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Database: UniProt/SWISS-PROT
Entry: DCEB_ECOLI
LinkDB: DCEB_ECOLI
Original site: DCEB_ECOLI 
ID   DCEB_ECOLI              Reviewed;         466 AA.
AC   P69910; P28302; P76873;
DT   04-JAN-2005, integrated into UniProtKB/Swiss-Prot.
DT   04-JAN-2005, sequence version 1.
DT   25-OCT-2017, entry version 113.
DE   RecName: Full=Glutamate decarboxylase beta;
DE            Short=GAD-beta;
DE            EC=4.1.1.15;
GN   Name=gadB; OrderedLocusNames=b1493, JW1488;
OS   Escherichia coli (strain K12).
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC   Enterobacteriaceae; Escherichia.
OX   NCBI_TaxID=83333;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC   STRAIN=K12;
RX   PubMed=1522060; DOI=10.1128/jb.174.18.5820-5826.1992;
RA   Smith D.K., Kassam T., Singh B., Elliott J.F.;
RT   "Escherichia coli has two homologous glutamate decarboxylase genes
RT   that map to distinct loci.";
RL   J. Bacteriol. 174:5820-5826(1992).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX   PubMed=9097039; DOI=10.1093/dnares/3.6.363;
RA   Aiba H., Baba T., Fujita K., Hayashi K., Inada T., Isono K., Itoh T.,
RA   Kasai H., Kashimoto K., Kimura S., Kitakawa M., Kitagawa M.,
RA   Makino K., Miki T., Mizobuchi K., Mori H., Mori T., Motomura K.,
RA   Nakade S., Nakamura Y., Nashimoto H., Nishio Y., Oshima T., Saito N.,
RA   Sampei G., Seki Y., Sivasundaram S., Tagami H., Takeda J.,
RA   Takemoto K., Takeuchi Y., Wada C., Yamamoto Y., Horiuchi T.;
RT   "A 570-kb DNA sequence of the Escherichia coli K-12 genome
RT   corresponding to the 28.0-40.1 min region on the linkage map.";
RL   DNA Res. 3:363-377(1996).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=K12 / MG1655 / ATCC 47076;
RX   PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA   Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA   Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA   Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J.,
RA   Mau B., Shao Y.;
RT   "The complete genome sequence of Escherichia coli K-12.";
RL   Science 277:1453-1462(1997).
RN   [4]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX   PubMed=16738553; DOI=10.1038/msb4100049;
RA   Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA   Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT   "Highly accurate genome sequences of Escherichia coli K-12 strains
RT   MG1655 and W3110.";
RL   Mol. Syst. Biol. 2:E1-E5(2006).
RN   [5]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-318.
RC   STRAIN=K12;
RX   PubMed=9116051; DOI=10.1016/S0300-9084(97)84334-9;
RA   Turlin E., Gasser F., Biville F.;
RT   "Sequence and functional analysis of an Escherichia coli DNA fragment
RT   able to complement pqqE and pqqF mutants from Methylobacterium
RT   organophilum.";
RL   Biochimie 78:823-831(1996).
RN   [6]
RP   PROTEIN SEQUENCE OF 1-15.
RC   STRAIN=K12;
RX   PubMed=8455549; DOI=10.1007/BF00282791;
RA   Yoshida T., Ueguchi C., Yamada H., Mizuno T.;
RT   "Function of the Escherichia coli nucleoid protein, H-NS: molecular
RT   analysis of a subset of proteins whose expression is enhanced in a hns
RT   deletion mutant.";
RL   Mol. Gen. Genet. 237:113-122(1993).
RN   [7]
RP   TRANSCRIPTIONAL REGULATION.
RC   STRAIN=ATCC 11246;
RX   PubMed=10383761; DOI=10.1046/j.1365-2958.1999.01430.x;
RA   De Biase D., Tramonti A., Bossa F., Visca P.;
RT   "The response to stationary-phase stress conditions in Escherichia
RT   coli: role and regulation of the glutamic acid decarboxylase system.";
RL   Mol. Microbiol. 32:1198-1211(1999).
RN   [8]
RP   MUTAGENESIS OF LYS-276.
RC   STRAIN=K12 / JM109 / ATCC 53323;
RX   PubMed=12383249; DOI=10.1046/j.1432-1033.2002.03149.x;
RA   Tramonti A., John R.A., Bossa F., De Biase D.;
RT   "Contribution of Lys276 to the conformational flexibility of the
RT   active site of glutamate decarboxylase from Escherichia coli.";
RL   Eur. J. Biochem. 269:4913-4920(2002).
RN   [9]
RP   TRANSCRIPTIONAL REGULATION.
RC   STRAIN=ATCC 11246;
RX   PubMed=11976288; DOI=10.1128/JB.184.10.2603-2613.2002;
RA   Tramonti A., Visca P., De Canio M., Falconi M., De Biase D.;
RT   "Functional characterization and regulation of gadX, a gene encoding
RT   an AraC/XylS-like transcriptional activator of the Escherichia coli
RT   glutamic acid decarboxylase system.";
RL   J. Bacteriol. 184:2603-2613(2002).
RN   [10]
RP   TRANSCRIPTIONAL REGULATION.
RC   STRAIN=K12 / MG1655 / ATCC 47076;
RX   PubMed=12399493; DOI=10.1128/JB.184.22.6225-6234.2002;
RA   Masuda N., Church G.M.;
RT   "Escherichia coli gene expression responsive to levels of the response
RT   regulator EvgA.";
RL   J. Bacteriol. 184:6225-6234(2002).
RN   [11]
RP   TRANSCRIPTIONAL REGULATION.
RC   STRAIN=K12;
RX   PubMed=12446650; DOI=10.1128/JB.184.24.7001-7012.2002;
RA   Ma Z., Richard H., Tucker D.L., Conway T., Foster J.W.;
RT   "Collaborative regulation of Escherichia coli glutamate-dependent acid
RT   resistance by two AraC-like regulators, GadX and GadW (YhiW).";
RL   J. Bacteriol. 184:7001-7012(2002).
RN   [12]
RP   TRANSCRIPTIONAL REGULATION.
RX   PubMed=12867478; DOI=10.1128/JB.185.15.4644-4647.2003;
RA   Waterman S.R., Small P.L.C.;
RT   "Transcriptional expression of Escherichia coli glutamate-dependent
RT   acid resistance genes gadA and gadBC in an hns rpoS mutant.";
RL   J. Bacteriol. 185:4644-4647(2003).
RN   [13]
RP   TRANSCRIPTIONAL REGULATION.
RC   STRAIN=K12 / MG1655 / ATCC 47076;
RX   PubMed=12694615; DOI=10.1046/j.1365-2958.2003.03477.x;
RA   Masuda N., Church G.M.;
RT   "Regulatory network of acid resistance genes in Escherichia coli.";
RL   Mol. Microbiol. 48:699-712(2003).
RN   [14]
RP   TRANSCRIPTIONAL REGULATION.
RC   STRAIN=K12;
RX   PubMed=12940989; DOI=10.1046/j.1365-2958.2003.03633.x;
RA   Ma Z., Gong S., Richard H., Tucker D.L., Conway T., Foster J.W.;
RT   "GadE (YhiE) activates glutamate decarboxylase-dependent acid
RT   resistance in Escherichia coli K-12.";
RL   Mol. Microbiol. 49:1309-1320(2003).
RN   [15]
RP   ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-446; LYS-453 AND LYS-464,
RP   AND IDENTIFICATION BY MASS SPECTROMETRY.
RC   STRAIN=K12 / JW1106, and K12 / MG1655 / ATCC 47076;
RX   PubMed=18723842; DOI=10.1074/mcp.M800187-MCP200;
RA   Zhang J., Sprung R., Pei J., Tan X., Kim S., Zhu H., Liu C.F.,
RA   Grishin N.V., Zhao Y.;
RT   "Lysine acetylation is a highly abundant and evolutionarily conserved
RT   modification in Escherichia coli.";
RL   Mol. Cell. Proteomics 8:215-225(2009).
RN   [16]
RP   X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS), SUBUNIT, AND SUBCELLULAR
RP   LOCATION.
RX   PubMed=12912902; DOI=10.1093/emboj/cdg403;
RA   Capitani G., De Biase D., Aurizi C., Gut H., Bossa F., Gruetter M.G.;
RT   "Crystal structure and functional analysis of Escherichia coli
RT   glutamate decarboxylase.";
RL   EMBO J. 22:4027-4037(2003).
CC   -!- FUNCTION: Converts glutamate to gamma-aminobutyrate (GABA),
CC       consuming one intracellular proton in the reaction. The gad system
CC       helps to maintain a near-neutral intracellular pH when cells are
CC       exposed to extremely acidic conditions. The ability to survive
CC       transit through the acidic conditions of the stomach is essential
CC       for successful colonization of the mammalian host by commensal and
CC       pathogenic bacteria.
CC   -!- CATALYTIC ACTIVITY: L-glutamate = 4-aminobutanoate + CO(2).
CC   -!- COFACTOR:
CC       Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC   -!- SUBUNIT: Homohexamer composed of three dimers.
CC       {ECO:0000269|PubMed:12912902}.
CC   -!- INTERACTION:
CC       P36879:yadG; NbExp=2; IntAct=EBI-549514, EBI-550911;
CC   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:12912902}.
CC       Membrane {ECO:0000269|PubMed:12912902}. Note=Localized exclusively
CC       in the cytoplasm at neutral pH, but is recruited to the membrane
CC       when the pH falls.
CC   -!- INDUCTION: By acidic conditions. Expression is regulated by a
CC       complex system involving RpoS, cAMP, CRP, EvgAS, H-NS, GadE, GadW
CC       and GadX. The level of involvement for each regulator varies
CC       depending upon the growth phase and the medium.
CC       {ECO:0000269|PubMed:10383761, ECO:0000269|PubMed:11976288,
CC       ECO:0000269|PubMed:12399493, ECO:0000269|PubMed:12446650,
CC       ECO:0000269|PubMed:12694615, ECO:0000269|PubMed:12867478,
CC       ECO:0000269|PubMed:12940989}.
CC   -!- MISCELLANEOUS: Changing Lys-276 to Ala increases thermal stability
CC       and protease resistance. The unfolding temperature is increased by
CC       11 degrees Celsius.
CC   -!- SIMILARITY: Belongs to the group II decarboxylase family.
CC       {ECO:0000305}.
DR   EMBL; M84025; AAA23834.1; -; Genomic_DNA.
DR   EMBL; U00096; AAC74566.1; -; Genomic_DNA.
DR   EMBL; AP009048; BAA15163.1; -; Genomic_DNA.
DR   EMBL; X71917; CAA50736.1; ALT_SEQ; Genomic_DNA.
DR   PIR; B43332; B43332.
DR   RefSeq; NP_416010.1; NC_000913.3.
DR   RefSeq; WP_000358930.1; NZ_LN832404.1.
DR   PDB; 1PMM; X-ray; 2.00 A; A/B/C/D/E/F=1-466.
DR   PDB; 1PMO; X-ray; 2.30 A; A/B/C/D/E/F=1-466.
DR   PDB; 2DGK; X-ray; 1.90 A; A/B/C/D/E/F=15-466.
DR   PDB; 2DGL; X-ray; 3.15 A; A/B/C/D/E/F=1-466.
DR   PDB; 2DGM; X-ray; 1.95 A; A/B/C/D/E/F=1-466.
DR   PDB; 3FZ6; X-ray; 2.82 A; A/B/C/D/E/F=1-466.
DR   PDB; 3FZ7; X-ray; 2.50 A; A/B/C/D/E/F=1-466.
DR   PDB; 3FZ8; X-ray; 3.00 A; A/B/C/D/E/F=1-466.
DR   PDBsum; 1PMM; -.
DR   PDBsum; 1PMO; -.
DR   PDBsum; 2DGK; -.
DR   PDBsum; 2DGL; -.
DR   PDBsum; 2DGM; -.
DR   PDBsum; 3FZ6; -.
DR   PDBsum; 3FZ7; -.
DR   PDBsum; 3FZ8; -.
DR   ProteinModelPortal; P69910; -.
DR   SMR; P69910; -.
DR   DIP; DIP-36202N; -.
DR   IntAct; P69910; 16.
DR   MINT; MINT-1256225; -.
DR   STRING; 316385.ECDH10B_1624; -.
DR   iPTMnet; P69910; -.
DR   PaxDb; P69910; -.
DR   PRIDE; P69910; -.
DR   EnsemblBacteria; AAC74566; AAC74566; b1493.
DR   EnsemblBacteria; BAA15163; BAA15163; BAA15163.
DR   GeneID; 946058; -.
DR   KEGG; ecj:JW1488; -.
DR   KEGG; eco:b1493; -.
DR   PATRIC; fig|1411691.4.peg.774; -.
DR   EchoBASE; EB1453; -.
DR   EcoGene; EG11490; gadB.
DR   eggNOG; ENOG4105CVK; Bacteria.
DR   eggNOG; COG0076; LUCA.
DR   HOGENOM; HOG000070228; -.
DR   InParanoid; P69910; -.
DR   KO; K01580; -.
DR   PhylomeDB; P69910; -.
DR   BioCyc; EcoCyc:GLUTDECARBOXB-MONOMER; -.
DR   BioCyc; MetaCyc:GLUTDECARBOXB-MONOMER; -.
DR   BRENDA; 4.1.1.15; 2026.
DR   EvolutionaryTrace; P69910; -.
DR   PRO; PR:P69910; -.
DR   Proteomes; UP000000318; Chromosome.
DR   Proteomes; UP000000625; Chromosome.
DR   GO; GO:0005829; C:cytosol; IDA:UniProtKB.
DR   GO; GO:0016020; C:membrane; IDA:UniProtKB.
DR   GO; GO:0004351; F:glutamate decarboxylase activity; IDA:EcoCyc.
DR   GO; GO:0030170; F:pyridoxal phosphate binding; IEA:InterPro.
DR   GO; GO:0006536; P:glutamate metabolic process; IEA:InterPro.
DR   GO; GO:0051454; P:intracellular pH elevation; IMP:EcoCyc.
DR   Gene3D; 3.40.640.10; -; 1.
DR   Gene3D; 3.90.1150.10; -; 1.
DR   InterPro; IPR010107; Glutamate_decarboxylase.
DR   InterPro; IPR002129; PyrdxlP-dep_de-COase.
DR   InterPro; IPR015424; PyrdxlP-dep_Trfase.
DR   InterPro; IPR015421; PyrdxlP-dep_Trfase_major_sub1.
DR   InterPro; IPR015422; PyrdxlP-dep_Trfase_sub2.
DR   InterPro; IPR021115; Pyridoxal-P_BS.
DR   PANTHER; PTHR43321; PTHR43321; 1.
DR   Pfam; PF00282; Pyridoxal_deC; 1.
DR   SUPFAM; SSF53383; SSF53383; 1.
DR   TIGRFAMs; TIGR01788; Glu-decarb-GAD; 1.
DR   PROSITE; PS00392; DDC_GAD_HDC_YDC; 1.
PE   1: Evidence at protein level;
KW   3D-structure; Acetylation; Complete proteome; Cytoplasm;
KW   Decarboxylase; Direct protein sequencing; Lyase; Membrane;
KW   Pyridoxal phosphate; Reference proteome.
FT   CHAIN         1    466       Glutamate decarboxylase beta.
FT                                /FTId=PRO_0000146982.
FT   REGION      126    127       Pyridoxal phosphate binding.
FT   BINDING      62     62       Substrate.
FT   BINDING      83     83       Substrate.
FT   BINDING     212    212       Pyridoxal phosphate.
FT   BINDING     275    275       Pyridoxal phosphate.
FT   MOD_RES     276    276       N6-(pyridoxal phosphate)lysine.
FT   MOD_RES     446    446       N6-acetyllysine.
FT                                {ECO:0000269|PubMed:18723842}.
FT   MOD_RES     453    453       N6-acetyllysine.
FT                                {ECO:0000269|PubMed:18723842}.
FT   MOD_RES     464    464       N6-acetyllysine.
FT                                {ECO:0000269|PubMed:18723842}.
FT   MUTAGEN     276    276       K->A: Strongly reduces pyridoxal
FT                                phosphate binding and increases stability
FT                                of the polypeptide.
FT                                {ECO:0000269|PubMed:12383249}.
FT   MUTAGEN     276    276       K->H: Abolishes pyridoxal phosphate
FT                                binding. {ECO:0000269|PubMed:12383249}.
FT   HELIX         4     14       {ECO:0000244|PDB:2DGM}.
FT   TURN         17     19       {ECO:0000244|PDB:2DGM}.
FT   HELIX        21     23       {ECO:0000244|PDB:2DGM}.
FT   STRAND       25     28       {ECO:0000244|PDB:3FZ8}.
FT   STRAND       29     31       {ECO:0000244|PDB:1PMO}.
FT   HELIX        39     49       {ECO:0000244|PDB:2DGK}.
FT   HELIX        50     52       {ECO:0000244|PDB:2DGK}.
FT   HELIX        56     58       {ECO:0000244|PDB:2DGM}.
FT   HELIX        70     78       {ECO:0000244|PDB:2DGK}.
FT   TURN         79     81       {ECO:0000244|PDB:2DGK}.
FT   TURN         87     89       {ECO:0000244|PDB:2DGK}.
FT   HELIX        91    107       {ECO:0000244|PDB:2DGK}.
FT   STRAND      114    116       {ECO:0000244|PDB:1PMO}.
FT   STRAND      119    125       {ECO:0000244|PDB:2DGK}.
FT   HELIX       126    147       {ECO:0000244|PDB:2DGK}.
FT   STRAND      156    161       {ECO:0000244|PDB:2DGK}.
FT   HELIX       164    172       {ECO:0000244|PDB:2DGK}.
FT   STRAND      176    179       {ECO:0000244|PDB:2DGK}.
FT   HELIX       191    197       {ECO:0000244|PDB:2DGK}.
FT   STRAND      202    206       {ECO:0000244|PDB:2DGK}.
FT   STRAND      208    210       {ECO:0000244|PDB:2DGK}.
FT   TURN        212    214       {ECO:0000244|PDB:2DGK}.
FT   HELIX       220    234       {ECO:0000244|PDB:2DGK}.
FT   STRAND      240    243       {ECO:0000244|PDB:2DGK}.
FT   HELIX       247    249       {ECO:0000244|PDB:2DGK}.
FT   HELIX       251    254       {ECO:0000244|PDB:2DGK}.
FT   STRAND      267    273       {ECO:0000244|PDB:2DGK}.
FT   TURN        274    278       {ECO:0000244|PDB:2DGK}.
FT   STRAND      285    291       {ECO:0000244|PDB:2DGK}.
FT   HELIX       292    294       {ECO:0000244|PDB:2DGK}.
FT   HELIX       297    299       {ECO:0000244|PDB:2DGK}.
FT   STRAND      301    303       {ECO:0000244|PDB:2DGK}.
FT   STRAND      310    312       {ECO:0000244|PDB:2DGK}.
FT   HELIX       322    358       {ECO:0000244|PDB:2DGK}.
FT   STRAND      361    368       {ECO:0000244|PDB:2DGK}.
FT   TURN        371    373       {ECO:0000244|PDB:2DGK}.
FT   STRAND      374    382       {ECO:0000244|PDB:2DGK}.
FT   HELIX       392    401       {ECO:0000244|PDB:2DGK}.
FT   STRAND      408    410       {ECO:0000244|PDB:2DGK}.
FT   HELIX       413    415       {ECO:0000244|PDB:2DGM}.
FT   STRAND      419    424       {ECO:0000244|PDB:2DGK}.
FT   HELIX       431    450       {ECO:0000244|PDB:2DGK}.
FT   HELIX       452    454       {ECO:0000244|PDB:2DGK}.
SQ   SEQUENCE   466 AA;  52668 MW;  8E653330A3C5B4ED CRC64;
     MDKKQVTDLR SELLDSRFGA KSISTIAESK RFPLHEMRDD VAFQIINDEL YLDGNARQNL
     ATFCQTWDDE NVHKLMDLSI NKNWIDKEEY PQSAAIDLRC VNMVADLWHA PAPKNGQAVG
     TNTIGSSEAC MLGGMAMKWR WRKRMEAAGK PTDKPNLVCG PVQICWHKFA RYWDVELREI
     PMRPGQLFMD PKRMIEACDE NTIGVVPTFG VTYTGNYEFP QPLHDALDKF QADTGIDIDM
     HIDAASGGFL APFVAPDIVW DFRLPRVKSI SASGHKFGLA PLGCGWVIWR DEEALPQELV
     FNVDYLGGQI GTFAINFSRP AGQVIAQYYE FLRLGREGYT KVQNASYQVA AYLADEIAKL
     GPYEFICTGR PDEGIPAVCF KLKDGEDPGY TLYDLSERLR LRGWQVPAFT LGGEATDIVV
     MRIMCRRGFE MDFAELLLED YKASLKYLSD HPKLQGIAQQ NSFKHT
//
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