gene reactions comment
B0084 MCTP1App,MCTP2App (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]|)
B0260 MMETt2pp (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]|)
B0323 CBMKr (No information about this protein was found by a literature search conducted on 23 July 2003.)
B0335 ACCOAL (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]|. )
B0411 DCYTtex,DADNtex,ADNtex,INStex,GUAtex,URItex,DURItex (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]|.)
B0433 AGM4Pt2pp,AGM3Pt2pp,AGMt2pp (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]|.)
B0484 CU1abcpp (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.)
B0511 ALLTNt2rpp (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.)
B0521 CBMKr (The Pseudomonas aeruginosa ArcC carbamate kinase has been characterized |CITS: [3040889], [2537202]|.)
B0572 AGt3,CUt3 (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]| )
B0573 AGt3,CUt3 (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]| )
B0574 AGt3,CUt3 (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]| )
B0635 MCTP1App,MCTP2App (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]|. )
B0650 NTP1 (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]|.)
B0655 GLUabcpp,ASPabcpp (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]|. )
B0657 ALPATE160pp,ALPATG160pp (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]|.)
B0684 RNTR4c,FLDR,RNTR1c,RNTR3c,RNTR2c NIL
B0732 MANPGH (The mngB gene encodes an alpha-mannosidase |CITS: [14645248]|.)
B0760 TUNGSabcpp,MOBDabcpp (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.)
B0839 MDDCP4pp,MDDCP2pp,MDDCP1pp,MDDCP3pp,MDDCP5pp (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]|.)
B0849 RNDR4b,PAPSR2,GRXR,RNDR2b,RNDR3b,RNDR1b (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]|)
B0933 ETHSO3abcpp,ISETACabcpp,MSO3abcpp,SULFACabcpp,BUTSO3abcpp (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.)
B0934 SULFACabcpp,MSO3abcpp,ISETACabcpp,ETHSO3abcpp,BUTSO3abcpp (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.)
B0936 ETHSO3abcpp,ISETACabcpp,SULFACabcpp,MSO3abcpp,BUTSO3abcpp (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.)
B0957 H2Otex (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]|.)
B1006 URAt2rpp (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]| )
B1064 RNDR4b,RNDR2b,RNDR3b,GRXR,ASR,PAPSR2,RNDR1b (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]|.)
B1094 AACPS1,AACPS3,AACPS4,AACPS7,UAGAAT,ACOATA,AACPS6,AACPS5,AACPS9,MCOATA,AACPS8,AACPS2 (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]|.)
B1193 MLTGY3pp,MLTGY4pp,MLTGY2pp,MLTGY1pp (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]|.)
B1226 NO3R2pp,NO3R1pp (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]|)
B1296 PTRCt2pp (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]|.)
B1325 ALAGLUE (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]|.)
B1329 3PEPTabcpp (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]|. )
B1440 SPMDabcpp,PTRCabcpp (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.)
B1441 SPMDabcpp,PTRCabcpp (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 PTRCabcpp,SPMDabcpp (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.)
B1443 SPMDabcpp,PTRCabcpp (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.)
B1466 NO3R1pp,NO3R2pp (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]|. )
B1483 ALAALAabcpp (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.)
B1484 ALAALAabcpp (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 ALAALAabcpp (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 ALAALAabcpp (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 ALAALAabcpp (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.)
B1605 ARGORNt7pp (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.)
B1621 GLCptspp,MALTptspp (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]|.
)
B1654 RNDR2b,RNDR1b,GRXR,RNDR3b,PAPSR2,RNDR4b (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]|)
B1677 ALPATE160pp,ALPATG160pp (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]|.)
B1773 FBA (No information about this protein was found by a literature search conducted on December 28, 2005. )
B1800 MALDDH (No information about this protein was found by a literature search conducted on December 28, 2005. )
B1801 GLYBt2pp,CHLt2pp,GLYt2pp (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.)
B2027 O16AP3pp,O16AP1pp,O16AP2pp (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]|)
B2032 O16GLCT1 (No information about this protein was found by a literature search conducted on November 29, 2005.)
B2033 O16AT (No information about this protein was found by a literature search conducted on February 26, 2004.)
B2034 O16GALFT (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 O16AP2pp,O16AP1pp,O16AP3pp (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]|.)
B2045 GALKr (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.)
B2128 CHLabcpp,GLYBabcpp (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]|.)
B2129 GLYBabcpp,CHLabcpp (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 GLYBabcpp,CHLabcpp (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]|.)
B2131 GLYBabcpp,CHLabcpp (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]|.)
B2223 BUTt2rpp,ACACt2pp,HEXt2rpp (No information about this protein was found by a literature search conducted on June 13, 2005. )
B2413 SULabcpp (A cysZ mutant is deficient in sulfate assimilation |CITS: [6302202]|.)
B2458 PTAr (No information about this protein was found by a literature search conducted on January 20, 2006.)
B2490 FHL (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.)
B2492 FORtppi,FORt2pp (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.)
B2519 MPTG2,MPTG (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]|.)
B2523 AMPTASEPG,AMPTASECG (The pepB gene encodes an aminopeptidase (AP) |CITS: [372108]|.)
B2536 PPPNt2rpp (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]|.)
B2579 OBTFL,PFL (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]|.)
B2582 RNDR2,THIORDXi,TRDR,PAPSR,METSOXR1,RNDR1,RNDR4,METSOXR2,DSBDR,RNDR3 NIL
B2687 RHCCE (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]|. )
B2690 PGMT (Phosphatase activity of YqaB was discovered in a high-throughput screen of purified proteins |CITS: [15808744]|. )
B2701 MLTGY2pp,MLTGY4pp,MLTGY1pp,MLTGY3pp (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]|.)
B2710 NHFRBO (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]|.)
B2738 FCLPA (No information about this protein was found by a literature search conducted on April 25, 2006.)
B2788 GLCRD (No information about this protein was found by a literature search conducted on January 9, 2006.)
B2789 GLCRt2rpp,GLYCAt2rpp,GALCTt2rpp (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.)
B2813 MLTGY4pp,MLTGY3pp,MLTGY2pp,MLTGY1pp (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]|.)
B2835 2AGPE160tipp,2AGPG180tipp,2AGPA160tipp,2AGPE161tipp,2AGPG160tipp,2AGPA181tipp,2AGPE180tipp,2AGPG181tipp,2AGPA120tipp,2AGPG141tipp,2AGPG140tipp,2AGPE140tipp,2AGPA161tipp,2AGPA140tipp,2AGPA141tipp,2AGPG161tipp,2AGPE141tipp,2AGPE120tipp,2AGPE181tipp,2AGPG120tipp,2AGPA180tipp (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]|.)
B2874 CBMKr (No information about this protein was found by a literature search conducted on January 10, 2006.)
B2895 RNTR4c,RNTR3c,RNTR1c,FLDR,RNTR2c NIL
B2923 ARGt3pp,LYSt3pp (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]|)
B2963 MLTGY3pp,MLTGY2pp,MLTGY1pp,MLTGY4pp (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]|)
B2979 GLYCTO2,GLYCTO4,GLYCTO3 (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]|.)
B3127 GALCTt2rpp,GLCRt2rpp,GLYCAt2rpp (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.)
B3290 Kt2pp (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]|.)
B3370 FRULYSt2pp,PSCLYSt2pp (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]|.)
B3380 PPM (No information about this protein was found by a literature search conducted on December 22, 2005.)
B3396 MPTG,MPTG2,MCTP2App,MCTP1App,MCTP1Bpp (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]|.)
B3469 COBALT2abcpp,ZN2abcpp,HG2abcpp,NI2abcpp,CU2abcpp,CD2abcpp (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]|.)
B3577 XYLUt2pp (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]|.)
B3578 XYLUt2pp (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]|.)
B3579 XYLUt2pp (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]|.)
B3610 GRXR,RNDR2b,RNDR4b,RNDR3b,PAPSR2,RNDR1b NIL
B3622 O16A4Lpp,ECA4OALpp (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]|)
B3679 INOSTt4pp (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.)
B3739 ATPS4rpp (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]|.)
B3748 RIBabcpp (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]|. )
B3781 RNDR4,PAPSR,DSBDR,RNDR2,METSOXR2,RNDR3,TRDR,RNDR1,METSOXR1,THIORDXi (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]|)
B3785 ECAP2pp,ECAP1pp,ECAP3pp (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.)
B3792 ECAtpp (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 ECAP2pp,ECAP3pp,ECAP1pp (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.)
B3803 UPP3MT (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]|.)
B3875 H2Otex (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]|)
B3951 PFL (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]|.)
B3952 PFL (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]|.)
B4192 ASCBPL (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]|.)
B4227 RIBabcpp (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.)
B4230 RIBabcpp (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.)
B4231 RIBabcpp (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.)
B4301 RPE (No information about this protein was found by a literature search conducted on September 19, 2005.)
B4356 GALCTNLt2pp (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.)
B4358 GALCTLO (YjjN did not show dehydrogenase activity in a high-throughput screen of purified proteins |CITS: [15808744]|. )
B4392 MLTGY2pp,MLTGY1pp,MLTGY4pp,MLTGY3pp (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]| )
B4407 THZPSN (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]|)
B4467 GLYCTO3,GLYCTO4,GLYCTO2 (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]|.)
B4468 GLYCTO4,GLYCTO2,GLYCTO3 (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]|.)
B4485 RIBabcpp (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.)