_D2','THRA2i','THRAi','ALATA_L2','GHMT2r',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B0674' : {'ecocyc-rxns': {"""ASNSYNB-RXN""": """L-glutamine + L-aspartate + ATP + H2O -> L-glutamate + L-asparagine + diphosphate + AMP""",},'ucsd-rxns' : ['ASNS1',], 'protein-comments' : ["""(AsnB belongs to the family of glutamine amidotransferases |CITS: [9559052]|. The crystal structure of AsnB has
been determined at 2.0 A resolution |CITS: [10587437]|.
Mutational studies in Klebsiella aerogenes show that in the absence of asparagine synthetase B, the
ammonia-dependent asparagine synthetase A enzyme is not sufficient for growth on poor nitrogen sources. The
asnA asnB double mutant is an asparagine auxotroph |CITS: [6125499]|.
)""","""NIL""",]},
'B3709' : {'ecocyc-rxns': {"""TRANS-RXN-76""": """L-tryptophan[periplasmic space] + H+[periplasmic space] =L-tryptophan[cytosol] + H+[cytosol] """,},'ucsd-rxns' : ['TRPt2rpp',], 'protein-comments' : ["""(TnaB is one of three known transporters for tryptophan in E. coli,
the others being Mtr and AroP. The tnaB gene is located in an operon
with the tnaA gene, encoding tryptophanase |CITS: [82007678]
[90264301] [91216998]|. Transcription of the tnaAB operon is
regulated by tryptophan-induced transcriptional antitermination
and is subject to catabolite repression |CITS: [82007678] [90264301]|.
Whole cell transport experiments have indicated that TnaB is a low affinity
tryptophan transporter (Km of about 70 μM) |CITS: [BURROUS1963] [82284004]|.
TnaB is a member of the ArAAAP family of amino acid transporters and is
homologous to the Mtr and TyrP transporters of E. coli |CITS: [91216998]|.
Examination of mtr, aroP and tnaB mutants under
various growth conditions has shown that TnaB is essential for growth
on tryptophan as the sole carbon source |CITS: [92011357]| and its primary
role is probably uptake of tryptophan for catabolic purposes.
Imported tryptophan can be utilised as a carbon and nitrogen source following
its degradation to indole, pyruvate and ammonia by tryptophanase.)""",]},
'B3708' : {'ecocyc-rxns': {"""LCYSDESULF-RXN""": """L-cysteine + H2O = pyruvate + ammonia + hydrogen sulfide""","""TRYPTOPHAN-RXN""": """L-tryptophan + H2O = indole + pyruvate + ammonia""",},'ucsd-rxns' : ['TRPAS2','CYSDS','SERD_L',], 'protein-comments' : ["""(Several distinct proteins exhibit cysteine desulfhydrase activity, which is involved in cysteine degradation |CITS: [12883870]|. The tnaA and metC genes each encode a cysteine desulfhydrase, as does an additional, as-yet unidentified gene |CITS: [12883870]|.
Regulation has been described |CITS: [12883870]|. Production of the protein is induced by L-cysteine |CITS: [12883870]|.)""","""NIL""",]},
'B4131' : {'ecocyc-rxns': {"""LYSDECARBOX-RXN""": """L-lysine = CO2 + cadaverine""",},'ucsd-rxns' : ['LYSDC',], 'protein-comments' : ["""NIL""","""(Lysine decarboxylase is a biodegradative enzyme. It is induced under acidic pH conditions and is thought to play a
role in maintaining pH homeostasis or extending the growth period by detoxification of the extracellular medium.
The enzyme is a polydimer with fivefold symmetry. The resulting decamer can dissociate reversibly into five dimers or
aggregate further to higher molecular weight species, appearing as stacks of decamers |CITS: [74086943]|.
There are two lysine decarboxylases in E. coli, encoded by the cadA and ldcC genes
|CITS: [9534244][9339543][9226257]|. The CO2 produced by CadA may be physiologically important
when the TCA cycle is down-regulated under conditions of anaerobiosis and low pH, and its CO2
production is therefore reduced |CITS: [8022268]|. Overproduction of CadA affects the growth rate |CITS: [9531770]|.
A speA speB speC speD cadA quintuple mutant is viable, albeit slow growing, on media deficient in amines,
indicating that polyamines are not required for growth |CITS: [7002915]|.
Loss of CadA is involved in virulence of Shigella species |CITS: [9520472][11207548][11705922]|; the cadAB
operon has similarity to the Salmonella typhimurium cadAB operon, which is involved in the acid
tolerance response (ATR) |CITS: [8736539]|.
Regulation has been described |CITS: [2527331], [1556086], [8381784], [8022268],
[8195083], [7830562], [7836317], [9075621], [9172436], [9171439], [9692215], [9692215], [8808945], [6767681], [7001435], [1370290]|.)""",]},
'B1241' : {'ecocyc-rxns': {"""PFLDEACTIV-RXN""": """pyruvate formate-lyase -> pyruvate formate-lyase (inactive)""","""ALCOHOL-DEHYDROG-GENERIC-RXN""": """an alcohol + NAD+ = NADH + an aldehyde or ketone""","""ALCOHOL-DEHYDROG-RXN""": """acetaldehyde + NADH = ethanol + NAD+""","""ACETALD-DEHYDROG-RXN""": """NAD+ + coenzyme A + acetaldehyde = NADH + acetyl-CoA""",},'ucsd-rxns' : ['ALCD2x','ACALD',], 'protein-comments' : ["""NIL""","""(A homopolymeric protein with three
Fe++-dependent catalytic functions: alcohol dehydrogenase,
acetaldehyde dehydrogenase and pyruvate formate-lyase deactivase. The
homopolymeric structure is unusual in that about 40 subunits are
helically arranged to form a rod-like ultrastructure. |CITS: [92388175]|)""",]},
'B0696' : {'ecocyc-rxns': {"""TRANS-RXN-2""": """K+[periplasmic space] + ATP + H2O =K+[cytosol] + ADP + phosphate """,},'ucsd-rxns' : ['Kabcpp',], 'protein-comments' : ["""NIL""","""(The kdpFABC genes encode an ATP-dependent high affinity P-Type ATPase potassium ion
transporter |CITS: [89078396] [89174642]|. The transporter has a high affinity and substrate specificity for
potassium ion (Km= 10 μM). It is activated by magnesium ion with an affinity constant of
80 μM |CITS: [89078396]|. ATP-driven potassium ion transport has been observed when the Kdp
complex is reconstituted in vesicles |CITS: [95204461]|. Kdp is unusual among P- type ATPases in
having three subunits: one for energy coupling (KdpB), one for substrate binding and transport (KdpA),
and one for associating the first two subunits together (KdpC) |CITS: [95204461]|. The largest subunit,
KdpB, is the homologue of other P-type ATPases. Neither of the other two subunits, KdpA or KdpC, has
homologues in other P-type ATPases. Mutation experiments have shown that all three subunits are
required for normal Kdp activity |CITS: [95204461]|. KdpA is highly hydrophobic with many predicted
membrane-spanning segments |CITS:[95204461]|. The fact that most mutants displaying lower affinity for
potassium ion had mutations that altered KdpA implies that KdpA has a major role in determining affinity for
potassium ion |CITS: [95204461]|. A truncated version of KdpA with only the N-terminal 135 amino acids
(which contains two transmembrane segments) is able to rescue a K+ transporter mutant in
media with low K+ concentration even without KdpA and KdpB. This is predicted to occur in
response to the membrane potential |CITS:[11344160]|. KdpC is predicted to have only a single
membrane-spanning segment |CITS:[95204461]|. Complementation experiments with complete and
truncated KdpC proteins and hybrids as well as sequence analysis of KdpC proteins have identified 4
major parts to the protein. There are two highly conserved regions (regions 2 and 4) and two highly
variable regions (1 and 3). Region 1, the N-terminal region, is predicted to be the membrane spanning
segment |CITS:[11248697]|. Mutational analysis also showed that KdpC is involved in linking KdpA and
KdpB together, serving to assemble and stabilize the KdpFABC complex |CITS: [99077600]|. A fourth gene
on the same operon, kdpF, encodes a small non-essential polypeptide, which was shown by
SDS-polyacrylamide gel analysis of the transporter complex to be associated with and stabilize the
KdpFABC complex in vivo |CITS: [99005984] [20076462]|. The kdp genes are expressed
when growth is limited by the availability of potassium ion |CITS:[89078396]|. Two other important
potassium ion uptake systems in E. coli include Trk and Kup |CITS: [95204461]|.)""",]},
'B0104' : {'ecocyc-rxns': {"""GMP-REDUCT-RXN""": """ammonia + inosine-5'-phosphate + NADP+ -> GMP + NADPH""",},'ucsd-rxns' : ['GMPR',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B1592' : {'ecocyc-rxns': {"""TRANS-RXN-139""": """chloride[periplasmic space] =chloride[cytosol] """,},'ucsd-rxns' : ['CLt3_2pp',], 'protein-comments' : ["""(YnfJ is an uncharacterized member of the
ClC family of chloride ion channels |CITS: [99184734]|.
Based on sequence similarity it may function as a
chloride ion channel.)""",]},
'B0031' : {'ecocyc-rxns': {"""DIHYDROPICRED-RXN""": """tetrahydrodipicolinate + NAD(P)+ -> L-2,3-dihydrodipicolinate + NAD(P)H + H+""",},'ucsd-rxns' : ['DHDPRy',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B1590' : {'ecocyc-rxns': {"""DIMESULFREDUCT-RXN""": """dimethyl sulfoxide + H+ + menaquinol -> dimethylsulfide + H2O + menaquinone-8""",},'ucsd-rxns' : ['TMAOR1','DMSOR1',], 'protein-comments' : ["""(YnfH contains eight potential transmembrane helices and is similar to DmsC, the membrane anchor subunit of the
dimethyl sulfoxide reductase heterotrimer. When expressed together with DmsA and either DmsB or YnfG in a
plasmid expression system, YnfH can form a complex with DmsA and DmsB/YnfG and support growth on DMSO
|CITS: [14522592]|.)""","""(A strain carrying a deletion of dmsABC and containing ynfFGH on a multicopy plasmid is able to grow
poorly under anaerobic conditions utilizing dimethyl sulfoxide as a terminal oxidant. The physiological substrate for
this enzyme is unknown |CITS: [14522592]|.)""",]},
'B4138' : {'ecocyc-rxns': {"""TRANS-RXN-106C""": """a C4-dicarboxylate[periplasmic space] + succinate[cytosol] =succinate[periplasmic space] + a C4-dicarboxylate[cytosol] ""","""TRANS-RXN-106B""": """a C4-dicarboxylate[periplasmic space] + malate[cytosol] =malate[periplasmic space] + a C4-dicarboxylate[cytosol] ""","""TRANS-RXN-106A""": """a C4-dicarboxylate[periplasmic space] + L-aspartate[cytosol] =L-aspartate[periplasmic space] + a C4-dicarboxylate[cytosol] ""","""TRANS-RXN-106""": """a C4-dicarboxylate[periplasmic space] + fumarate[cytosol] =fumarate[periplasmic space] + a C4-dicarboxylate[cytosol] """,},'ucsd-rxns' : ['ASPt2_3pp','MALt2_3pp','SUCFUMtpp','SUCCt2_3pp','FUMt2_3pp',], 'protein-comments' : ["""(The DcuA transporter is one of three transporters known to be
responsible for the uptake of C4-dicarboxylates such as fumarate under
anaerobic conditions. DcuA and DcuB are homologous transporters
which function as independent and mutually redundant C4-dicarboxylate
(aspartate, malate, fumarate and succinate) transporters. The third
anaerobic dicarboxylate transporter is DcuC. Mutations in either
dcuA or dcuB did not greatly affect anaerobic
growth on C4 dicarboxylates, but a double dcuA dcuB mutant
was severely impaired |CITS: [95050204]|. Whole cell transport
experiments have indicated that both DcuA and DcuB catalyse C4
dicarboxylate exchange, for instance fumarate uptake in exchange
for succinate with a Km for fumarate of approx 30 μM |CITS: [95050204]|.
dcuA is located downstream of aspA encoding aspartase and
dcuB is upstream of fumB encoding anaerobic fumarase implying
their physiological functions may be to catalyze aspartate:fumarate and
fumarate:malate exchange during the anaerobic utilization of aspartate and
fumarate, respectively |CITS: [95050204]|. However, their transport
specificities do not fully support this notion.
DcuA and DcuB are the prototype representatives of the Dcu family of
dicarboxylate transporters.
Expression of dcuA has been shown to be constitutive while
expression of dcuB is induced anaerobically by FNR and by
C-4 dicarboxylates |CITS: [99069334]|.
)""",]},
'B2436' : {'ecocyc-rxns': {"""RXN0-1461""": """coproporphyrinogen III + O2 + 2 H+ = protoporphyrinogen IX + 2 CO2 + 2 H2O""",},'ucsd-rxns' : ['CPPPGO',], 'protein-comments' : ["""NIL""",]},
'B0677' : {'ecocyc-rxns': {"""NAG6PDEACET-RXN""": """H2O + N-acetyl-D-glucosamine-6-phosphate -> acetate + D-glucosamine-6-phosphate""",},'ucsd-rxns' : ['AGDC',], 'protein-comments' : ["""(Regulation has been described |CITS: [12813061]|. Transcription is regulated by Mg2+ |CITS: [12813061]|. Transcription is regulated by PhoP |CITS: [12813061]|.)""","""NIL""",]},
'B1759' : {'ecocyc-rxns': {"""RXN0-383""": """CTP + H2O = CMP + diphosphate""",},'ucsd-rxns' : ['NTPP4','NTPP3',], 'protein-comments' : ["""(NudG is a member of the Nudix hydrolase family and shows high specificity for hydrolysis of pyrimidine
(deoxy)nucleoside triphosphates |CITS: [21101911]|. The enzyme hydrolyzes oxidized nucleotides and is therefore
expected to function in DNA damage avoidance |CITS: [11676470]|. Its preferred substrate appears to be
5-hydroxy-CTP |CITS: [12509230]|.
A nudG deletion strain exhibits a 2-3-fold elevated rate of H2O2-induced mutations, while overexpression of
nudG suppressed mutations |CITS: [14750949]|. Site-directed mutagenesis of various conserved amino acid
residues has been performed |CITS: [15381107]|, and residues involved in substrate binding have been identified
|CITS: [15823026]|.)""",]},
'B1693' : {'ecocyc-rxns': {"""3-DEHYDROQUINATE-DEHYDRATASE-RXN""": """3-dehydroquinate = H2O + 3-dehydro-shikimate""",},'ucsd-rxns' : ['DHQD',], 'protein-comments' : ["""(Comparisons of the coli
3-dehydroquinase sequence and with the partial sequence of arom gene
of aspergillus nidulans, which is known to include the
3-dehydroquinase domain, reveals significant homologies.)""","""NIL""",]},
'B1692' : {'ecocyc-rxns': {"""SHIKIMATE-5-DEHYDROGENASE-RXN""": """NADP+ + shikimate = NADPH + 3-dehydro-shikimate""",},'ucsd-rxns' : ['SHK3Dr',], 'protein-comments' : ["""(The ydiB gene encodes a quinate/shikimate dehydrogenase |CITS: [12637497]|.
Crystal structures of the enzyme are presented at 2.3 A resolution |CITS: [12624088]| and 2.5 A resolution |CITS: [12637497]|. The structure is discussed with respect to the enzyme catalytic mechanism |CITS: [12624088], [12637497]|. YdiB copurifies with NAD |CITS: [12624088]| and can use NAD or NADP in the reaction |CITS: [12637497]|.)""",]},
'B1463' : {'ecocyc-rxns': {"""2.3.1.118-RXN""": """an N-hydroxy-arylamine + acetyl-CoA = an N-acetoxyarylamine + coenzyme A""",},'ucsd-rxns' : ['ACANTHAT',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B2049' : {'ecocyc-rxns': {"""MANNPGUANYLTRANGDP-RXN""": """α-D-mannose 1-phosphate + GDP = GDP-D-mannose + phosphate""",},'ucsd-rxns' : ['MAN1PT2',], 'protein-comments' : ["""NIL""",]},
'B3752' : {'ecocyc-rxns': {"""RIBOKIN-RXN""": """D-ribose + ATP -> D-ribose-5-phosphate + ADP""",},'ucsd-rxns' : ['RBK',], 'protein-comments' : ["""(A crystal structure of ribokinase has been determined. The structure suggested that ion binding leads to a
conformational change and activation of the enzyme |CITS: [11786021]|.
The significance of ribokinase for utilization of ribose has been studied |CITS: [4889152]|.)""",]},
'B1713' : {'ecocyc-rxns': {"""PHENYLALANINE--TRNA-LIGASE-RXN""": """tRNAphe + L-phenylalanine + ATP -> L-phenylalanyl-tRNAphe + diphosphate + AMP""",},'ucsd-rxns' : ['PHETRS',], 'protein-comments' : ["""(The β subunit of PheRS contains the Phe-tRNAPhe binding site |CITS: [7043240][3893548]|. The
editing site of the enzyme localizes to the B3/B4 domain of the β subunit |CITS: [15526031]|.
Isolated β subunits exist primarily as monomers |CITS: [1915899]|.)""","""(Phenylalanyl-tRNA synthetase (PheRS) is a member of the family of aminoacyl-tRNA synthetases, which interpret the
genetic code by covalently linking amino acids to their specific tRNA molecules. The reaction is driven by ATP
hydrolysis. PheRS belongs to the Class II aminoacyl tRNA synthetases, which share three regions of homology
|CITS: [2203971][1852601]|.
PheRS is a tetramer consisting of two α and two β subunits. Both subunits are required for catalytic
activity |CITS: [4603142][6360212]|. Two molecules of tRNAPhe bind to one PheRS complex
|CITS: [6337625]|, and both binding sites are active sites |CITS: [170267][793866]|. Binding is not dependent on
Mg2+ |CITS: [1100384]|.
The reaction mechanism of PheRS includes the formation of an aminoacyl adenylate intermediate, which then serves
as the animo acid donor in the aminoacyl-tRNA synthetase reaction |CITS: [320199]|. Binding of
tRNAPhe to PheRS induces a conformational change in the tRNA |CITS: [383142]| as well as in PheRS
|CITS: [7011376]|. Aminoacylation is limited by the kinetics of a conformational change of the
PheRS-Phe-tRNAPhe complex |CITS: [7046786][7046787]|. PheRS can aminoacylate a synthetic
substrate with a deoxyribose backbone (tDNA) |CITS: [2455342]|.
Specificity determinants within tRNAPhe that are important for recognition by PheRS and for attenuation
have been identified
|CITS: [776674][365576][3894009][3311746][2643111][2231729][2023934][1420156][7687542][8082771][8089840]|.
A synthetically constructed tRNAPhe(AAA) is not a good substrate for PheRS |CITS: [1370814]|.
Specificity determinants and residues within PheRS that are important for catalytic activity have been investigated
|CITS: [2823880]|. The Ala294 residue of the α subunit is involved in binding phenylalanine and influences
amino acid specificity by determining of the size of the binding pocket |CITS: [8003476]|.
A proofreading mechanism hydrolyzes a PheRS-tyrosine adenylate complex and Tyr-tRNAPhe
|CITS: [8003476][15526031]|. The editing site localizes to the B3/B4 domain of the β subunit |CITS: [15526031]|.
PheRS of E. coli B contains a proofreading activity which deacylates misacylated Ile-tRNAPhe
|CITS: [4558664][6222761]|.
Expression of pheST is derepressed by an attenuation mechanism when the level of aminoacylated
tRNAPhe is low |CITS: [6317865][6317866][6426518][3126825]| and by high levels of PheRS
|CITS: [3158742]|.
Review: |CITS: [10966471]|
)""",]},
'B2215' : {'ecocyc-rxns': {"""RXN0-2481""": """hydrophilic solute or ion < 600 Da[extracellular space] =hydrophilic solute or ion < 600 Da[periplasmic space] """,},'ucsd-rxns' : ['Htex','LEUtex','ALAALAtex','LYStex','ORNtex','O2Stex','UMPtex','GAMAN6Ptex','UDPACGALtex','INDOLEtex','3AMPtex','ACtex','GALBDtex','XTSNtex','THMtex','TRPtex','SERtex','CRNtex','SO4tex','ARGtex','ETHAtex','23CGMPtex','CLtex','ACSERtex','METSOX2tex','ACMANAtex','NOtex','DGSNtex','UDPGtex','23DAPPAtex','GLYCtex','MELIBtex','SO2tex','12PPDStex','GALURtex','23CAMPtex','GLUtex','DGMPtex','GSNtex','THYMtex','GLYBtex','NMNtex','GLCNtex','FE2tex','12PPDRtex','DALAtex','ALAtex','Zn2tex','HCINNMtex','ACGAL1Ptex','TSULtex','THMDtex','ACNAMtex','CGLYtex','DOPAtex','GTHRDtex','AGMtex','G3PStex','PSCLYStex','HOMtex','GBBTNtex','DMStex','HG2tex','PItex','IDONtex','GLCtex','TYRtex','MOBDtex','ASNtex','ACGALtex','NO3tex','NAtex','PACALDtex','PPPNtex','DSERtex','ACMUMtex','PPALtex','HIStex','DINStex','TCYNTtex','SULFACtex','OCTAtex','CD2tex','URAtex','GALCTtex','TUNGStex','SO3tex','METDtex','TMAOtex','CYANtex','MSO3tex','TMAtex','GALCTNLtex','ALLtex','PYRtex','D-LACtex','BUTtex','XMPtex','MMETtex','5DGLCNtex','ALLTNtex','G3PCtex','CYStex','GLYCAtex','MNtex','G3PEtex','ASO3tex','TYRPtex','GLYtex','L-LACtex','FORtex','PNTOtex','ETOHtex','SPMDtex','HPPPNtex','GDPtex','BALAtex','FRULYStex','TARTRtex','3GMPtex','MNLtex','DCMPtex','AMPtex','ACGAtex','ACACtex','SUCCtex','FALDtex','PEAMNtex','SUCRtex','UDPGALtex','PPAtex','PROtex','XANtex','PPTtex','ASPtex','HXAtex','SKMtex','HYXNtex','TREtex','CO2tex','PROGLYtex','MALtex','ILEtex','GLCUR1Ptex','UREAtex','DAPtex','GLNtex','CSNtex','PTRCtex','XYLtex','O2tex','DAMPtex','G3PGtex','3PEPTtex','VALtex','AKGtex','METtex','ASCBtex','SBTtex','3CMPtex','GLYC2Ptex','GLYALDtex','G6Ptex','NO2tex','PSERtex','CYTDtex','H2tex','MANGLYCtex','DUMPtex','LYXtex','34dhpactex','R5Ptex','ARBtex','GAL1Ptex','FRUURtex','MG2tex','METSOX1tex','TAURtex','GALTtex','UDPGLCURtex','CYNTtex','23CCMPtex','G1Ptex','GLCRtex','IMPtex','RMNtex','DHAtex','GTPtex','FUCtex','ANHGMtex','GLYCLTtex','GALtex','CITtex','23CUMPtex','LCTStex','H2O2tex','OROTtex','DCAtex','NACtex','ACALDtex','CYSDtex','G3PItex','ISETACtex','ACGAM1Ptex','INSTtex','ABUTtex','GTHOXtex','DMSOtex','F6Ptex','GALCTNtex','26DAHtex','MAN6Ptex','GAMtex','GLYC3Ptex','GLCURtex','NI2tex','DIMPtex','THRPtex','MANtex','GMPtex','CU2tex','THRtex','XYLUtex','DTMPtex','TYMtex','4PEPTtex','ADEtex','RIBtex','H2Otex','ETHSO3tex','CA2tex','BUTSO3tex','3UMPtex','CUtex','4HOXPACDtex','NH4tex','UACGAMtex','Ktex','FE3tex','MALDtex','FRUtex','PHEtex','FUMtex','N2Otex','H2Stex','CMPtex','DDGLCNtex','COBALT2tex','CHLtex',], 'protein-comments' : ["""(OmpC is a member of the GMP family. It forms a trimeric porin allowing for ions and other hydrophilic solutes to cross the outer membrane.
(Neidhardt, F.C. Escherichia coli and Salmonella Cellular and Molecular Biology) The solutes tend to
be less than 500 Daltons or less. OmpC is tightly but noncovalently associated with the peptidoglycan layer. |CITS: [2903556]|
Double OmpC-OmpF mutants and OmpR mutants (incapable of synthesizing OmpC and OmpF) survive poorly in comparison to
single mutants of OmpC or OmpF when suspended in filtered-autoclaved water or sea water. This suggests that these two porins are crucial for entry into survival mode. |CITS: [14633108]|)""",]},
'B0612' : {'ecocyc-rxns': {"""TRANS-RXN-201""": """succinate[cytosol] + citrate[periplasmic space] =citrate[cytosol] + succinate[periplasmic space] """,},'ucsd-rxns' : ['CITt7pp',], 'protein-comments' : ["""(CitT is a probable citrate/succinate antiporter, responsible for
the uptake of citrate. In aerobic conditions, most E. coli strains do not utilise citrate
due to lack of citrate transport, although some strains carry a plasmid-encoded
citrate transporter |CITS: [86059247]|. Under anaerobic conditions, citrate
can be utilised if an oxidizable cosubstrate is present suchas glycerol or
glucose. Expression of the cloned citT gene conferred the ability to
utilise citrate in aerobic conditions. Whole cell transport assays indicated
that CitT mediated exchange of citrate with citrate, succinate, tartrate or
fumarate |CITS: [98361905]|. Since succinate is the end product of citrate
fermentation, it seems probable that CitT functions physiologically as a
citrate/succinate exchanger in anaerobic conditions |CITS: [98361905]|.
Consistent with this supposition, CitT is a member of the DASS family of
di- and tri-carboxylic acid transporters. The citT gene is located in
an operon including the genes for citrate lyase.)""",]},
'B0974' : {'ecocyc-rxns': {"""RXN0-4141""": """H2 + an acceptor = 2 H+ + a reduced acceptor""",},'ucsd-rxns' : ['HYD1pp','HYD2pp','HYD3pp',], 'protein-comments' : ["""(The hyaC gene product is very hydrophobic, rich in aromatic residues, and has four putative hydrophobic
membrane-spanning regions |CITS: [90202716]|.
An in-frame deletion in the hyaC gene results in wild-type levels of hydrogenase 1 activity, although resulting
in the appearance of multiple forms of the enzyme |CITS: [1856178]|.
Review: |CITS: [15119826]|
)""","""(Hydrogenase 1 mediates hydrogen uptake in the presence of high-potential acceptors such as ferricyanide and
phenazine methosulfate, but not low-potential acceptors |CITS: [11506918]|. The enzyme is more tolerant to oxygen
than hydrogenase 2, providing complementary redox properties to the cell |CITS: [12420163]|.
Hydrogenase 1 contains a [3Fe-4S] or [4Fe-4S] cluster (depending on oxidation state) and nickel |CITS: [8858127]|.
The substrate specificity of hydrogenase 1 for various quinones is unknown |CITS: [11506918]|.
HybG |CITS: [11292801]| and HybF |CITS: [12081959]| are involved in maturation of hydrogenase 1.
Review: |CITS: [15119826]|)""",]},
'B0973' : {'ecocyc-rxns': {"""RXN0-4141""": """H2 + an acceptor = 2 H+ + a reduced acceptor""",},'ucsd-rxns' : ['HYD1pp','HYD2pp','HYD3pp',], 'protein-comments' : ["""(HyaB is the large subunit of hydrogenase 1; it is thought to bind the Ni-Fe active site cofactor. Processing of HyaB
at the C terminus is required for the formation of active hydrogenase |CITS: [1856178]|; the cleavage is proposed to
take place at the conserved His582 residue |CITS: [8405419]|. Nickel binding is one of the requirements for C
terminal processing of the large subunit |CITS: [1558764]|.
Expression of the hya operon is induced under anaerobic conditions and by the presence of formate, but
repressed by nitrate |CITS: [8071220][10537212]|. Expression is increased under acidic conditions
|CITS: [10464194]|.
A hyaB in-frame deletion mutant does not have a defect in anaerobic growth with hydrogen and fumarate as
sole energy and carbon sources, while a hyaB hybC double mutant did not grow under these conditions
|CITS: [DUBINI02]|.
Review: |CITS: [15119826]|
)""","""(Hydrogenase 1 mediates hydrogen uptake in the presence of high-potential acceptors such as ferricyanide and
phenazine methosulfate, but not low-potential acceptors |CITS: [11506918]|. The enzyme is more tolerant to oxygen
than hydrogenase 2, providing complementary redox properties to the cell |CITS: [12420163]|.
Hydrogenase 1 contains a [3Fe-4S] or [4Fe-4S] cluster (depending on oxidation state) and nickel |CITS: [8858127]|.
The substrate specificity of hydrogenase 1 for various quinones is unknown |CITS: [11506918]|.
HybG |CITS: [11292801]| and HybF |CITS: [12081959]| are involved in maturation of hydrogenase 1.
Review: |CITS: [15119826]|)""",]},
'B0972' : {'ecocyc-rxns': {"""RXN0-4141""": """H2 + an acceptor = 2 H+ + a reduced acceptor""",},'ucsd-rxns' : ['HYD1pp','HYD2pp','HYD3pp',], 'protein-comments' : ["""(HyaA is the small subunit of hydrogenase 1. Insertion of the C-terminal transmembrane domain of HyaA into the
inner membrane is due to the Tat translocation system |CITS: [9660752][12940994]|.
Expression of the hya operon is induced under anaerobic conditions and by the presence of formate, but
repressed by nitrate |CITS: [8071220][10537212]|. Expression is increased under acidic conditions
|CITS: [10464194]|.
Review: |CITS: [15119826]|
)""","""(Hydrogenase 1 mediates hydrogen uptake in the presence of high-potential acceptors such as ferricyanide and
phenazine methosulfate, but not low-potential acceptors |CITS: [11506918]|. The enzyme is more tolerant to oxygen
than hydrogenase 2, providing complementary redox properties to the cell |CITS: [12420163]|.
Hydrogenase 1 contains a [3Fe-4S] or [4Fe-4S] cluster (depending on oxidation state) and nickel |CITS: [8858127]|.
The substrate specificity of hydrogenase 1 for various quinones is unknown |CITS: [11506918]|.
HybG |CITS: [11292801]| and HybF |CITS: [12081959]| are involved in maturation of hydrogenase 1.
Review: |CITS: [15119826]|)""",]},
'B2199' : {'ecocyc-rxns': {"""TRANS-RXN0-162""": """protoheme IX[cytosol] + ATP + H2O =phosphate + ADP + protoheme IX[periplasmic space] """,},'ucsd-rxns' : ['PHEMEabcpp',], 'protein-comments' : ["""(ccmC is a member of an operon whose gene products (CcmA-H) have been shown to be cytoplasmic membrane proteins required for cytochrome c maturation |CITS:[7635817]|. In ccmAB deletion mutants, heme incorporation into CcmE was found to take place provided that substantial amounts of CcmC was available |CITS:[10339610]|. A ccmC deletion mutant is deficient in its ability to produce c-type cytochromes |CITS:[9237661]|. CcmC is a membrane protein whose topology has been determined in homologues in other species |CITS:[9560218]| to consist of six transmembrane domains with two cytoplasmic and three periplasmic loops |CITS:[11384983]|. Studies using point mutations of conserved residues suggest that a hydrophobic, periplasmically situated surface of CcmC is critical for the binding of heme and its presentation to CcmE |CITS:[10998170]| which then binds heme covalently and transfers it to apocytochrome c |CITS:[10339610]|. Fusion protein studies suggest that CcmC is important in not only the transfer of heme to CcmE but also in its delivery to cytochrome c |CITS:[14532274]|.)""","""(The CcmABC (Cytochrome C Maturation proteins) putative transporter is a member of the ATP-Binding
Cassette (ABC) transporter superfamily |CITS: [98254124]|. Sequence analysis suggest that CcmA is the
ATP binding subunit and occurs as a homodimer and CcmB and CcmC are transmembrane domains.
CcmABC has been proposed to function as a heme exporter, which exports heme to the periplasm where it
is incorporated into cytochrome c apoproteins |CITS: [97438699]|. However, CcmC has been shown
to function independently and is essential for heme attachment to CcmE, a periplasmic heme chaperone,
that binds heme covalently in the periplasm and then acts as a heme donor for ligation to apocytochrome
c |CITS:[99272716]|. Analysis of a ccmA deletion mutant has suggested that CcmAB is not
essential for heme export |CITS: [20170685]|.)""","""(Type c cytochrome in Escherichia coli is only synthesized during anaerobic growth conditions |CITS:[8039676]|. CcmA-H in E. coli are cytoplasmic membrane proteins which together make up a type 1 cytochrome c biogenesis system |CITS:[7635817]|. All eight proteins have been shown to be required for cytochrome c maturation |CITS:[8830238]|, |CITS:[7635817]|. In cytochrome c biogenesis, apocytochrome c, is translocated across the cytoplasmic membrane into the periplasm through the sec secretion system |CITS:[9720859]| where it complexes with heme, also transported across the cytoplasmic membrane. While CcmA and CcmB have been shown to constitute an ABC transporter, and are required for proper cytochrome c maturation, they have not been shown to be required for heme transport |CITS:[10708391]|. An intramolecular disulfide bond in the apocyctochrome c must be reduced in order for the covalent attachment of heme cofactor to occur. CcmG and CcmH have been identified as having the characteristic C-X-X-C motif of oxidoreductases and to function in the redox pathway of cytochrome c maturation |CITS:[10841975]|, |CITS:[9914305]|. CcmE acts as a periplasmic heme chaperone, binding heme covalently and transferring it to apocytochrome c |CITS:[10339610]|. Heme binding to CcmE is dependent on the presence of CcmC while the small integral membrane protein CcmD has been shown to play a role in CcmE stabilization |CITS:[10339610]|. Results of mutation deletion studies suggest that a periplasmically-situated hydrophobic surface of CcmC binds heme and presents it to CcmE in the periplasm |CITS:[10998170]|. Studies of ccmD deletion mutants have shown that CcmD affects the level of CcmE in the cytoplasmic membrane and is critical for CcmE function |CITS:[10998170]|. Deletion mutation and immunoprecipitation studies suggest that CcmE shuttles between CcmC and CcmF for heme transfer to apocytochrome c |CITS:[14532274]|.)""",]},
'B0979' : {'ecocyc-rxns': {"""CYT-UBIQUINOL-OXID-RXN""": """ubiquinol-8 + O2 = ubiquinone-8 + 2 H2O""",},'ucsd-rxns' : ['CYTBDpp','CYTBD2pp',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B0477' : {'ecocyc-rxns': {"""GUANOSINEKIN-RXN""": """guanosine + ATP -> GMP + ADP""","""INOSINEKIN-RXN""": """inosine + ATP = inosine-5'-phosphate + ADP""",},'ucsd-rxns' : ['INSK','GSNK',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B2261' : {'ecocyc-rxns': {"""O-SUCCINYLBENZOATE-COA-SYN-RXN""": """2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate = O-succinylbenzoate + H2O""",},'ucsd-rxns' : ['SUCBZS',], 'protein-comments' : ["""NIL""",]},
'B3457' : {'ecocyc-rxns': {"""ABC-36-RXN""": """ATP + L-valine[periplasmic space] + H2O =ADP + phosphate + L-valine[cytosol] ""","""ABC-15-RXN""": """ATP + L-isoleucine[periplasmic space] + H2O =ADP + phosphate + L-isoleucine[cytosol] ""","""ABC-35-RXN""": """ATP + L-leucine[periplasmic space] + H2O =ADP + phosphate + L-leucine[cytosol] """,},'ucsd-rxns' : ['VALabcpp','THRabcpp','ALAabcpp','ILEabcpp','LEUabcpp','LEUabcpp',], 'protein-comments' : ["""NIL""","""(LivFGHMJ and LivFGHMK are two ATP-dependent high-affinity branched-chain amino acid transport
system and are members of the ATP Binding Cassette (ABC) Superfamily of transporters |CITS: [20053876]|.
The two systems are responsible for the high affinity transport of branched-chain amino acids in
E. coli. They have shared membrane and ATP-binding components but have distinctive periplasmic
binding proteins. Due to the different periplasmic binding components, the two complexes differ in their
binding specificity: LivFGHMK is specific for the transport of leucine, while LivFGHMJ is a transporter for
leucine, isoleucine, and valine |CITS: [85288998]|. Based on sequence similarity and hydrophobicity
analysis, LivJ and LivK are the two periplasmic animo acid-binding proteins, LivH and LivM are the
membrane components, and LivG and LivF are the ATP-binding component of the ABC transport
complexes |CITS: [90307651]|. Deletions each of the liv genes resulted in the inability to transport
leucine |CITS: [90307651]|. In addition, a deletion strain that does not express any of the liv genes
was unable to carry out high-affinity transport of leucine unless one of the binding protein genes and all of
the membrane complex genes were provided on a plasmid |CITS: [90307651]|. In a separate experiment,
liv gene mutants were found to be resistant to a toxic analog of leucine, azaleucine, due to its
inability in branched-chain amino acid transport |CITS: [85288998]|.)""","""(LivFGHMJ and LivFGHMK are two ATP-dependent high-affinity branched-chain amino acid transport
system and are members of the ATP Binding Cassette (ABC) Superfamily of transporters |CITS: [20053876]|.
The two systems are responsible for the high affinity transport of branched-chain amino acids in E. coli.
They have shared membrane and ATP-binding components but have distinctive periplasmic binding proteins.
Due to the different periplasmic binding components, the two complexes differ in their binding specificity:
LivFGHMK is specific for the transport of leucine, while LivFGHMJ is a transporter for leucine, isoleucine,
and valine |CITS: [85288998]|. Based on sequence similarity and hydrophobicity analysis, LivJ and LivK
are the two periplasmic animo acid-binding proteins, LivH and LivM are the membrane components, and
LivG and LivF are the ATP-binding component of the ABC transport complexes |CITS: [90307651]|.
Deletions each of the liv genes resulted in the inability to transport leucine |CITS: [90307651]|. In
addition, a deletion strain that does not express any of the liv genes was unable to carry out high-
affinity transport of leucine unless one of the binding protein genes and all of the membrane complex genes
were provided on a plasmid |CITS: [90307651]|. In a separate experiment, liv gene mutants were
found to be resistant to a toxic analog of leucine, azaleucine, due to its inability in branched-chain amino
acid transport |CITS: [85288998]|. This system has also been shown |CITS:[14702302]| to serve as a third (along
with the AroP and PheP systems) complex for transport of phenylanine across the inner membrane.)""",]},
'B3475' : {'ecocyc-rxns': {"""HOLO-ACP-SYNTH-RXN""": """apo-[acyl-carrier protein] + coenzyme A = adenosine-3',5'-bisphosphate + acyl carrier protein""",},'ucsd-rxns' : ['ACPS1',], 'protein-comments' : ["""NIL""",]},
'B2048' : {'ecocyc-rxns': {"""PHOSMANMUT-RXN""": """α-D-mannose 1-phosphate = mannose-6-phosphate""",},'ucsd-rxns' : ['PMANM',], 'protein-comments' : ["""NIL""",]},
'B0475' : {'ecocyc-rxns': {"""PROTOHEMEFERROCHELAT-RXN""": """Fe2+ + protoporphyrin IX = 2 H+ + protoheme IX""",},'ucsd-rxns' : ['FCLT',], 'protein-comments' : ["""(An hemH mutant shows a defect in iron incorporation into porphyrin that results in a
defect in assembly of membrane-associated succinate-ubiquinone reductase |CITS: [11405622]|.)""",]},
'B0181' : {'ecocyc-rxns': {"""UDPNACETYLGLUCOSAMACYLTRANS-RXN""": """(R)-3-hydroxymyristoyl-ACP + UDP-N-acetyl-D-glucosamine = UDP-3-O-(3-hydroxymyristoyl)-N-acetylglucosamine + acyl carrier protein""",},'ucsd-rxns' : ['UAGAAT',], 'protein-comments' : ["""(The structure of LpxA has been determined by X-ray crystallography to a resolution of 2.6 angstroms
|CITS:[7481807]|. Regulation has been described |CITS: [11544210]|. Transcription is induced by nalidixic
acid, but not by mitomycin C, and induction does not require LexA |CITS: [11544210]|.)""","""NIL""",]},
'B3182' : {'ecocyc-rxns': {"""RXN0-3461""": """EC# 3.4.99.-""","""3.4.16.4-RXN""": """D-alanyl-D-alanine + H2O = 2 D-alanine""",},'ucsd-rxns' : ['MDDCP2pp','MDDEP3pp','MDDEP2pp','MDDCP1pp','MDDEP4pp','MDDCP5pp','MDDCP4pp','MDDEP1pp','MDDCP3pp',], 'protein-comments' : ["""(DacB is a penicillin-sensitive protein that catalyzes both D-alanyl-D-alanine carboxypeptidase
and D-alanyl-D-alanine endopeptidase activities, though the former has been shown to
occur at low levels |CITS: [2046551][331322][16402224]|.
DacB has a twenty-residue amino-terminal signal sequence which is cleaved in mature protein.
It also has the characteristic β-lactamase / penicillin-binding protein active site
motifs of serine-x-x-lysine, serine-x-asparagine and lysine-threonine-glycine |CITS: [2040429]|.
DacB may also have two disulfide bridges, formed by the pairs cysteine-139-cysteine-153 and
cysteine-197-cysteine-214 |CITS: [1577694]|.
DacB forms an alpha helical structure in the presence of lipid, but unlike DacA appears to favor
surface rather than deep interaction with membranes |CITS: [12444970]|. This interaction
involves electrostatic rather than hydrophobic forces |CITS: [9858668]|.
DacB can be purified with the dye cibacron navyblue 2G-E |CITS: [1833192]|. It has also been
successfully crystallized on its own and bound to various antibiotics |CITS: [7707365][16411754]|.
Quadruple dacA dacB dacC dacD mutants are viable, as are strains deleted for eight of the known penicillin-binding
proteins, dacB among them |CITS: [8955390][10383966]|. DacB is not required for viability |CITS: [16402224]|.
Overexpression of DacB during early exponential growth leads to cell lysis |CITS: [11325933]|.)""",]},
'B2429' : {'ecocyc-rxns': {"""RXN0-17""": """N-acetylmuramate[periplasmic space] + phosphoenolpyruvate =MurNAc-6-P[cytoplasm] + pyruvate """,},'ucsd-rxns' : ['ACMUMptspp','SUCptspp',], 'protein-comments' : ["""(contains PTS Enzyme IIBC domains)""","""(MurP, the N-acetymuramic acid PTS permease, belongs to the functional superfamily of the
phosphoenolpyruvate (PEP)-dependent, sugar transporting phosphotransferase system (PTS). The PTS
transports and simultaneously phosphorylates its sugar substrates in a process called group translocation.
murP encodes the PTS EIIB and -C sugar-specific domains. The PTS EIIAGlc domain
is also required for transport. MurP functions in the uptake of exogenous N-acetylmuramic acid (MurNAc),
releasing the phosphate ester into the cell cytoplasm in preparation for metabolism. MurP and
EIIAGlc are required for growth on MurNAc as the sole carbon and energy source
|CITS:[15060041]|.
The overall PTS-mediated phosphoryl transfer reaction, requiring the two general energy coupling proteins
of the PTS, Enzyme I and HPr, as well as the three domains of the Enzyme II complex is:
PEP--> Enzyme I(his~~P) --> HPr(his~~P) --> IIA(his~~P) --> IIB(cys~~P) -(IIC)-> N-acetylmuramic acid-6-P.
)""",]},
'B3187' : {'ecocyc-rxns': {"""OPPSYN-RXN""": """a trans-polyisoprenyln-PP + Δ3-isopentenyl-PP = trans-polyisoprenyln+1-PP + diphosphate""",},'ucsd-rxns' : ['OCTDPS',], 'protein-comments' : ["""(The subunit structure is not known.)""",]},
'B1250' : {'ecocyc-rxns': {"""TRANS-RXN-143""": """K+[periplasmic space] =K+[cytosol] """,},'ucsd-rxns' : ['Kt2pp',], 'protein-comments' : ["""(Kch is an uncharacterized member of the Voltage-gated Ion Channel (VIC) Superfamily of transporters
|CITS: [94345058]|. The regulation and functional properties of the protein have not been extensively studied;
however, comparisons have often been made between Kch and the eukaryotic potassium channel proteins
|CITS: [98319474] [96421576] [94224769]|. Kch was solubilized and purified, and the biochemical properties
and structure of the protein were examined |CITS: [98319474]|. The primary structure of Kch shows the
presence of six apparent transmembrane regions with low overall sequence similarity to eukaryotic channels.
However, the potassium specific pore region (P-region) is 60-70% identical to corresponding regions in
various eukaryotic potassium channel proteins |CITS: [94224769]|. Although Kch shares similarities with
eukaryotic potassium channels, the actual physiological functions of the protein are unclear.
Kch was found, in random transposon mutagenesis studies, to be required for growth in optimum (rich
medium at 37 degrees C) growth conditions but not under cold conditions (15 degrees C) or in minimal
medium |CITS:[15380559]|.)""",]},
'B3956' : {'ecocyc-rxns': {"""PEPCARBOX-RXN""": """oxaloacetate + phosphate = phosphoenolpyruvate + H2O + CO2""",},'ucsd-rxns' : ['PPC',], 'protein-comments' : ["""(Mutants in the ppc gene have been isolated and studied |CITS: [1765093][2016273][3902793][7490260]|.
Overexpression of Ppc improves the growth yield on glucose |CITS: [8285716]| and increases production of
succinate from glucose by fermentation |CITS: [8633880]|. A ppc null mutant was also reported to show improved
growth yield on glucose |CITS: [14963616]|. Gene expression, enzyme activities, metabolite concentrations and
metabolic flux have been measured in a ppc mutant |CITS: [14963616][15158257]|.)""","""NIL""",]},
'B1252' : {'ecocyc-rxns': {"""RXN0-2121""": """cob(I)alamin[extracellular space] =cob(I)alamin[cytosol] ""","""RXN0-1565""": """cob(I)alamin[extracellular space] =cob(I)alamin[periplasmic space] ""","""RXN0-2181""": """ferric enterobactin[extracellular space] =ferric enterobactin[cytosol] ""","""RXN0-1682""": """ferric enterobactin[extracellular space] =ferric enterobactin[periplasmic space] ""","""RXN0-2241""": """iron (III) hydroxamate complex[extracellular space] =iron (III) hydroxamate complex[cytosol] ""","""RXN0-1701""": """iron (III) hydroxamate complex[extracellular space] =iron (III) hydroxamate complex[periplasmic space] ""","""RXN0-2261""": """ferric dicitrate[extracellular space] =ferric dicitrate[cytosol] ""","""RXN0-1684""": """ferric dicitrate[extracellular space] =ferric dicitrate[periplasmic space] """,},'ucsd-rxns' : ['FEENTERtonex','CPGNtonex','CBItonex','FE3DHBZStonex','FE3DHBZStonex','FEOXAMtonex','CBL1tonex','FECRMtonex','FE3HOXtonex','ADOCBLtonex','FE3DCITtonex',], 'protein-comments' : ["""(TonB is a cytoplasmic membrane protein which transduces the proton motive force (pmf) of the cytoplasmic
membrane to the outer membrane active transporters thus providing the energy source required for the import
of iron-siderophore complexes and vitamin B12 across the outer membrane |CITS:[9159515]|. TonB functions
as part of an energy transduction complex with ExbB and ExbD |CITS:[11934617]|. The crystal structure of a
92-residue fragment of TonB (TonB-92) has been determined to 1.13 A resolution |CITS:[15522863]|.)""","""(TonB is a cytoplasmic membrane protein which transduces the proton motive force (pmf) of the cytoplasmic
membrane to the outer membrane active transporters thus providing the energy source required for the import
of iron-siderophore complexes and vitamin B12 across the outer membrane |CITS:[9159515]|.
The amino-terminal signal sequence of TonB is thought to span the cytoplasmic membrane, with the rest
of the protein residing within the periplasmic space |CITS:[8316087]|. TonB has been shown to come into
close contact with proteins located in both membranes |CITS:[8344918]|. Sucrose density gradient
centrifugation studies found that TonB is distributed approximately equally in the inner and outer
membrane fractions |CITS:[9159515]|. In conjunction with cytoplasmic membrane proteins ExbB
and ExbD, TonB forms an energy transduction complex which interacts with a variety of outer membrane
active transporter proteins |CITS:[11934617]|. When complexed with ExbB and ExbD, TonB is
thought to adopt an energized conformation which is subsequently released from the cytoplasmic
membrane to the outer membrane whereupon it interacts with an array of outer membrane
proteins |CITS:[11872715]|. TonB is then thought to respond to the conformational changes
induced in the active transport proteins upon substrate binding |CITS:[9353297]|, releasing its
stored energy to the active transporters and reassociating with ExbB and ExbD at the cytoplasmic
membrane to be re-energized |CITS:[12823822]|.)""","""(The Outer Membrane Ferric Citrate Transport System is responsible for the transport of ferric
citrate across the outer membrane by FecA energized by the TonB energy transducing system.)""","""NIL""","""NIL""","""NIL""","""NIL""","""(FepA is a 22-stranded membrane-spanning beta barrel protein in the outer membrane. FepA is a TonB dependent active transporter
that recognizes ferric enterobactin and translocates the molecule across the outer membrane into the periplasm. FepB is a
periplasmic binding protein that binds ferric enterobactin for transport across the inner membrane by the FepCDG ABC transporter.)""","""NIL""","""NIL""",]},
'B2423' : {'ecocyc-rxns': {"""ABC-7-RXN""": """ATP + thiosulfate[periplasmic space] + H2O =ADP + phosphate + thiosulfate[cytosol] ""","""ABC-70-RXN""": """sulfate[periplasmic space] + H2O + ATP =sulfate[cytosol] + phosphate + ADP """,},'ucsd-rxns' : ['TSULabcpp','TSULabcpp','SULabcpp','SULabcpp',], 'protein-comments' : ["""NIL""","""(CysATWP-Sbp is a sulfate transporter that is a member of the ATP-Binding Cassette (ABC) Superfamily
of transporters |CITS: [96381453]|. Based on sequence similarity, CysA is the ATP-binding component;
CysT and CysW are the membrane components, CysP is the periplasmic thiosulfate-binding component,
and Sbp is the periplasmic sulfate-binding component of the ABC transporter |CITS: [90264334] [95332222]|.
Single cysP and spb insertional mutants are able to utilized both sulfate and thiosulfate as a
sole sulfur source; however, both mutants have impaired growth compared with the wild-type strain,
suggesting that both proteins are required for the normal transport of these ions |CITS: [95332222]|. The
inactivation of both cysP and spb genes blocks the transport of both sulfate and thiosulfate,
and the transport activity is restored by the presence of intact copies of either the cysP or sbp
gene |CITS:[95332222]|. These results indicate that the two binding proteins have partially overlapping
activities, and that a single mutation, inactivating only one of them does not completely inactivate
thiosulfate and sulfate uptake. CysP and Sbp are therefore an example of periplasmic binding proteins
having overlapping activities and interacting with the common membrane proteins, CysATW.)""","""(CysATWP-Sbp is a sulfate transporter that is a member of the ATP-Binding Cassette (ABC) Superfamily of
transporters |CITS: [96381453]|. Based on sequence similarity, CysA is the ATP-binding component; CysT
and CysW are the membrane components, CysP is the periplasmic thiosulfate-binding component, and
Sbp is the periplasmic sulfate-binding component of the ABC transporter |CITS: [90264334] [95332222]|.
Single cysP and spb insertional mutants are able to utilized both sulfate and thiosulfate as a
sole sulfur source; however, both mutants have impaired growth compared with the wild-type strain,
suggesting that both proteins are required for the normal transport of these ions |CITS: [95332222]|. The
inactivation of both cysP and spb genes blocks the transport of both sulfate and thiosulfate,
and the transport activity is restored by the presence of intact copies of either the cysP or sbp
gene |CITS:[95332222]|. These results indicate that the two binding proteins have partially overlapping
activities, and that a single mutation, inactivating only one of them does not completely inactivate
thiosulfate and sulfate uptake. CysP and Sbp are therefore an example of periplasmic binding proteins
having overlapping activities and interacting with the common membrane proteins, CysATW.)""",]},
'B2422' : {'ecocyc-rxns': {"""ABC-7-RXN""": """ATP + thiosulfate[periplasmic space] + H2O =ADP + phosphate + thiosulfate[cytosol] ""","""ABC-70-RXN""": """sulfate[periplasmic space] + H2O + ATP =sulfate[cytosol] + phosphate + ADP """,},'ucsd-rxns' : ['TSULabcpp','TSULabcpp','SULabcpp','SULabcpp',], 'protein-comments' : ["""NIL""","""(CysATWP-Sbp is a sulfate transporter that is a member of the ATP-Binding Cassette (ABC) Superfamily
of transporters |CITS: [96381453]|. Based on sequence similarity, CysA is the ATP-binding component;
CysT and CysW are the membrane components, CysP is the periplasmic thiosulfate-binding component,
and Sbp is the periplasmic sulfate-binding component of the ABC transporter |CITS: [90264334] [95332222]|.
Single cysP and spb insertional mutants are able to utilized both sulfate and thiosulfate as a
sole sulfur source; however, both mutants have impaired growth compared with the wild-type strain,
suggesting that both proteins are required for the normal transport of these ions |CITS: [95332222]|. The
inactivation of both cysP and spb genes blocks the transport of both sulfate and thiosulfate,
and the transport activity is restored by the presence of intact copies of either the cysP or sbp
gene |CITS:[95332222]|. These results indicate that the two binding proteins have partially overlapping
activities, and that a single mutation, inactivating only one of them does not completely inactivate
thiosulfate and sulfate uptake. CysP and Sbp are therefore an example of periplasmic binding proteins
having overlapping activities and interacting with the common membrane proteins, CysATW.)""","""(CysATWP-Sbp is a sulfate transporter that is a member of the ATP-Binding Cassette (ABC) Superfamily of
transporters |CITS: [96381453]|. Based on sequence similarity, CysA is the ATP-binding component; CysT
and CysW are the membrane components, CysP is the periplasmic thiosulfate-binding component, and
Sbp is the periplasmic sulfate-binding component of the ABC transporter |CITS: [90264334] [95332222]|.
Single cysP and spb insertional mutants are able to utilized both sulfate and thiosulfate as a
sole sulfur source; however, both mutants have impaired growth compared with the wild-type strain,
suggesting that both proteins are required for the normal transport of these ions |CITS: [95332222]|. The
inactivation of both cysP and spb genes blocks the transport of both sulfate and thiosulfate,
and the transport activity is restored by the presence of intact copies of either the cysP or sbp
gene |CITS:[95332222]|. These results indicate that the two binding proteins have partially overlapping
activities, and that a single mutation, inactivating only one of them does not completely inactivate
thiosulfate and sulfate uptake. CysP and Sbp are therefore an example of periplasmic binding proteins
having overlapping activities and interacting with the common membrane proteins, CysATW.)""",]},
'B3189' : {'ecocyc-rxns': {"""UDPNACETYLGLUCOSAMENOLPYRTRANS-RXN""": """UDP-N-acetyl-D-glucosamine + phosphoenolpyruvate = UDP-GlcNAc-enolpyruvate + phosphate""",},'ucsd-rxns' : ['UAGCVT',], 'protein-comments' : ["""NIL""",]},
'B2425' : {'ecocyc-rxns': {"""ABC-70-RXN""": """sulfate[periplasmic space] + H2O + ATP =sulfate[cytosol] + phosphate + ADP ""","""ABC-7-RXN""": """ATP + thiosulfate[periplasmic space] + H2O =ADP + phosphate + thiosulfate[cytosol] """,},'ucsd-rxns' : ['TSULabcpp','SULabcpp',], 'protein-comments' : ["""NIL""","""(CysATWP-Sbp is a sulfate transporter that is a member of the ATP-Binding Cassette (ABC) Superfamily of
transporters |CITS: [96381453]|. Based on sequence similarity, CysA is the ATP-binding component; CysT
and CysW are the membrane components, CysP is the periplasmic thiosulfate-binding component, and
Sbp is the periplasmic sulfate-binding component of the ABC transporter |CITS: [90264334] [95332222]|.
Single cysP and spb insertional mutants are able to utilized both sulfate and thiosulfate as a
sole sulfur source; however, both mutants have impaired growth compared with the wild-type strain,
suggesting that both proteins are required for the normal transport of these ions |CITS: [95332222]|. The
inactivation of both cysP and spb genes blocks the transport of both sulfate and thiosulfate,
and the transport activity is restored by the presence of intact copies of either the cysP or sbp
gene |CITS:[95332222]|. These results indicate that the two binding proteins have partially overlapping
activities, and that a single mutation, inactivating only one of them does not completely inactivate
thiosulfate and sulfate uptake. CysP and Sbp are therefore an example of periplasmic binding proteins
having overlapping activities and interacting with the common membrane proteins, CysATW.)""",]},
'B2424' : {'ecocyc-rxns': {"""ABC-7-RXN""": """ATP + thiosulfate[periplasmic space] + H2O =ADP + phosphate + thiosulfate[cytosol] ""","""ABC-70-RXN""": """sulfate[periplasmic space] + H2O + ATP =sulfate[cytosol] + phosphate + ADP """,},'ucsd-rxns' : ['TSULabcpp','TSULabcpp','SULabcpp','SULabcpp',], 'protein-comments' : ["""NIL""","""(CysATWP-Sbp is a sulfate transporter that is a member of the ATP-Binding Cassette (ABC) Superfamily
of transporters |CITS: [96381453]|. Based on sequence similarity, CysA is the ATP-binding component;
CysT and CysW are the membrane components, CysP is the periplasmic thiosulfate-binding component,
and Sbp is the periplasmic sulfate-binding component of the ABC transporter |CITS: [90264334] [95332222]|.
Single cysP and spb insertional mutants are able to utilized both sulfate and thiosulfate as a
sole sulfur source; however, both mutants have impaired growth compared with the wild-type strain,
suggesting that both proteins are required for the normal transport of these ions |CITS: [95332222]|. The
inactivation of both cysP and spb genes blocks the transport of both sulfate and thiosulfate,
and the transport activity is restored by the presence of intact copies of either the cysP or sbp
gene |CITS:[95332222]|. These results indicate that the two binding proteins have partially overlapping
activities, and that a single mutation, inactivating only one of them does not completely inactivate
thiosulfate and sulfate uptake. CysP and Sbp are therefore an example of periplasmic binding proteins
having overlapping activities and interacting with the common membrane proteins, CysATW.)""","""(CysATWP-Sbp is a sulfate transporter that is a member of the ATP-Binding Cassette (ABC) Superfamily of
transporters |CITS: [96381453]|. Based on sequence similarity, CysA is the ATP-binding component; CysT
and CysW are the membrane components, CysP is the periplasmic thiosulfate-binding component, and
Sbp is the periplasmic sulfate-binding component of the ABC transporter |CITS: [90264334] [95332222]|.
Single cysP and spb insertional mutants are able to utilized both sulfate and thiosulfate as a
sole sulfur source; however, both mutants have impaired growth compared with the wild-type strain,
suggesting that both proteins are required for the normal transport of these ions |CITS: [95332222]|. The
inactivation of both cysP and spb genes blocks the transport of both sulfate and thiosulfate,
and the transport activity is restored by the presence of intact copies of either the cysP or sbp
gene |CITS:[95332222]|. These results indicate that the two binding proteins have partially overlapping
activities, and that a single mutation, inactivating only one of them does not completely inactivate
thiosulfate and sulfate uptake. CysP and Sbp are therefore an example of periplasmic binding proteins
having overlapping activities and interacting with the common membrane proteins, CysATW.)""",]},
'B1493' : {'ecocyc-rxns': {"""GLUTDECARBOX-RXN""": """L-glutamate -> CO2 + 4-aminobutyrate""",},'ucsd-rxns' : ['GLUDC',], 'protein-comments' : ["""(There are two distinct E. coli GAD polypeptides which are
highly similar to one another. They map to different positions and
neither is where the gene gadS is said to be located. |CITS: [92394884]|
Regulation has been described |CITS: [12940989]|.)""","""NIL""",]},
'B0038' : {'ecocyc-rxns': {"""RXN0-3601""": """L-carnitine + γ-butyrobetainyl-CoA = L-carnitinyl-CoA + γ-butyrobetaine""",},'ucsd-rxns' : ['CRNBTCT','CRNCBCT',], 'protein-comments' : ["""NIL""","""(The crystal structure of CaiB has been solved and shows that two monomers form an interlaced dimer
|CITS: [15518548]|.
CaiB was thought to be a carnitine dehydratase (|CITS: [2663076][8188598]|), but was later shown to be a type III
CoA transferase |CITS: [11551212]|. The purified CaiB likely contained small amounts of CaiD, accounting for the
observed activity |CITS: [11551212]|.
In E. coli strain O44 K74, the caiB gene product forms a complex with the caiA gene product,
crotonobetaine reductase. |CITS: [99227081]|)""",]},
'B3430' : {'ecocyc-rxns': {"""GLUC1PADENYLTRANS-RXN""": """α-D-glucose 1-phosphate + ATP -> ADP-D-glucose + diphosphate""",},'ucsd-rxns' : ['GLGC',], 'protein-comments' : ["""(Review: |CITS: [12794190]|)""","""NIL""",]},
'B3792' : {'ecocyc-rxns': {},'ucsd-rxns' : ['ECAtpp',], 'protein-comments' : ["""(WzxE is a "flippase" responsible for movement of lipid III
(Fuc4NAc-ManNAcA-GlcNAc-P-P-undecaprenol)
across the membrane bilayer |CITS: [12621029]|.
The determinants of WzxE recognition of its substrate
have been examined |CITS: [12621029]|.
A wzxE mutant exhibits buildup of lipid III |CITS: [12621029]|.
A wzxE mutant also exhibits a defect in transport of an
N-acetylglucosaminylpyrophosphorylnerol substrate across
membranes in an in vitro system |CITS: [12621029]|.)""","""(The Enterobacterial Common Antigen biosynthesis protein complex is responsible for synthesizing ECA
polysaccharide chains from Lipid III precursors that have been transferred accross the inner membrane.)""",]},
'B3793' : {'ecocyc-rxns': {},'ucsd-rxns' : ['ECAP3pp','ECAP1pp','ECAP2pp',], 'protein-comments' : ["""(wzyE has been proposed to encode the polymerase involved in the assembly of linear ECA polysaccharide
chains |CITS: [11673418][12618464][12621029]|. A wzyE null mutant was reported to be unable to synthesize
ECA and to accumulate lipid III |CITS: [11673418]|.
A larger open reading frame in this region was originally thought to exist and encode the
4-alpha-L-fucosyltransferase, which is in fact encoded by the gene directly upstream of wzyE, rffT
|CITS: [11673418]|.)""","""(The Enterobacterial Common Antigen biosynthesis protein complex is responsible for synthesizing ECA
polysaccharide chains from Lipid III precursors that have been transferred accross the inner membrane.)""",]},
'B3790' : {'ecocyc-rxns': {"""TDPFUCACTRANS-RXN""": """dTDP-D-fucosamine + acetyl-CoA = dTDP-4-acetamido-4,6-dideoxy-D-galactose + coenzyme A""",},'ucsd-rxns' : ['TDPADGAT',], 'protein-comments' : ["""(The subunit structure is unknown.)""",]},
'B0811' : {'ecocyc-rxns': {"""ABC-12-RXN""": """ATP + L-glutamine[periplasmic space] + H2O =ADP + phosphate + L-glutamine[cytosol] """,},'ucsd-rxns' : ['GLNabcpp',], 'protein-comments' : ["""NIL""","""(The GlnHPQ high-affinity glutamine transport system is a member of the ATP-Binding Cassette (ABC)
Superfamily of transporters |CITS: [96381453]|. Based on sequence similarity, GlnH is the periplasmic
glutamine-binding protein, GlnQ is the ATP-binding component, and GlnP is the membrane component
of the ABC transporter. Mutation of glnP results in the impaired ability to transport glutamine as well
as the inability to utilized glutamine as a sole source of carbon |CITS: [82007680] [87115160]|. Expression
of the cloned glnHPQ genes on a plasmid vector restored the glnH, glnP, and
glnQ mutants' abilities to transport glutamine and utilize glutamine as a sole carbon source
|CITS: [87115160]|.)""",]},
'B0032' : {'ecocyc-rxns': {"""CARBPSYN-RXN""": """2 ATP + L-glutamine + CO2 + 2 H2O = carbamoyl-phosphate + L-glutamate + phosphate + 2 ADP""",},'ucsd-rxns' : ['CBPS',], 'protein-comments' : ["""(The small subunit is the amidotransferase
component of the enzyme. |CITS: [99190825]|)""","""NIL""",]},
'B0033' : {'ecocyc-rxns': {"""CARBPSYN-RXN""": """2 ATP + L-glutamine + CO2 + 2 H2O = carbamoyl-phosphate + L-glutamate + phosphate + 2 ADP""",},'ucsd-rxns' : ['CBPS',], 'protein-comments' : ["""(The large subunit is the synthetase component of the enzyme.
The large subunit alone can catalyze carbamyl phosphate
synthesis from ammonia, but not from glutamine. |CITS: [87166060]
[99190825]|)""","""NIL""",]},
'B0030' : {'ecocyc-rxns': {"""URIDINE-NUCLEOSIDASE-RXN""": """uridine + H2O -> uracil + D-ribose""","""RXN0-363""": """xanthosine + H2O -> xanthine + D-ribose""","""INOSINE-NUCLEOSIDASE-RXN""": """inosine + H2O -> hypoxanthine + D-ribose""","""ADENOSINE-NUCLEOSIDASE-RXN""": """adenosine + H2O -> adenine + D-ribose""","""RXN0-361""": """cytidine + H2O -> cytosine + D-ribose""","""RXN0-366""": """guanosine + H2O -> guanine + D-ribose""",},'ucsd-rxns' : ['XTSNH','ADNUC','URIH','CYTDH','INSH',], 'protein-comments' : ["""(The rihC gene encodes a ribonucleoside hydrolase
with a broad substrate specificity |CITS: [21125610]|. It has decreasing
activity in the order uridine > xanthosine > inosine >
adenosine > cytidine > guanosine |CITS: [21125610]|. There are two
other ribonucleoside hydrolases present in E. coli
encoded by the rihA and rihB genes, which have
different specificities |CITS: [21125610]|.
An rihA rihB rihC triple mutant does not exhibit an obvious growth defect |CITS: [11027694]|.
Regulation has been described |CITS: [11027694], [11544210]|. The rihA and rihC genes are subject to catabolite repression |CITS: [11027694]|. Transcription is induced by nalidixic acid, but not by mitomycin C, and induction does not require LexA |CITS: [11544210]|.
)""",]},
'B1528' : {'ecocyc-rxns': {"""TRANS-RXN-40""": """α-L-arabinose[cytosol] + H+[periplasmic space] =α-L-arabinose[periplasmic space] + H+[cytosol] """,},'ucsd-rxns' : ['MELIBt3ipp','ARBt3ipp','LCTSt3ipp',], 'protein-comments' : ["""(YdeA is a member of the major facilitator superfamily (MFS) of
transporters |CITS: [98190790]|. Overexpression of ydeA
interferes with induction of the arabinose operon and greatly
decreases levels of intracellular arabinose |CITS: [99194728]|.
This suggests that YdeA may function in arabinose efflux. Consistent with this,
YdeA shows greatest sequence similarity to AraJ and to bacterial
drug efflux proteins.
Disruption of ydeA suggests it is non-essential |CITS: [99194728]|.)""",]},
'B0036' : {'ecocyc-rxns': {"""RXN0-3561""": """L-carnitinyl-CoA = crotonobetainyl-CoA + H2O""","""CARNCOARACE-RXN""": """D-carnitinyl-CoA = L-carnitinyl-CoA""",},'ucsd-rxns' : ['CRNCAR','CRNCDH',], 'protein-comments' : ["""(CaiD is a member of the crotonase superfamily; it catalyzes the hydration of crotonobetainyl-CoA to carnityl-CoA and
can use crotonyl-CoA, but not crotonobetaine, as an alternative substrate |CITS: [11551212]|.
)""",]},
'B0037' : {'ecocyc-rxns': {"""DCARNCOALIG-RXN""": """coenzyme A + D-carnitine = D-carnitinyl-CoA + H2O""","""CROTCOALIG-RXN""": """coenzyme A + crotono-betaine = crotonobetainyl-CoA + H2O""","""LCARNCOALIG-RXN""": """coenzyme A + L-carnitine = L-carnitinyl-CoA + H2O""",},'ucsd-rxns' : ['CTBTCAL2','CRNCAL2','CRNDCAL2',], 'protein-comments' : ["""NIL""",]},
'B2954' : {'ecocyc-rxns': {"""RXN0-1603""": """XTP + H2O -> xanthosine-5-phosphate + diphosphate""","""RXN0-1602""": """dITP + H2O -> dIMP + diphosphate""",},'ucsd-rxns' : ['NTPP9','NTPP11','NTPP10',], 'protein-comments' : ["""(Purified RdgB exhibits nucleoside triphosphatase activity toward deoxyinosine triphosphate (dITP) and xanthosine
triphosphate (XTP), mutagenic products of purine nucleotide deamination, and may therefore act to reduce the
abundance of nucleotides that can be misincorporated during DNA replication
|CITS: [12730170][12791149][12297000]|. RdgB does not exhibit strong activity toward a dATP, dCTP, dGTP, or dTTP
substrate |CITS: [12297000]|.
An rdgB mutant exhibits increased intrachromosomal recombination, compared to wild type |CITS: [2442140]|.
An rdgB mutation causes SOS induction |CITS: [2442140]|. The elevated recombination and the SOS induction
of an rdgB mutant are suppressed by purA expression |CITS: [1991730]|. A recA200 rdgB double
mutant is inviable at elevated temperatures that are nonpermissive for the recA200 allele; under
nonpermissive conditions the double mutant exhibits DNA degradation and a defect in DNA replication, but no defect
in protein translation |CITS: [2442140]|. A moa rdgB double mutant exhibits hypersensitivity to
N-6-hydroxylaminopurine (HAP) that is suppressed by an nfi (endonuclease V) mutation; however, this strain
exhibits a high rate of mutation |CITS: [12730170]|. A rdgB recBC triple mutation is lethal while a rdgB
recF mutation is not, and a rdgB recBC mutant exhibits a chromosomal fragmentation phenotype that is
suppressed by an nfi mutation; taken together, these results indicate that the rdgB mutation results in
double-strand DNA breaks due to endonuclease V action, consistent with misincorporation of hypoxanthine and/or
xanthine during DNA replication |CITS: [12791149]|.
RdgB is similar to a purine-preferring Methanococcus jannaschii deoxyribonucleotide triphosphate
pyrophosphatase |CITS: [12730170][12297000]|.
RdgB: "Rec-dependent growth" |CITS: [2442140]|.)""",]},
'B0120' : {'ecocyc-rxns': {"""SAMDECARB-RXN""": """S-adenosyl-L-methionine = CO2 + S-adenosyl-L-methioninamine""",},'ucsd-rxns' : ['ADMDC',], 'protein-comments' : ["""(Adenosylmethionine decarboxylase is first synthesized as a proenzyme which is
cleaved post-translationally into two smaller polypeptides. |CITS: [88058963]|)""","""NIL""","""NIL""","""NIL""","""(Adenosylmethionine decarboxylases belong to unique group of enzymes that contain a covalently bound
pyruvoyl prosthetic group.
The pyruvoyl group is thought to act analogously to pyridoxal phosphate cofactor by forming a Schiff base
with the amino group of the substrate and then serving as an electron sink to facilitate the
decarboxylation |CITS: [91208149]|.
Proteins that contain such group are expressed as a zymogen which is processed post-translationally
by a self-maturation cleavage called serinolysis. In this process the pyruvoul group is formed from a
serine residue, splitting the presursor protein into two parts.
The |FRAME:EG10962| gene of |FRAME:ECOLI| codes for a single polypeptide of 30.4 kDa.
S- adenosylmethionine decarboxylase is first formed as a 30.4 kDa polypeptide and
is then cleaved at the Lys111- Ser112 peptide bond to form a 12.4 kDa subunit and a 18 kDa
subunit. The latter subunit contains the pyruvoyl moiety |CITS:[3316212]|.
The final adenosylmethionine decarboxylase is a heterooctamer composed
of four alpha- and four beta-chains |CITS: [88058963]|.)""","""NIL""","""(Adenosylmethionine decarboxylases belong to unique group of enzymes that contain a covalently bound
pyruvoyl prosthetic group.
The pyruvoyl group is thought to act analogously to pyridoxal phosphate cofactor by forming a Schiff base
with the amino group of the substrate and then serving as an electron sink to facilitate the
decarboxylation |CITS: [91208149]|.
Proteins that contain such group are expressed as a zymogen which is processed post-translationally
by a self-maturation cleavage called serinolysis. In this process the pyruvoul group is formed from a
serine residue, splitting the presursor protein into two parts.
The |FRAME:EG10962| gene of |FRAME:ECOLI| codes for a single polypeptide of 30.4 kDa.
S- adenosylmethionine decarboxylase is first formed as a 30.4 kDa polypeptide and
is then cleaved at the Lys111- Ser112 peptide bond to form a 12.4 kDa subunit and a 18 kDa
subunit. The latter subunit contains the pyruvoyl moiety |CITS:[3316212]|.
The final adenosylmethionine decarboxylase is a heterooctamer composed
of four alpha- and four beta-chains |CITS: [88058963]|.)""",]},
'B4383' : {'ecocyc-rxns': {"""D-PPENTOMUT-RXN""": """deoxyribose-1-phosphate = deoxyribose-5-phosphate""","""PPENTOMUT-RXN""": """ribose-1-phosphate = D-ribose-5-phosphate""",},'ucsd-rxns' : ['PPM2','PPM',], 'protein-comments' : ["""NIL""",]},
'B3940' : {'ecocyc-rxns': {"""ASPARTATEKIN-RXN""": """L-aspartate + ATP = L-aspartyl-4-phosphate + ADP""","""HOMOSERDEHYDROG-RXN""": """homoserine + NAD(P)+ = L-aspartate-semialdehyde + NAD(P)H + H+""",},'ucsd-rxns' : ['HSDy','ASPK',], 'protein-comments' : ["""NIL""","""(This reaction, the phosphorylation of aspartate, is the first step in the biosynthesis of 4 different amino acids,
namely lysine, methionine and threonine (through homoserine), and isoleucine (which is synthesized from threonine).
In E. coli there are three isozymes that catalyze this step, namely aspartate
kinase I, II and III. Each of the kinases is controlled by one of the end products of the different pathways
(threonine, methionine and lysine, respectively). Two of the three enzymes (aspartate kinase I and II) are
multifunctional proteins, also catalyzing the reaction of homoserine dehydrogenase |CITS: [4148765]|.
Aspartate kinase III does not have an associated homoserine dehydrogenase activity (it is not part of the lysine
biosynthesis pathway).
The two catalytic activities of aspartate kinase II are organized in two separate
domains |CITS: [78026516]|.
Synthesis of the enzyme is repressed by the MetJ protein and S-adenosylmethionine |CITS: [86103348]|.)""",]},
'B1119' : {'ecocyc-rxns': {"""N-ACETYLGLUCOSAMINE-KINASE-RXN""": """N-acetyl-D-glucosamine + ATP = N-acetyl-D-glucosamine-6-phosphate + ADP""",},'ucsd-rxns' : ['ACGAMK',], 'protein-comments' : ["""(N-acetyl-D-glucosamine (GlcNAc) is released in the cytoplasm during murein recycling. NagK is the only known
cytoplasmic GlcNAc kinase in E. coli |CITS: [15489439]|. The enzyme was originally purified and studied by
Asensio and Ruiz-Amil |CITS: [ASENSIO66]|.
Overexpression of nagK rescues the glucose auxotrophy of a glucokinase mutant, and the NagK protein
functions as a rudimentary glucokinase in vitro |CITS: [15157072]|. The Km of NagK for glucose
is 100-fold higher than its Km for GlcNAc |CITS: [15489439]|.
)""",]},
'B4245' : {'ecocyc-rxns': {"""ASPCARBTRANS-RXN""": """L-aspartate + carbamoyl-phosphate = carbamoyl-L-aspartate + phosphate""",},'ucsd-rxns' : ['ASPCT',], 'protein-comments' : ["""NIL""","""(The catalytic subunit is enzymatically active but lacks the
homotropic response to the substates, and is insensitive to inhibition
by CTP |CITS: [ColiSalII]|.)""","""(The enzyme is made up of two catalytic trimers (encoded by
the gene pyrB) and three regulatory dimers (encoded by the gene pyrI)
|CITS: [Prosite] [ColiSalII] [86033987]|.)""",]},
'B1033' : {'ecocyc-rxns': {"""GLYOXYLATE-REDUCTASE-(NADP+)-RXN""": """glycolate + NADP+ = NADPH + glyoxylate""","""RXN0-300""": """glycerate + NADP+ = hydroxypyruvate + NADPH""",},'ucsd-rxns' : ['GLYCLTDy','GLYCLTDx','HPYRRy','HPYRRx',], 'protein-comments' : ["""NIL""",]},
'B0273' : {'ecocyc-rxns': {"""ORNCARBAMTRANSFER-RXN""": """L-ornithine + carbamoyl-phosphate = citrulline + phosphate""",},'ucsd-rxns' : ['OCBT',], 'protein-comments' : ["""NIL""","""(In the test tube, not in the cell, a family of four isoenzymes forms by assortment of two
closely similar polypeptides, the chain F-monomer and chain I-monomer,
to give active trimers FFF, FFI, FII, and III. |CITS:
[77028751]|)""",]},
'B3751' : {'ecocyc-rxns': {"""ABC-28-RXN""": """ATP + D-ribose[periplasmic space] + H2O =ADP + phosphate + D-ribose[cytosol] """,},'ucsd-rxns' : ['RIBabcpp',], 'protein-comments' : ["""NIL""","""(RbsABC is an ATP-dependent ribose transporter that is a member of the ATP-Binding Cassette (ABC)
Superfamily of transporters |CITS: [99121048]|. Based on sequence similarity, RbsA is the ATP-binding
constituent, RbsB is the periplasmic substrate-binding protein, and RbsC form the transmembrane
constituent of the transporter |CITS: [99121048]|. Mutations in each of the components eliminated transport
of ribose at external concentration of 1 μM, indicating that the components make up a transport system
that is responsible for high-affinity ribose transport. However, these mutants are able to grow normally on
high concentrations of the sugar, suggesting that there is at least a second, low-affinity transport system for
ribose in E. coli |CITS: [84212237]|. Hydrophobicity analysis has shown that RbsC contains six
transmembrane helices, while alkaline phosphatase fusions and the use of inside-out vesicles with proteolysis
have shown that the C and N termini are both on the cytoplasmic side of the membrane.)""",]},
'B4244' : {'ecocyc-rxns': {"""ASPCARBTRANS-RXN""": """L-aspartate + carbamoyl-phosphate = carbamoyl-L-aspartate + phosphate""",},'ucsd-rxns' : ['ASPCT',], 'protein-comments' : ["""NIL""","""(The regulatory subunit is catalytically inactive but
contains the common binding site for the allosteric effectors CTP and
ATP |CITS: [ColiSalII]|.)""","""(The enzyme is made up of two catalytic trimers (encoded by
the gene pyrB) and three regulatory dimers (encoded by the gene pyrI)
|CITS: [Prosite] [ColiSalII] [86033987]|.)""",]},
'B1131' : {'ecocyc-rxns': {"""AICARSYN-RXN""": """5'-phosphoribosyl-4-(N-succinocarboxamide)-5-aminoimidazole = fumarate + AICAR""","""AMPSYN-RXN""": """adenylo-succinate = fumarate + AMP""",},'ucsd-rxns' : ['ADSL2r','ADSL1r',], 'protein-comments' : ["""NIL""",]},
'B1134' : {'ecocyc-rxns': {"""GUANOSINE-DIPHOSPHATASE-RXN""": """GDP + H2O -> GMP + phosphate""","""RXN0-3543""": """4-amino-2-methyl-5-hydroxymethylpyrimidine pyrophosphate -> 4-amino-2-methyl-5-hydroxymethylpyrimidine phosphate + phosphate""","""RXN0-3542""": """thiamine diphosphate + H2O -> thiamine-phosphate + phosphate""",},'ucsd-rxns' : ['2MAHMP','TDP',], 'protein-comments' : ["""(The nudJ gene product is a member of the Nudix hydrolase superfamily. Unlike the other Nudix nucleoside
triphosphatases in E. coli, the product of the reaction is phosphate instead of pyrophosphate. NudJ is a
promiscuous enzyme with no preference for deoxyribose or ribose, and nucleoside di- and tri-phosphates serve as
substrates equally. The enzyme is a monomer in solution |CITS: [16766526]|.
Overexpression of NudJ from a multicopy plasmid leads to resistance to the HMP
(4-amino-2-methyl-5-hydroxymethylpyrimidine) analog bacimethrin (MeO-HMP). The enzyme is involved in the
hydrolysis of HMP-PP and TPP, intermediates in thiamin biosynthesis |CITS: [15292217]|.
Review: |CITS: [16378245]|
)""",]},
'B2170' : {'ecocyc-rxns': {"""TRANS-RXN-82""": """lactose[cytosol] + H+[periplasmic space] =lactose[periplasmic space] + H+[cytosol] """,},'ucsd-rxns' : ['LCTSt3ipp',], 'protein-comments' : ["""(SetB is a probable efflux transporter for sugars such as lactose and IPTG.
Everted membrane vesicles prepared from cells overexpressing setB
exhibit lactose transport activity which is abolished by uncouplers |CITS:[99226230]|.
SetB is a member of the major facilitator superfamily (MFS) of transporters,
and it probably functions as a proton/sugar antiporter.
SetB also appears to play a role in chromosome segregation. Deletion of
setB resulted in smaller cells with a minor defect in chromosome
segregation increasing the time required for segregation to occur.
Overexpression of setB resulted in cell elongation, filamentation,
and stretched or fragmented nucleoids. At high copy number, setB
suppresses a mutation in the ParC subunit of topoisomerase IV. Deletion of
setB combined with mutation of ftsK, responsible for segregation
of dimeric chromosomes, resulted in reduced growth rates, increased
filamentation, and increased the incidence of large nucleoids and
condensed DNA in the middle of the cell. SetB-GFP fusions showed
a helical localization pattern similar to MreB. Co-expression of SetB-GFP
and Myc-MreB showed that the two proteins co-localized. Yeast
two-hybrid experiments revealed that SetB and MreB interact. SetB is
involved in protein segregation and likely acts somewhere in the linkage
of chromosomes to the force required to separate them |CITS:[14617174]|.
)""",]},
'B1136' : {'ecocyc-rxns': {"""ISOCITDEH-RXN""": """isocitrate + NADP+ = NADPH + α-ketoglutarate + CO2""",},'ucsd-rxns' : ['ICDHyr',], 'protein-comments' : ["""NIL""","""NIL""","""(There are marked differences in the properties of enzymes from different sources. The E. coli enzyme is not an
allosteric protein as isocitrate dehydrogenases from other sources are, and it is cold sensitive. IcdA is observed to
have several distinct isoforms |CITS: [9298646]|. Phosphorylation of the
enzyme on a serine residue by isocitrate dehydrogenase kinase/phosphatase inactivates it, and dephosphorylation
by the phosphatase reactivates it |CITS: [85022438] [89374109] [90046847]|. Phosphorylation affects the binding of
NADP. This is the first bacterial enzyme shown to be regulated by phosphorylation/dephosphosphorylation
|CITS: [85022438]|. The 3D structure of the enzyme has been elucidated |CITS: [90046847]|.)""",]},
'B2710' : {'ecocyc-rxns': {},'ucsd-rxns' : ['NHFRBO',], 'protein-comments' : ["""NIL""","""NIL""","""(Flavorubredoxin (FlRd) is a multidomain protein containing an amino-terminal β-lactamase-like module with a
non-heme di-iron site as the catalytic center, a short chain flavodoxin-like module and a rubredoxin-like
extension. FlRd participates in a reaction that reduces nitric oxide |CITS: [20573621][12101220][11751865]|.
Regulation has been described |CITS: [12529359]|.)""",]},
'B0573' : {'ecocyc-rxns': {},'ucsd-rxns' : ['CUt3','AGt3',], 'protein-comments' : ["""(CusF is a periplasmic copper-binding protein that interacts with the CusCBA copper efflux complex. |CITS: [12813074]|
CusF is a pink copper-binding protein. The UV-vis spectrum of copper-containing CusF showed a absorption maximum
around 510 nm, which has not been reported for any other copper proteins. It is believed that CusF may contain a novel
type of copper binding site. |CITS: [12813074]|
The cusABFCRS gene cluster has similarity to a gene cluster contained on a silver resistance plasmid from a clinical Salmonella isolate |CITS: [12829274]|.
Agr: "Ag(I) resistance" |CITS: [12829274]|.)""","""(The Copper transporting efflux system, CusCFBA, is one of at least three systems involved in copper resistance.
CusB is a member of the membrane fusion protein (MFP) family. CusC is the outer membrane factor which forms a channel in the outer membrane.
CusA is the resistance-nodulation-division (RND) permease. CusF is the periplasmic copper binding protein.
The CusCFBA complex may translocate copper from the cytoplasm to the extracellular enviornment across both the inner and outer membrane. Alternatively, the Cus complex
may capture copper in the periplasm and export it outside. Evidence that supports the alternative claim includes the
periplasmic localization of the copper binding protein, CusF, and the assumption that copper access to the RND protein, CusA, may be possible from the cytoplasm as well as the periplasm. |CITS: [12374972]|
)""",]},
'B0572' : {'ecocyc-rxns': {},'ucsd-rxns' : ['CUt3','AGt3',], 'protein-comments' : ["""(CusC is the outer membrane factor for the CusCFBA copper efflux system.
The cusABFCRS gene cluster has similarity to a gene cluster contained on a silver resistance plasmid from a clinical Salmonella isolate |CITS: [12829274]|.
Agr: "Ag(I) resistance" |CITS: [12829274]|.)""","""(The Copper transporting efflux system, CusCFBA, is one of at least three systems involved in copper resistance.
CusB is a member of the membrane fusion protein (MFP) family. CusC is the outer membrane factor which forms a channel in the outer membrane.
CusA is the resistance-nodulation-division (RND) permease. CusF is the periplasmic copper binding protein.
The CusCFBA complex may translocate copper from the cytoplasm to the extracellular enviornment across both the inner and outer membrane. Alternatively, the Cus complex
may capture copper in the periplasm and export it outside. Evidence that supports the alternative claim includes the
periplasmic localization of the copper binding protein, CusF, and the assumption that copper access to the RND protein, CusA, may be possible from the cytoplasm as well as the periplasm. |CITS: [12374972]|
)""",]},
'B0242' : {'ecocyc-rxns': {"""PROLINE-MULTI""": """L-glutamate + ATP + NADPH -> ADP + L-glutamate γ-semialdehyde + NADP+ + phosphate""","""GLUTKIN-RXN""": """L-glutamate + ATP -> L-glutamate-5-phosphate + ADP""",},'ucsd-rxns' : ['GLU5K',], 'protein-comments' : ["""NIL""","""NIL""","""NIL""",]},
'B0576' : {'ecocyc-rxns': {"""TRANS-RXN-56""": """H+[periplasmic space] + L-phenylalanine[periplasmic space] =H+[cytosol] + L-phenylalanine[cytosol] """,},'ucsd-rxns' : ['PHEt2rpp','TYRt2rpp',], 'protein-comments' : ["""(PheP is a phenylalanine transporter that is a member of the Amino Acid-Polyamine-Organocation (APC)
Superfamily of transporters |CITS: [20200359]|. Complementation of a pheP mutant restored
phenylalanine-specific transport activity, indicating that PheP is normally responsible for phenylalanine
transport |CITS: [91267923]|. Experiments with oxidative phosphorylation uncouplers and E. coli
strains deficient in the F0F1-ATPase suggest that PheP-mediated transport is
driven by the proton motive force |CITS: [20200359]|. PheP probably functions as a phenylalanine/proton
symporter. PheP shares sequence similarity with AroP, which is a general aromatic amino acid transport
system, responsible for phenylalanine, tyrosine, and tryptophan transport |CITS: [91267923]|. Hydropathy
analysis and PhoA fusion suggests that PheP have a 12 transmembrane segment topology
|CITS: [96196173]|.)""",]},
'B3350' : {'ecocyc-rxns': {"""TRANS-RXN-42""": """H+[periplasmic space] + K+[cytosol] =H+[cytosol] + K+[periplasmic space] """,},'ucsd-rxns' : ['Kt3pp',], 'protein-comments' : ["""(KefB and KefC are two independent glutathione-regulated potassium efflux
systems, which play a role in responding to changes in osmotic
pressure and in protecting the cell from electrophile toxicity. Mutations
in kefB and kefC affect potassium efflux at neutral pH, can
be complemented by the cloned genes and probably function via potassium/proton
antiport |CITS: [85200098] [87279929]|. Potassium efflux by KefB or KefC
is activated by adducts formed by reaction of glutathione with electrophilic
compounds such as N-ethylmaleimide, methylglyoxal and
chlorodinitrobenzene |CITS: [95020661] [90286917]|. Potassium efflux mediated by
KefB and KefC leads to acidification of the cytoplasm, which protects the cell
from electrophile toxicity |CITS: [97175522] [96130836]|. KefB and KefC differ
in their activation by methylglyoxal, with KefC only weakly activated
|CITS: [99194803]|. KefB is a member of the CPA2 family of monovalent cation/proton
antiporters.
In addition to KefB and KefC, additional unidentified potassium efflux systems
exist.
)""",]},
'B0574' : {'ecocyc-rxns': {},'ucsd-rxns' : ['CUt3','AGt3',], 'protein-comments' : ["""(CusB is the membrane fusion protein in the CusCFBA copper efflux system. The function of a membrane fusion protein
like CusB may be to bring the outer membrane factor, CusC, closer to the resistance-nodulation-division permease, CusA.
The cusABFCRS gene cluster has similarity to a gene cluster contained on a silver resistance plasmid from a clinical Salmonella isolate |CITS: [12829274]|.
Agr: "Ag(I) resistance" |CITS: [12829274]|.)""","""(The Copper transporting efflux system, CusCFBA, is one of at least three systems involved in copper resistance.
CusB is a member of the membrane fusion protein (MFP) family. CusC is the outer membrane factor which forms a channel in the outer membrane.
CusA is the resistance-nodulation-division (RND) permease. CusF is the periplasmic copper binding protein.
The CusCFBA complex may translocate copper from the cytoplasm to the extracellular enviornment across both the inner and outer membrane. Alternatively, the Cus complex
may capture copper in the periplasm and export it outside. Evidence that supports the alternative claim includes the
periplasmic localization of the copper binding protein, CusF, and the assumption that copper access to the RND protein, CusA, may be possible from the cytoplasm as well as the periplasm. |CITS: [12374972]|
)""",]},
'B3451' : {'ecocyc-rxns': {"""ABC-34-RXN""": """ATP + sn-glycerol-3-phosphate[periplasmic space] + H2O =ADP + phosphate + sn-glycerol-3-phosphate[cytosol] """,},'ucsd-rxns' : ['G3PEabcpp','GLYC3Pabcpp','G3PCabcpp','G3PGabcpp','G3PIabcpp','G3PSabcpp',], 'protein-comments' : ["""NIL""","""(The UgpABCE glycerol-3-phosphate uptake system is a member of the ATP-Binding Cassette (ABC)
Superfamily |CITS:[96381453]|. Glycerol-3-phosphate can be used as a carbon source and a phosphate
source |CITS: [82189841]|, and is also an essential intermediate in phospholipid biosynthesis
|CITS: [98377424]|. Using 32P-labeled glycerol-3-phosphate,glycerol-3-phosphate uptake via the Ugp
system was observed in whole cell experiments |CITS: [94110221]|. Based on sequence similarity, UgpC is
the ATP-binding protein, UgpA and UgpE are the membrane components, and UgpB is the periplasmic
binding protein. Transcription of the ugp system is under the control of the pho regulon
|CITS:[94110221]|. The statement of ugp genes cloned in a plasmid were shown to be
phoB-dependent |CITS:[94012527]|. The Ugp system, even though capable of transporting glycerol-
3-phosphate, is unable to supply enough carbon for bacterial growth |CITS: [98377424]|. The concentration
of internal inorganic phosphate was monitored by nuclear magnetic resonance (NMR) imaging, and the
uptake of glycerol-3-phosphate via the Ugp system lead to a dramatic increase in the internal phosphate
concentration up to about 20 mM. This, in turn, inhibits the Ugp-mediated uptake of glycerol-3-phosphate
|CITS: [98377424]|. This feedback inhibition of Ugp by internal phosphate explains why glycerol-3-phosphate
transported by the Ugp system can only serve as the sole phosphate source but not the sole carbon source
|CITS: [98377424]|. Thus, the Ugp system is ideally geared for scavenging phosphate-containing compounds
|CITS:[98377424]|.)""",]},
'B3450' : {'ecocyc-rxns': {"""ABC-34-RXN""": """ATP + sn-glycerol-3-phosphate[periplasmic space] + H2O =ADP + phosphate + sn-glycerol-3-phosphate[cytosol] """,},'ucsd-rxns' : ['G3PEabcpp','GLYC3Pabcpp','G3PCabcpp','G3PGabcpp','G3PIabcpp','G3PSabcpp',], 'protein-comments' : ["""NIL""","""(The UgpABCE glycerol-3-phosphate uptake system is a member of the ATP-Binding Cassette (ABC)
Superfamily |CITS:[96381453]|. Glycerol-3-phosphate can be used as a carbon source and a phosphate
source |CITS: [82189841]|, and is also an essential intermediate in phospholipid biosynthesis
|CITS: [98377424]|. Using 32P-labeled glycerol-3-phosphate,glycerol-3-phosphate uptake via the Ugp
system was observed in whole cell experiments |CITS: [94110221]|. Based on sequence similarity, UgpC is
the ATP-binding protein, UgpA and UgpE are the membrane components, and UgpB is the periplasmic
binding protein. Transcription of the ugp system is under the control of the pho regulon
|CITS:[94110221]|. The statement of ugp genes cloned in a plasmid were shown to be
phoB-dependent |CITS:[94012527]|. The Ugp system, even though capable of transporting glycerol-
3-phosphate, is unable to supply enough carbon for bacterial growth |CITS: [98377424]|. The concentration
of internal inorganic phosphate was monitored by nuclear magnetic resonance (NMR) imaging, and the
uptake of glycerol-3-phosphate via the Ugp system lead to a dramatic increase in the internal phosphate
concentration up to about 20 mM. This, in turn, inhibits the Ugp-mediated uptake of glycerol-3-phosphate
|CITS: [98377424]|. This feedback inhibition of Ugp by internal phosphate explains why glycerol-3-phosphate
transported by the Ugp system can only serve as the sole phosphate source but not the sole carbon source
|CITS: [98377424]|. Thus, the Ugp system is ideally geared for scavenging phosphate-containing compounds
|CITS:[98377424]|.)""",]},
'B3453' : {'ecocyc-rxns': {"""ABC-34-RXN""": """ATP + sn-glycerol-3-phosphate[periplasmic space] + H2O =ADP + phosphate + sn-glycerol-3-phosphate[cytosol] """,},'ucsd-rxns' : ['G3PEabcpp','GLYC3Pabcpp','G3PCabcpp','G3PGabcpp','G3PIabcpp','G3PSabcpp',], 'protein-comments' : ["""NIL""","""(The UgpABCE glycerol-3-phosphate uptake system is a member of the ATP-Binding Cassette (ABC)
Superfamily |CITS:[96381453]|. Glycerol-3-phosphate can be used as a carbon source and a phosphate
source |CITS: [82189841]|, and is also an essential intermediate in phospholipid biosynthesis
|CITS: [98377424]|. Using 32P-labeled glycerol-3-phosphate,glycerol-3-phosphate uptake via the Ugp
system was observed in whole cell experiments |CITS: [94110221]|. Based on sequence similarity, UgpC is
the ATP-binding protein, UgpA and UgpE are the membrane components, and UgpB is the periplasmic
binding protein. Transcription of the ugp system is under the control of the pho regulon
|CITS:[94110221]|. The statement of ugp genes cloned in a plasmid were shown to be
phoB-dependent |CITS:[94012527]|. The Ugp system, even though capable of transporting glycerol-
3-phosphate, is unable to supply enough carbon for bacterial growth |CITS: [98377424]|. The concentration
of internal inorganic phosphate was monitored by nuclear magnetic resonance (NMR) imaging, and the
uptake of glycerol-3-phosphate via the Ugp system lead to a dramatic increase in the internal phosphate
concentration up to about 20 mM. This, in turn, inhibits the Ugp-mediated uptake of glycerol-3-phosphate
|CITS: [98377424]|. This feedback inhibition of Ugp by internal phosphate explains why glycerol-3-phosphate
transported by the Ugp system can only serve as the sole phosphate source but not the sole carbon source
|CITS: [98377424]|. Thus, the Ugp system is ideally geared for scavenging phosphate-containing compounds
|CITS:[98377424]|.)""",]},
'B3452' : {'ecocyc-rxns': {"""ABC-34-RXN""": """ATP + sn-glycerol-3-phosphate[periplasmic space] + H2O =ADP + phosphate + sn-glycerol-3-phosphate[cytosol] """,},'ucsd-rxns' : ['G3PEabcpp','GLYC3Pabcpp','G3PCabcpp','G3PGabcpp','G3PIabcpp','G3PSabcpp',], 'protein-comments' : ["""NIL""","""(The UgpABCE glycerol-3-phosphate uptake system is a member of the ATP-Binding Cassette (ABC)
Superfamily |CITS:[96381453]|. Glycerol-3-phosphate can be used as a carbon source and a phosphate
source |CITS: [82189841]|, and is also an essential intermediate in phospholipid biosynthesis
|CITS: [98377424]|. Using 32P-labeled glycerol-3-phosphate,glycerol-3-phosphate uptake via the Ugp
system was observed in whole cell experiments |CITS: [94110221]|. Based on sequence similarity, UgpC is
the ATP-binding protein, UgpA and UgpE are the membrane components, and UgpB is the periplasmic
binding protein. Transcription of the ugp system is under the control of the pho regulon
|CITS:[94110221]|. The statement of ugp genes cloned in a plasmid were shown to be
phoB-dependent |CITS:[94012527]|. The Ugp system, even though capable of transporting glycerol-
3-phosphate, is unable to supply enough carbon for bacterial growth |CITS: [98377424]|. The concentration
of internal inorganic phosphate was monitored by nuclear magnetic resonance (NMR) imaging, and the
uptake of glycerol-3-phosphate via the Ugp system lead to a dramatic increase in the internal phosphate
concentration up to about 20 mM. This, in turn, inhibits the Ugp-mediated uptake of glycerol-3-phosphate
|CITS: [98377424]|. This feedback inhibition of Ugp by internal phosphate explains why glycerol-3-phosphate
transported by the Ugp system can only serve as the sole phosphate source but not the sole carbon source
|CITS: [98377424]|. Thus, the Ugp system is ideally geared for scavenging phosphate-containing compounds
|CITS:[98377424]|.)""",]},
'B3455' : {'ecocyc-rxns': {"""ABC-36-RXN""": """ATP + L-valine[periplasmic space] + H2O =ADP + phosphate + L-valine[cytosol] ""","""ABC-15-RXN""": """ATP + L-isoleucine[periplasmic space] + H2O =ADP + phosphate + L-isoleucine[cytosol] ""","""ABC-35-RXN""": """ATP + L-leucine[periplasmic space] + H2O =ADP + phosphate + L-leucine[cytosol] """,},'ucsd-rxns' : ['VALabcpp','THRabcpp','ALAabcpp','ILEabcpp','LEUabcpp','LEUabcpp',], 'protein-comments' : ["""NIL""","""(LivFGHMJ and LivFGHMK are two ATP-dependent high-affinity branched-chain amino acid transport
system and are members of the ATP Binding Cassette (ABC) Superfamily of transporters |CITS: [20053876]|.
The two systems are responsible for the high affinity transport of branched-chain amino acids in
E. coli. They have shared membrane and ATP-binding components but have distinctive periplasmic
binding proteins. Due to the different periplasmic binding components, the two complexes differ in their
binding specificity: LivFGHMK is specific for the transport of leucine, while LivFGHMJ is a transporter for
leucine, isoleucine, and valine |CITS: [85288998]|. Based on sequence similarity and hydrophobicity
analysis, LivJ and LivK are the two periplasmic animo acid-binding proteins, LivH and LivM are the
membrane components, and LivG and LivF are the ATP-binding component of the ABC transport
complexes |CITS: [90307651]|. Deletions each of the liv genes resulted in the inability to transport
leucine |CITS: [90307651]|. In addition, a deletion strain that does not express any of the liv genes
was unable to carry out high-affinity transport of leucine unless one of the binding protein genes and all of
the membrane complex genes were provided on a plasmid |CITS: [90307651]|. In a separate experiment,
liv gene mutants were found to be resistant to a toxic analog of leucine, azaleucine, due to its
inability in branched-chain amino acid transport |CITS: [85288998]|.)""","""(LivFGHMJ and LivFGHMK are two ATP-dependent high-affinity branched-chain amino acid transport
system and are members of the ATP Binding Cassette (ABC) Superfamily of transporters |CITS: [20053876]|.
The two systems are responsible for the high affinity transport of branched-chain amino acids in E. coli.
They have shared membrane and ATP-binding components but have distinctive periplasmic binding proteins.
Due to the different periplasmic binding components, the two complexes differ in their binding specificity:
LivFGHMK is specific for the transport of leucine, while LivFGHMJ is a transporter for leucine, isoleucine,
and valine |CITS: [85288998]|. Based on sequence similarity and hydrophobicity analysis, LivJ and LivK
are the two periplasmic animo acid-binding proteins, LivH and LivM are the membrane components, and
LivG and LivF are the ATP-binding component of the ABC transport complexes |CITS: [90307651]|.
Deletions each of the liv genes resulted in the inability to transport leucine |CITS: [90307651]|. In
addition, a deletion strain that does not express any of the liv genes was unable to carry out high-
affinity transport of leucine unless one of the binding protein genes and all of the membrane complex genes
were provided on a plasmid |CITS: [90307651]|. In a separate experiment, liv gene mutants were
found to be resistant to a toxic analog of leucine, azaleucine, due to its inability in branched-chain amino
acid transport |CITS: [85288998]|. This system has also been shown |CITS:[14702302]| to serve as a third (along
with the AroP and PheP systems) complex for transport of phenylanine across the inner membrane.)""",]},
'B3454' : {'ecocyc-rxns': {"""ABC-35-RXN""": """ATP + L-leucine[periplasmic space] + H2O =ADP + phosphate + L-leucine[cytosol] ""","""ABC-36-RXN""": """ATP + L-valine[periplasmic space] + H2O =ADP + phosphate + L-valine[cytosol] ""","""ABC-15-RXN""": """ATP + L-isoleucine[periplasmic space] + H2O =ADP + phosphate + L-isoleucine[cytosol] """,},'ucsd-rxns' : ['VALabcpp','THRabcpp','ALAabcpp','ILEabcpp','LEUabcpp','LEUabcpp',], 'protein-comments' : ["""NIL""","""(LivFGHMJ and LivFGHMK are two ATP-dependent high-affinity branched-chain amino acid transport
system and are members of the ATP Binding Cassette (ABC) Superfamily of transporters |CITS: [20053876]|.
The two systems are responsible for the high affinity transport of branched-chain amino acids in E. coli.
They have shared membrane and ATP-binding components but have distinctive periplasmic binding proteins.
Due to the different periplasmic binding components, the two complexes differ in their binding specificity:
LivFGHMK is specific for the transport of leucine, while LivFGHMJ is a transporter for leucine, isoleucine,
and valine |CITS: [85288998]|. Based on sequence similarity and hydrophobicity analysis, LivJ and LivK
are the two periplasmic animo acid-binding proteins, LivH and LivM are the membrane components, and
LivG and LivF are the ATP-binding component of the ABC transport complexes |CITS: [90307651]|.
Deletions each of the liv genes resulted in the inability to transport leucine |CITS: [90307651]|. In
addition, a deletion strain that does not express any of the liv genes was unable to carry out high-
affinity transport of leucine unless one of the binding protein genes and all of the membrane complex genes
were provided on a plasmid |CITS: [90307651]|. In a separate experiment, liv gene mutants were
found to be resistant to a toxic analog of leucine, azaleucine, due to its inability in branched-chain amino
acid transport |CITS: [85288998]|. This system has also been shown |CITS:[14702302]| to serve as a third (along
with the AroP and PheP systems) complex for transport of phenylanine across the inner membrane.)""","""(LivFGHMJ and LivFGHMK are two ATP-dependent high-affinity branched-chain amino acid transport
system and are members of the ATP Binding Cassette (ABC) Superfamily of transporters |CITS: [20053876]|.
The two systems are responsible for the high affinity transport of branched-chain amino acids in
E. coli. They have shared membrane and ATP-binding components but have distinctive periplasmic
binding proteins. Due to the different periplasmic binding components, the two complexes differ in their
binding specificity: LivFGHMK is specific for the transport of leucine, while LivFGHMJ is a transporter for
leucine, isoleucine, and valine |CITS: [85288998]|. Based on sequence similarity and hydrophobicity
analysis, LivJ and LivK are the two periplasmic animo acid-binding proteins, LivH and LivM are the
membrane components, and LivG and LivF are the ATP-binding component of the ABC transport
complexes |CITS: [90307651]|. Deletions each of the liv genes resulted in the inability to transport
leucine |CITS: [90307651]|. In addition, a deletion strain that does not express any of the liv genes
was unable to carry out high-affinity transport of leucine unless one of the binding protein genes and all of
the membrane complex genes were provided on a plasmid |CITS: [90307651]|. In a separate experiment,
liv gene mutants were found to be resistant to a toxic analog of leucine, azaleucine, due to its
inability in branched-chain amino acid transport |CITS: [85288998]|.)""",]},
'B0474' : {'ecocyc-rxns': {"""ADENYL-KIN-RXN""": """AMP + ATP = 2 ADP""",},'ucsd-rxns' : ['ADNK1','ADK1','NDPK4','ADK4','ADK3','DADK','NDPK8','NDPK2','NDPK3','NDPK1','NDPK6','NDPK7','NDPK5',], 'protein-comments' : ["""NIL""",]},
'B3456' : {'ecocyc-rxns': {"""ABC-36-RXN""": """ATP + L-valine[periplasmic space] + H2O =ADP + phosphate + L-valine[cytosol] ""","""ABC-15-RXN""": """ATP + L-isoleucine[periplasmic space] + H2O =ADP + phosphate + L-isoleucine[cytosol] ""","""ABC-35-RXN""": """ATP + L-leucine[periplasmic space] + H2O =ADP + phosphate + L-leucine[cytosol] """,},'ucsd-rxns' : ['VALabcpp','THRabcpp','ALAabcpp','ILEabcpp','LEUabcpp','LEUabcpp',], 'protein-comments' : ["""NIL""","""(LivFGHMJ and LivFGHMK are two ATP-dependent high-affinity branched-chain amino acid transport
system and are members of the ATP Binding Cassette (ABC) Superfamily of transporters |CITS: [20053876]|.
The two systems are responsible for the high affinity transport of branched-chain amino acids in
E. coli. They have shared membrane and ATP-binding components but have distinctive periplasmic
binding proteins. Due to the different periplasmic binding components, the two complexes differ in their
binding specificity: LivFGHMK is specific for the transport of leucine, while LivFGHMJ is a transporter for
leucine, isoleucine, and valine |CITS: [85288998]|. Based on sequence similarity and hydrophobicity
analysis, LivJ and LivK are the two periplasmic animo acid-binding proteins, LivH and LivM are the
membrane components, and LivG and LivF are the ATP-binding component of the ABC transport
complexes |CITS: [90307651]|. Deletions each of the liv genes resulted in the inability to transport
leucine |CITS: [90307651]|. In addition, a deletion strain that does not express any of the liv genes
was unable to carry out high-affinity transport of leucine unless one of the binding protein genes and all of
the membrane complex genes were provided on a plasmid |CITS: [90307651]|. In a separate experiment,
liv gene mutants were found to be resistant to a toxic analog of leucine, azaleucine, due to its
inability in branched-chain amino acid transport |CITS: [85288998]|.)""","""(LivFGHMJ and LivFGHMK are two ATP-dependent high-affinity branched-chain amino acid transport
system and are members of the ATP Binding Cassette (ABC) Superfamily of transporters |CITS: [20053876]|.
The two systems are responsible for the high affinity transport of branched-chain amino acids in E. coli.
They have shared membrane and ATP-binding components but have distinctive periplasmic binding proteins.
Due to the different periplasmic binding components, the two complexes differ in their binding specificity:
LivFGHMK is specific for the transport of leucine, while LivFGHMJ is a transporter for leucine, isoleucine,
and valine |CITS: [85288998]|. Based on sequence similarity and hydrophobicity analysis, LivJ and LivK
are the two periplasmic animo acid-binding proteins, LivH and LivM are the membrane components, and
LivG and LivF are the ATP-binding component of the ABC transport complexes |CITS: [90307651]|.
Deletions each of the liv genes resulted in the inability to transport leucine |CITS: [90307651]|. In
addition, a deletion strain that does not express any of the liv genes was unable to carry out high-
affinity transport of leucine unless one of the binding protein genes and all of the membrane complex genes
were provided on a plasmid |CITS: [90307651]|. In a separate experiment, liv gene mutants were
found to be resistant to a toxic analog of leucine, azaleucine, due to its inability in branched-chain amino
acid transport |CITS: [85288998]|. This system has also been shown |CITS:[14702302]| to serve as a third (along
with the AroP and PheP systems) complex for transport of phenylanine across the inner membrane.)""",]},
'B3925' : {'ecocyc-rxns': {"""F16BDEPHOS-RXN""": """fructose-1,6-bisphosphate + H2O = D-fructose-6-phosphate + phosphate""",},'ucsd-rxns' : ['FBP',], 'protein-comments' : ["""NIL""","""NIL""",]},
'B3924' : {'ecocyc-rxns': {"""NRDACTMULTI-RXN""": """reduced flavodoxin + inactive ribonucleoside triphosphate reductase + S-adenosyl-L-methionine = 5'-deoxyadenosine + oxidized flavodoxin + active ribonucleoside triphosphate reductase + L-methionine""","""FLAVONADPREDUCT-RXN""": """reduced flavodoxin + NADP+ = oxidized flavodoxin + NADPH + H+""",},'ucsd-rxns' : ['RNTR3c','RNTR3c','FLDR','FLDR','RNTR4c','RNTR4c','RNTR1c','RNTR1c','RNTR2c','RNTR2c',], 'protein-comments' : ["""NIL""","""(The anaerobic nucleoside-triphosphate reductase activating
system is composed of three enzymes and several compounds. Anaerobic
nucleoside-triphosphate reductase is activated through the action of a
specific activating enzyme, nucleoside-triphosphate reductase
activase, flavodoxin NADP+ reductase, S-adenosylmethionine, flavodoxin
and NADPH. All of these components form a multi-enzyme complex with
the ribonucleoside reductase itself. |CITS: [93194782] [95155298]|)""",]},
'B3927' : {'ecocyc-rxns': {"""TRANS-RXN-131""": """glycerol[periplasmic space] =glycerol[cytosol] """,},'ucsd-rxns' : ['GLYCtpp','GLYALDtpp','UREAtpp',], 'protein-comments' : ["""(The glycerol facilitator, GlpF, allows the facilitated diffusion of glycerol into the cell. It is
a member of the major intrinsic protein (MIP) family of transmembrane channel proteins,
along with AqpZ, a water channel. GlpF forms a tetramer of 4 channels |CITS:[14630323]|. The structure of GlpF
has been determined using cryo-electron microscopy of 2 dimensional crystals to a resolution of 6.9
angstroms. The GlpF channel contains hydrophobic residues on one side and hydrophilic residues on the
other side, possibly limiting water permeation |CITS:[11162735]|. Real time molecular dynamics simulations
indicate GlpF is a two stage filter. The first is a selectivity-determining region, and the second is a proton
filter. In order to prevent water transport, it is believed GlpF has a glycerol-mediated induced fit gating
motion |CITS:[11743202]|. Complementation studies have demonstrated that
the cloned glpF gene can complement glycerol transport mutants |CITS: [90094250]|. Voltage
clamp experiments showed that GlpF was not voltage-activated for ion transport; it
mediates glycerol diffusion via a pore type mechanism |CITS: [9421629]|.)""",]},
'B3926' : {'ecocyc-rxns': {"""GLYCEROL-KIN-RXN""": """glycerol + ATP -> sn-glycerol-3-phosphate + ADP""",},'ucsd-rxns' : ['GLYK',], 'protein-comments' : ["""NIL""","""(The enzyme can undergo a reversible subunit dissociation
between tetramer and dimer |CITS: [79082770]|.)""",]},
'B0323' : {'ecocyc-rxns': {},'ucsd-rxns' : ['CBMKr',], 'protein-comments' : ["""(No information about this protein was found by a literature search
conducted on 23 July 2003.)""",]},
'B3599' : {'ecocyc-rxns': {"""TRANS-RXN-156""": """phosphoenolpyruvate + mannitol[periplasmic space] =mannitol-1-phosphate[cytosol] + pyruvate """,},'ucsd-rxns' : ['MNLptspp',], 'protein-comments' : ["""(contains PTS Enzyme IIA, IIB and IIC domains)""","""(MtlA, the mannitol PTS permease, belongs to the functional superfamily
of the phosphoenolpyruvate (PEP)-dependent, sugar transporting
phosphotransferase system (PTS). The PTS transports and simultaneously
phosphorylates its sugar substrates in a process called group
translocation. MtlA takes up exogenous mannitol, releasing the
phosphate ester, mannitol-1-P, into the cell cytoplasm in preparation
for oxidation to fructose-6-P by the NAD-dependent mannitol-P
dehydrogenase (MtlD). Subsequent metabolism is primarily via
glycolysis |CITS: [94066914]|.
MtlA, the Enzyme IIMtl complex, possesses
three domains in a single polypeptide chain with the domain order
IIC-IIB-IIA |CITS: [83291014]|. It is homologous to FruAB, the fructose-specific
PTS Enzyme II. The secondary structure of IIAMtl
has been solved by NMR |CITS: [94004470]|. MtlA has been reported to possess
6 transmembrane α-helical segments
in its IIC domain |CITS: [92052139]|. The IIB and IIA domains are localized
to the cytoplasmic side of the membrane. The overall PTS-mediated
phosphoryl transfer reaction, requiring the two general energy
coupling proteins of the PTS, Enzyme I and HPr, as well as the
three domains of the Enzyme II complex is:
PEP --> Enzyme I(his~~P)
--> HPr(his~~P)
--> IIA(his~~P) -->
IIB(cys~~P) -(IIC)-> mannitol-1-P.
MtlA transports mannitol with low micromolar affinity.
The mtl operon (mtlADR) is inducible (~~20x) by
growth of wild type E. coli K12 in the presence of mannitol.
The MtlR protein is a negative transcriptional regulator of the
operon |CITS: [94131964]|. The operon is also positively controlled by the cyclic
AMP-cyclic AMP receptor protein (CRP) complex and negatively by
the catabolite repressor/activator (Cra) protein.
)""",]},
'B0241' : {'ecocyc-rxns': {"""RXN0-2481""": """hydrophilic solute or ion < 600 Da[extracellular space] =hydrophilic solute or ion < 600 Da[periplasmic space] """,},'ucsd-rxns' : ['Htex','LEUtex','ALAALAtex','LYStex','ORNtex','O2Stex','UMPtex','GAMAN6Ptex','UDPACGALtex','INDOLEtex','3AMPtex','ACtex','GALBDtex','XTSNtex','THMtex','TRPtex','SERtex','CRNtex','SO4tex','ARGtex','ETHAtex','23CGMPtex','CLtex','ACSERtex','METSOX2tex','ACMANAtex','NOtex','DGSNtex','UDPGtex','23DAPPAtex','GLYCtex','MELIBtex','SO2tex','12PPDStex','GALURtex','23CAMPtex','GLUtex','DGMPtex','GSNtex','THYMtex','GLYBtex','NMNtex','GLCNtex','FE2tex','12PPDRtex','DALAtex','ALAtex','Zn2tex','HCINNMtex','ACGAL1Ptex','TSULtex','THMDtex','CGLYtex','DOPAtex','GTHRDtex','AGMtex','G3PStex','PSCLYStex','HOMtex','GBBTNtex','DMStex','HG2tex','PItex','IDONtex','GLCtex','TYRtex','MOBDtex','ASNtex','ACGALtex','NO3tex','NAtex','PACALDtex','PPPNtex','DSERtex','ACMUMtex','PPALtex','HIStex','DINStex','TCYNTtex','SULFACtex','OCTAtex','CD2tex','URAtex','GALCTtex','TUNGStex','SO3tex','METDtex','TMAOtex','CYANtex','MSO3tex','TMAtex','GALCTNLtex','ALLtex','PYRtex','D-LACtex','BUTtex','XMPtex','MMETtex','5DGLCNtex','ALLTNtex','G3PCtex','CYStex','GLYCAtex','MNtex','G3PEtex','ASO3tex','TYRPtex','GLYtex','L-LACtex','FORtex','PNTOtex','ETOHtex','SPMDtex','HPPPNtex','GDPtex','BALAtex','FRULYStex','TARTRtex','3GMPtex','MNLtex','DCMPtex','AMPtex','ACGAtex','ACACtex','SUCCtex','FALDtex','PEAMNtex','SUCRtex','UDPGALtex','PPAtex','PROtex','XANtex','PPTtex','ASPtex','HXAtex','SKMtex','HYXNtex','TREtex','CO2tex','PROGLYtex','MALtex','ILEtex','GLCUR1Ptex','UREAtex','DAPtex','GLNtex','CSNtex','PTRCtex','XYLtex','O2tex','DAMPtex','G3PGtex','3PEPTtex','VALtex','AKGtex','METtex','ASCBtex','SBTtex','3CMPtex','GLYC2Ptex','GLYALDtex','G6Ptex','NO2tex','PSERtex','CYTDtex','H2tex','MANGLYCtex','DUMPtex','LYXtex','34dhpactex','R5Ptex','ARBtex','GAL1Ptex','FRUURtex','MG2tex','METSOX1tex','TAURtex','GALTtex','UDPGLCURtex','CYNTtex','23CCMPtex','G1Ptex','GLCRtex','IMPtex','RMNtex','DHAtex','GTPtex','FUCtex','ANHGMtex','GLYCLTtex','GALtex','CITtex','23CUMPtex','LCTStex','H2O2tex','OROTtex','DCAtex','NACtex','ACALDtex','CYSDtex','G3PItex','ISETACtex','ACGAM1Ptex','INSTtex','ABUTtex','GTHOXtex','DMSOtex','F6Ptex','GALCTNtex','26DAHtex','MAN6Ptex','GAMtex','GLYC3Ptex','GLCURtex','NI2tex','DIMPtex','THRPtex','MANtex','GMPtex','CU2tex','THRtex','XYLUtex','DTMPtex','TYMtex','4PEPTtex','ADEtex','RIBtex','H2Otex','ETHSO3tex','CA2tex','BUTSO3tex','3UMPtex','CUtex','4HOXPACDtex','NH4tex','UACGAMtex','Ktex','FE3tex','MALDtex','FRUtex','PHEtex','FUMtex','N2Otex','H2Stex','CMPtex','DDGLCNtex','COBALT2tex','CHLtex',], 'protein-comments' : ["""(PhoE is a member of the General Bacterial Porin (GBP) family. These proteins are present in the outer
membranes of Gram negative bacteria, mitochondria, and plastids. The structure consists of fourteen nearest-
neighbor antiparallel Β-strands. PhoE is believed to be a pore with specificity defined by the pore's composition.
In this case, PhoE is believed to have a preference for small anions due to a collection of positively charged
amino acids near the pore entrance. |CITS: [8988389]| Therefore, PhoE is not a specific transport system, rather
it is just a water filled channel allowing for passive diffusion of small molecules (~600 Da).
Targeting of PhoE to the Sec-translocase for transport across the inner membrane
is SecB-dependent |CITS:[16352602]|.)""",]},
'B0243' : {'ecocyc-rxns': {"""PROLINE-MULTI""": """L-glutamate + ATP + NADPH -> ADP + L-glutamate γ-semialdehyde + NADP+ + phosphate""","""GLUTSEMIALDEHYDROG-RXN""": """L-glutamate γ-semialdehyde + phosphate + NADP+ = L-glutamate-5-phosphate + NADPH + H+""",},'ucsd-rxns' : ['G5SD',], 'protein-comments' : ["""NIL""","""NIL""","""NIL""",]},
'B4242' : {'ecocyc-rxns': {"""ABC-20-RXN""": """Ni2+[periplasmic space] + ATP + H2O =Ni2+[cytosol] + ADP + phosphate ""","""TRANS-RXN-250""": """Mg2+[periplasmic space] + ATP + H2O =Mg2+[cytosol] + ADP + phosphate """,},'ucsd-rxns' : ['NI2uabcpp','MG2uabcpp',], 'protein-comments' : ["""(MgtA is a P-type ATPase involved in the uptake of magnesium ion |CITS: [98283691]|. MgtA has not been
experimentally characterized in E. coli, but its orthologue in Salmonella typhimurium has
been extensively characterized as follows. Strains with wild-type mgtA gene and mutation in other
loci that code for components of magnesium transporters were used to study the kinetics and specificity of ion
transport of the system |CITS: [89359107]|. MgtA was found to transport magnesium ion with, instead of
against, the magnesium electrochemical gradient with a Ka of 5-15 μM |CITS: [89359107]|.
MgtA also mediates the influx of nickel (II) ion. In addition, cobalt (II) ion, although not transported via
MgtA, was found to have an inhibitory effect on the transporter |CITS: [89359107]|. MgtA was found to have
10 transmembrane domains, as determined by fusion protein and epitope analysis |CITS: [98283691]|.
Regulation has been described |CITS: [12813061]|. Transcription is regulated by Mg2+ |CITS: [12813061]|.)""",]},
}