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Glutamate decarboxylase beta (GAD-beta) (EC 4.1.1.15)

 DCEB_ECOLI              Reviewed;         466 AA.
P69910; P28302; P76873;
04-JAN-2005, integrated into UniProtKB/Swiss-Prot.
04-JAN-2005, sequence version 1.
05-DEC-2018, entry version 117.
RecName: Full=Glutamate decarboxylase beta;
Short=GAD-beta;
EC=4.1.1.15;
Name=gadB; OrderedLocusNames=b1493, JW1488;
Escherichia coli (strain K12).
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
Enterobacteriaceae; Escherichia.
NCBI_TaxID=83333;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=K12;
PubMed=1522060; DOI=10.1128/jb.174.18.5820-5826.1992;
Smith D.K., Kassam T., Singh B., Elliott J.F.;
"Escherichia coli has two homologous glutamate decarboxylase genes
that map to distinct loci.";
J. Bacteriol. 174:5820-5826(1992).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
PubMed=9097039; DOI=10.1093/dnares/3.6.363;
Aiba H., Baba T., Fujita K., Hayashi K., Inada T., Isono K., Itoh T.,
Kasai H., Kashimoto K., Kimura S., Kitakawa M., Kitagawa M.,
Makino K., Miki T., Mizobuchi K., Mori H., Mori T., Motomura K.,
Nakade S., Nakamura Y., Nashimoto H., Nishio Y., Oshima T., Saito N.,
Sampei G., Seki Y., Sivasundaram S., Tagami H., Takeda J.,
Takemoto K., Takeuchi Y., Wada C., Yamamoto Y., Horiuchi T.;
"A 570-kb DNA sequence of the Escherichia coli K-12 genome
corresponding to the 28.0-40.1 min region on the linkage map.";
DNA Res. 3:363-377(1996).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / MG1655 / ATCC 47076;
PubMed=9278503; DOI=10.1126/science.277.5331.1453;
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J.,
Mau B., Shao Y.;
"The complete genome sequence of Escherichia coli K-12.";
Science 277:1453-1462(1997).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
PubMed=16738553; DOI=10.1038/msb4100049;
Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
"Highly accurate genome sequences of Escherichia coli K-12 strains
MG1655 and W3110.";
Mol. Syst. Biol. 2:E1-E5(2006).
[5]
NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-318.
STRAIN=K12;
PubMed=9116051; DOI=10.1016/S0300-9084(97)84334-9;
Turlin E., Gasser F., Biville F.;
"Sequence and functional analysis of an Escherichia coli DNA fragment
able to complement pqqE and pqqF mutants from Methylobacterium
organophilum.";
Biochimie 78:823-831(1996).
[6]
PROTEIN SEQUENCE OF 1-15.
STRAIN=K12;
PubMed=8455549; DOI=10.1007/BF00282791;
Yoshida T., Ueguchi C., Yamada H., Mizuno T.;
"Function of the Escherichia coli nucleoid protein, H-NS: molecular
analysis of a subset of proteins whose expression is enhanced in a hns
deletion mutant.";
Mol. Gen. Genet. 237:113-122(1993).
[7]
TRANSCRIPTIONAL REGULATION.
STRAIN=ATCC 11246;
PubMed=10383761; DOI=10.1046/j.1365-2958.1999.01430.x;
De Biase D., Tramonti A., Bossa F., Visca P.;
"The response to stationary-phase stress conditions in Escherichia
coli: role and regulation of the glutamic acid decarboxylase system.";
Mol. Microbiol. 32:1198-1211(1999).
[8]
MUTAGENESIS OF LYS-276.
STRAIN=K12 / JM109 / ATCC 53323;
PubMed=12383249; DOI=10.1046/j.1432-1033.2002.03149.x;
Tramonti A., John R.A., Bossa F., De Biase D.;
"Contribution of Lys276 to the conformational flexibility of the
active site of glutamate decarboxylase from Escherichia coli.";
Eur. J. Biochem. 269:4913-4920(2002).
[9]
TRANSCRIPTIONAL REGULATION.
STRAIN=ATCC 11246;
PubMed=11976288; DOI=10.1128/JB.184.10.2603-2613.2002;
Tramonti A., Visca P., De Canio M., Falconi M., De Biase D.;
"Functional characterization and regulation of gadX, a gene encoding
an AraC/XylS-like transcriptional activator of the Escherichia coli
glutamic acid decarboxylase system.";
J. Bacteriol. 184:2603-2613(2002).
[10]
TRANSCRIPTIONAL REGULATION.
STRAIN=K12 / MG1655 / ATCC 47076;
PubMed=12399493; DOI=10.1128/JB.184.22.6225-6234.2002;
Masuda N., Church G.M.;
"Escherichia coli gene expression responsive to levels of the response
regulator EvgA.";
J. Bacteriol. 184:6225-6234(2002).
[11]
TRANSCRIPTIONAL REGULATION.
STRAIN=K12;
PubMed=12446650; DOI=10.1128/JB.184.24.7001-7012.2002;
Ma Z., Richard H., Tucker D.L., Conway T., Foster J.W.;
"Collaborative regulation of Escherichia coli glutamate-dependent acid
resistance by two AraC-like regulators, GadX and GadW (YhiW).";
J. Bacteriol. 184:7001-7012(2002).
[12]
TRANSCRIPTIONAL REGULATION.
PubMed=12867478; DOI=10.1128/JB.185.15.4644-4647.2003;
Waterman S.R., Small P.L.C.;
"Transcriptional expression of Escherichia coli glutamate-dependent
acid resistance genes gadA and gadBC in an hns rpoS mutant.";
J. Bacteriol. 185:4644-4647(2003).
[13]
TRANSCRIPTIONAL REGULATION.
STRAIN=K12 / MG1655 / ATCC 47076;
PubMed=12694615; DOI=10.1046/j.1365-2958.2003.03477.x;
Masuda N., Church G.M.;
"Regulatory network of acid resistance genes in Escherichia coli.";
Mol. Microbiol. 48:699-712(2003).
[14]
TRANSCRIPTIONAL REGULATION.
STRAIN=K12;
PubMed=12940989; DOI=10.1046/j.1365-2958.2003.03633.x;
Ma Z., Gong S., Richard H., Tucker D.L., Conway T., Foster J.W.;
"GadE (YhiE) activates glutamate decarboxylase-dependent acid
resistance in Escherichia coli K-12.";
Mol. Microbiol. 49:1309-1320(2003).
[15]
ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-446; LYS-453 AND LYS-464,
AND IDENTIFICATION BY MASS SPECTROMETRY.
STRAIN=K12 / JW1106, and K12 / MG1655 / ATCC 47076;
PubMed=18723842; DOI=10.1074/mcp.M800187-MCP200;
Zhang J., Sprung R., Pei J., Tan X., Kim S., Zhu H., Liu C.F.,
Grishin N.V., Zhao Y.;
"Lysine acetylation is a highly abundant and evolutionarily conserved
modification in Escherichia coli.";
Mol. Cell. Proteomics 8:215-225(2009).
[16]
X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS), SUBUNIT, AND SUBCELLULAR
LOCATION.
PubMed=12912902; DOI=10.1093/emboj/cdg403;
Capitani G., De Biase D., Aurizi C., Gut H., Bossa F., Gruetter M.G.;
"Crystal structure and functional analysis of Escherichia coli
glutamate decarboxylase.";
EMBO J. 22:4027-4037(2003).
-!- FUNCTION: Converts glutamate to gamma-aminobutyrate (GABA),
consuming one intracellular proton in the reaction. The gad system
helps to maintain a near-neutral intracellular pH when cells are
exposed to extremely acidic conditions. The ability to survive
transit through the acidic conditions of the stomach is essential
for successful colonization of the mammalian host by commensal and
pathogenic bacteria.
-!- CATALYTIC ACTIVITY:
Reaction=H(+) + L-glutamate = 4-aminobutanoate + CO2;
Xref=Rhea:RHEA:17785, ChEBI:CHEBI:15378, ChEBI:CHEBI:16526,
ChEBI:CHEBI:29985, ChEBI:CHEBI:59888; EC=4.1.1.15;
-!- COFACTOR:
Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
-!- SUBUNIT: Homohexamer composed of three dimers.
{ECO:0000269|PubMed:12912902}.
-!- INTERACTION:
P36879:yadG; NbExp=2; IntAct=EBI-549514, EBI-550911;
-!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:12912902}.
Membrane {ECO:0000269|PubMed:12912902}. Note=Localized exclusively
in the cytoplasm at neutral pH, but is recruited to the membrane
when the pH falls.
-!- INDUCTION: By acidic conditions. Expression is regulated by a
complex system involving RpoS, cAMP, CRP, EvgAS, H-NS, GadE, GadW
and GadX. The level of involvement for each regulator varies
depending upon the growth phase and the medium.
{ECO:0000269|PubMed:10383761, ECO:0000269|PubMed:11976288,
ECO:0000269|PubMed:12399493, ECO:0000269|PubMed:12446650,
ECO:0000269|PubMed:12694615, ECO:0000269|PubMed:12867478,
ECO:0000269|PubMed:12940989}.
-!- MISCELLANEOUS: Changing Lys-276 to Ala increases thermal stability
and protease resistance. The unfolding temperature is increased by
11 degrees Celsius.
-!- SIMILARITY: Belongs to the group II decarboxylase family.
{ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; M84025; AAA23834.1; -; Genomic_DNA.
EMBL; U00096; AAC74566.1; -; Genomic_DNA.
EMBL; AP009048; BAA15163.1; -; Genomic_DNA.
EMBL; X71917; CAA50736.1; ALT_SEQ; Genomic_DNA.
PIR; B43332; B43332.
RefSeq; NP_416010.1; NC_000913.3.
RefSeq; WP_000358930.1; NZ_LN832404.1.
PDB; 1PMM; X-ray; 2.00 A; A/B/C/D/E/F=1-466.
PDB; 1PMO; X-ray; 2.30 A; A/B/C/D/E/F=1-466.
PDB; 2DGK; X-ray; 1.90 A; A/B/C/D/E/F=15-466.
PDB; 2DGL; X-ray; 3.15 A; A/B/C/D/E/F=1-466.
PDB; 2DGM; X-ray; 1.95 A; A/B/C/D/E/F=1-466.
PDB; 3FZ6; X-ray; 2.82 A; A/B/C/D/E/F=1-466.
PDB; 3FZ7; X-ray; 2.50 A; A/B/C/D/E/F=1-466.
PDB; 3FZ8; X-ray; 3.00 A; A/B/C/D/E/F=1-466.
PDBsum; 1PMM; -.
PDBsum; 1PMO; -.
PDBsum; 2DGK; -.
PDBsum; 2DGL; -.
PDBsum; 2DGM; -.
PDBsum; 3FZ6; -.
PDBsum; 3FZ7; -.
PDBsum; 3FZ8; -.
ProteinModelPortal; P69910; -.
SMR; P69910; -.
BioGrid; 4260788; 5.
DIP; DIP-36202N; -.
IntAct; P69910; 16.
MINT; P69910; -.
STRING; 316385.ECDH10B_1624; -.
iPTMnet; P69910; -.
PaxDb; P69910; -.
PRIDE; P69910; -.
EnsemblBacteria; AAC74566; AAC74566; b1493.
EnsemblBacteria; BAA15163; BAA15163; BAA15163.
GeneID; 946058; -.
KEGG; ecj:JW1488; -.
KEGG; eco:b1493; -.
PATRIC; fig|1411691.4.peg.774; -.
EchoBASE; EB1453; -.
EcoGene; EG11490; gadB.
eggNOG; ENOG4105CVK; Bacteria.
eggNOG; COG0076; LUCA.
HOGENOM; HOG000070228; -.
InParanoid; P69910; -.
KO; K01580; -.
PhylomeDB; P69910; -.
BioCyc; EcoCyc:GLUTDECARBOXB-MONOMER; -.
BioCyc; MetaCyc:GLUTDECARBOXB-MONOMER; -.
BRENDA; 4.1.1.15; 2026.
EvolutionaryTrace; P69910; -.
PRO; PR:P69910; -.
Proteomes; UP000000318; Chromosome.
Proteomes; UP000000625; Chromosome.
GO; GO:0005829; C:cytosol; HDA:UniProtKB.
GO; GO:0016020; C:membrane; HDA:UniProtKB.
GO; GO:0004351; F:glutamate decarboxylase activity; IDA:EcoCyc.
GO; GO:0030170; F:pyridoxal phosphate binding; IEA:InterPro.
GO; GO:0006538; P:glutamate catabolic process; IBA:GO_Central.
GO; GO:0051454; P:intracellular pH elevation; IMP:EcoCyc.
Gene3D; 3.40.640.10; -; 1.
InterPro; IPR010107; Glutamate_decarboxylase.
InterPro; IPR002129; PyrdxlP-dep_de-COase.
InterPro; IPR015424; PyrdxlP-dep_Trfase.
InterPro; IPR015421; PyrdxlP-dep_Trfase_major.
InterPro; IPR021115; Pyridoxal-P_BS.
PANTHER; PTHR43321; PTHR43321; 1.
Pfam; PF00282; Pyridoxal_deC; 1.
SUPFAM; SSF53383; SSF53383; 1.
TIGRFAMs; TIGR01788; Glu-decarb-GAD; 1.
PROSITE; PS00392; DDC_GAD_HDC_YDC; 1.
1: Evidence at protein level;
3D-structure; Acetylation; Complete proteome; Cytoplasm;
Decarboxylase; Direct protein sequencing; Lyase; Membrane;
Pyridoxal phosphate; Reference proteome.
CHAIN 1 466 Glutamate decarboxylase beta.
/FTId=PRO_0000146982.
REGION 126 127 Pyridoxal phosphate binding.
BINDING 62 62 Substrate.
BINDING 83 83 Substrate.
BINDING 212 212 Pyridoxal phosphate.
BINDING 275 275 Pyridoxal phosphate.
MOD_RES 276 276 N6-(pyridoxal phosphate)lysine.
MOD_RES 446 446 N6-acetyllysine.
{ECO:0000269|PubMed:18723842}.
MOD_RES 453 453 N6-acetyllysine.
{ECO:0000269|PubMed:18723842}.
MOD_RES 464 464 N6-acetyllysine.
{ECO:0000269|PubMed:18723842}.
MUTAGEN 276 276 K->A: Strongly reduces pyridoxal
phosphate binding and increases stability
of the polypeptide.
{ECO:0000269|PubMed:12383249}.
MUTAGEN 276 276 K->H: Abolishes pyridoxal phosphate
binding. {ECO:0000269|PubMed:12383249}.
HELIX 4 14 {ECO:0000244|PDB:2DGM}.
TURN 17 19 {ECO:0000244|PDB:2DGM}.
HELIX 21 23 {ECO:0000244|PDB:2DGM}.
STRAND 25 28 {ECO:0000244|PDB:3FZ8}.
STRAND 29 31 {ECO:0000244|PDB:1PMO}.
HELIX 39 49 {ECO:0000244|PDB:2DGK}.
HELIX 50 52 {ECO:0000244|PDB:2DGK}.
HELIX 56 58 {ECO:0000244|PDB:2DGM}.
HELIX 70 78 {ECO:0000244|PDB:2DGK}.
TURN 79 81 {ECO:0000244|PDB:2DGK}.
TURN 87 89 {ECO:0000244|PDB:2DGK}.
HELIX 91 107 {ECO:0000244|PDB:2DGK}.
STRAND 114 116 {ECO:0000244|PDB:1PMO}.
STRAND 119 125 {ECO:0000244|PDB:2DGK}.
HELIX 126 147 {ECO:0000244|PDB:2DGK}.
STRAND 156 161 {ECO:0000244|PDB:2DGK}.
HELIX 164 172 {ECO:0000244|PDB:2DGK}.
STRAND 176 179 {ECO:0000244|PDB:2DGK}.
HELIX 191 197 {ECO:0000244|PDB:2DGK}.
STRAND 202 206 {ECO:0000244|PDB:2DGK}.
STRAND 208 210 {ECO:0000244|PDB:2DGK}.
TURN 212 214 {ECO:0000244|PDB:2DGK}.
HELIX 220 234 {ECO:0000244|PDB:2DGK}.
STRAND 240 243 {ECO:0000244|PDB:2DGK}.
HELIX 247 249 {ECO:0000244|PDB:2DGK}.
HELIX 251 254 {ECO:0000244|PDB:2DGK}.
STRAND 267 273 {ECO:0000244|PDB:2DGK}.
TURN 274 278 {ECO:0000244|PDB:2DGK}.
STRAND 285 291 {ECO:0000244|PDB:2DGK}.
HELIX 292 294 {ECO:0000244|PDB:2DGK}.
HELIX 297 299 {ECO:0000244|PDB:2DGK}.
STRAND 301 303 {ECO:0000244|PDB:2DGK}.
STRAND 310 312 {ECO:0000244|PDB:2DGK}.
HELIX 322 358 {ECO:0000244|PDB:2DGK}.
STRAND 361 368 {ECO:0000244|PDB:2DGK}.
TURN 371 373 {ECO:0000244|PDB:2DGK}.
STRAND 374 382 {ECO:0000244|PDB:2DGK}.
HELIX 392 401 {ECO:0000244|PDB:2DGK}.
STRAND 408 410 {ECO:0000244|PDB:2DGK}.
HELIX 413 415 {ECO:0000244|PDB:2DGM}.
STRAND 419 424 {ECO:0000244|PDB:2DGK}.
HELIX 431 450 {ECO:0000244|PDB:2DGK}.
HELIX 452 454 {ECO:0000244|PDB:2DGK}.
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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