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 03-AUG-2022, entry version 139.
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 that map
RT 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., Makino K.,
RA Miki T., Mizobuchi K., Mori H., Mori T., Motomura K., Nakade S.,
RA Nakamura Y., Nashimoto H., Nishio Y., Oshima T., Saito N., Sampei G.,
RA Seki Y., Sivasundaram S., Tagami H., Takeda J., Takemoto K., Takeuchi Y.,
RA Wada C., Yamamoto Y., Horiuchi T.;
RT "A 570-kb DNA sequence of the Escherichia coli K-12 genome corresponding to
RT 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., Mau B.,
RA 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 MG1655
RT 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 able
RT to complement pqqE and pqqF mutants from Methylobacterium 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 coli:
RT 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 active
RT 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 an
RT AraC/XylS-like transcriptional activator of the Escherichia coli glutamic
RT 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 acid
RT 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 resistance in
RT 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, AND
RP 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 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 glutamate
RT decarboxylase.";
RL EMBO J. 22:4027-4037(2003).
CC -!- FUNCTION: Converts glutamate to gamma-aminobutyrate (GABA), consuming
CC one intracellular proton in the reaction. The gad system helps to
CC maintain a near-neutral intracellular pH when cells are exposed to
CC extremely acidic conditions. The ability to survive transit through the
CC acidic conditions of the stomach is essential for successful
CC colonization of the mammalian host by commensal and pathogenic
CC bacteria.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H(+) + L-glutamate = 4-aminobutanoate + CO2;
CC Xref=Rhea:RHEA:17785, ChEBI:CHEBI:15378, ChEBI:CHEBI:16526,
CC ChEBI:CHEBI:29985, ChEBI:CHEBI:59888; EC=4.1.1.15;
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 P69910; P36879: yadG; NbExp=2; IntAct=EBI-549514, EBI-550911;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:12912902}. Membrane
CC {ECO:0000269|PubMed:12912902}. Note=Localized exclusively in the
CC cytoplasm at neutral pH, but is recruited to the membrane when the pH
CC falls.
CC -!- INDUCTION: By acidic conditions. Expression is regulated by a complex
CC system involving RpoS, cAMP, CRP, EvgAS, H-NS, GadE, GadW and GadX. The
CC level of involvement for each regulator varies depending upon the
CC growth phase and the medium. {ECO:0000269|PubMed:10383761,
CC ECO:0000269|PubMed:11976288, ECO:0000269|PubMed:12399493,
CC ECO:0000269|PubMed:12446650, ECO:0000269|PubMed:12694615,
CC ECO:0000269|PubMed:12867478, ECO:0000269|PubMed:12940989}.
CC -!- MISCELLANEOUS: Changing Lys-276 to Ala increases thermal stability and
CC protease resistance. The unfolding temperature is increased by 11
CC degrees Celsius.
CC -!- SIMILARITY: Belongs to the group II decarboxylase family.
CC {ECO:0000305}.
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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_SSUV01000024.1.
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 AlphaFoldDB; P69910; -.
DR SMR; P69910; -.
DR BioGRID; 4260788; 5.
DR BioGRID; 850419; 2.
DR DIP; DIP-36202N; -.
DR IntAct; P69910; 16.
DR MINT; P69910; -.
DR STRING; 511145.b1493; -.
DR iPTMnet; P69910; -.
DR jPOST; P69910; -.
DR PaxDb; P69910; -.
DR PRIDE; P69910; -.
DR EnsemblBacteria; AAC74566; AAC74566; b1493.
DR EnsemblBacteria; BAA15163; BAA15163; BAA15163.
DR GeneID; 66674655; -.
DR GeneID; 946058; -.
DR KEGG; ecj:JW1488; -.
DR KEGG; eco:b1493; -.
DR PATRIC; fig|1411691.4.peg.774; -.
DR EchoBASE; EB1453; -.
DR eggNOG; COG0076; Bacteria.
DR HOGENOM; CLU_019582_0_0_6; -.
DR InParanoid; P69910; -.
DR OMA; TMAPHSE; -.
DR PhylomeDB; P69910; -.
DR BioCyc; EcoCyc:GLUTDECARBOXB-MON; -.
DR BioCyc; MetaCyc:GLUTDECARBOXB-MON; -.
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; HDA:UniProtKB.
DR GO; GO:0016020; C:membrane; HDA:UniProtKB.
DR GO; GO:0004351; F:glutamate decarboxylase activity; IDA:EcoCyc.
DR GO; GO:0030170; F:pyridoxal phosphate binding; IEA:InterPro.
DR GO; GO:0006538; P:glutamate catabolic process; IBA:GO_Central.
DR GO; GO:0051454; P:intracellular pH elevation; IMP:EcoCyc.
DR Gene3D; 3.40.640.10; -; 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.
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; Cytoplasm; Decarboxylase;
KW Direct protein sequencing; Lyase; Membrane; Pyridoxal phosphate;
KW Reference proteome.
FT CHAIN 1..466
FT /note="Glutamate decarboxylase beta"
FT /id="PRO_0000146982"
FT BINDING 62
FT /ligand="substrate"
FT BINDING 83
FT /ligand="substrate"
FT BINDING 126..127
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT BINDING 212
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT BINDING 275
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT MOD_RES 276
FT /note="N6-(pyridoxal phosphate)lysine"
FT MOD_RES 446
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000269|PubMed:18723842"
FT MOD_RES 453
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000269|PubMed:18723842"
FT MOD_RES 464
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000269|PubMed:18723842"
FT MUTAGEN 276
FT /note="K->A: Strongly reduces pyridoxal phosphate binding
FT and increases stability of the polypeptide."
FT /evidence="ECO:0000269|PubMed:12383249"
FT MUTAGEN 276
FT /note="K->H: Abolishes pyridoxal phosphate binding."
FT /evidence="ECO:0000269|PubMed:12383249"
FT HELIX 4..14
FT /evidence="ECO:0007829|PDB:2DGM"
FT TURN 17..19
FT /evidence="ECO:0007829|PDB:2DGM"
FT HELIX 21..23
FT /evidence="ECO:0007829|PDB:2DGM"
FT STRAND 25..28
FT /evidence="ECO:0007829|PDB:3FZ8"
FT STRAND 29..31
FT /evidence="ECO:0007829|PDB:1PMO"
FT HELIX 39..49
FT /evidence="ECO:0007829|PDB:2DGK"
FT HELIX 50..52
FT /evidence="ECO:0007829|PDB:2DGK"
FT HELIX 56..58
FT /evidence="ECO:0007829|PDB:2DGM"
FT HELIX 70..78
FT /evidence="ECO:0007829|PDB:2DGK"
FT TURN 79..81
FT /evidence="ECO:0007829|PDB:2DGK"
FT TURN 87..89
FT /evidence="ECO:0007829|PDB:2DGK"
FT HELIX 91..107
FT /evidence="ECO:0007829|PDB:2DGK"
FT STRAND 114..116
FT /evidence="ECO:0007829|PDB:1PMO"
FT STRAND 119..125
FT /evidence="ECO:0007829|PDB:2DGK"
FT HELIX 126..147
FT /evidence="ECO:0007829|PDB:2DGK"
FT STRAND 156..161
FT /evidence="ECO:0007829|PDB:2DGK"
FT HELIX 164..172
FT /evidence="ECO:0007829|PDB:2DGK"
FT STRAND 176..179
FT /evidence="ECO:0007829|PDB:2DGK"
FT HELIX 191..197
FT /evidence="ECO:0007829|PDB:2DGK"
FT STRAND 202..206
FT /evidence="ECO:0007829|PDB:2DGK"
FT STRAND 208..210
FT /evidence="ECO:0007829|PDB:2DGK"
FT TURN 212..214
FT /evidence="ECO:0007829|PDB:2DGK"
FT HELIX 220..234
FT /evidence="ECO:0007829|PDB:2DGK"
FT STRAND 240..243
FT /evidence="ECO:0007829|PDB:2DGK"
FT HELIX 247..249
FT /evidence="ECO:0007829|PDB:2DGK"
FT HELIX 251..254
FT /evidence="ECO:0007829|PDB:2DGK"
FT STRAND 267..273
FT /evidence="ECO:0007829|PDB:2DGK"
FT TURN 274..278
FT /evidence="ECO:0007829|PDB:2DGK"
FT STRAND 285..291
FT /evidence="ECO:0007829|PDB:2DGK"
FT HELIX 292..294
FT /evidence="ECO:0007829|PDB:2DGK"
FT HELIX 297..299
FT /evidence="ECO:0007829|PDB:2DGK"
FT STRAND 301..303
FT /evidence="ECO:0007829|PDB:2DGK"
FT STRAND 310..312
FT /evidence="ECO:0007829|PDB:2DGK"
FT HELIX 322..358
FT /evidence="ECO:0007829|PDB:2DGK"
FT STRAND 361..368
FT /evidence="ECO:0007829|PDB:2DGK"
FT TURN 371..373
FT /evidence="ECO:0007829|PDB:2DGK"
FT STRAND 374..382
FT /evidence="ECO:0007829|PDB:2DGK"
FT HELIX 392..401
FT /evidence="ECO:0007829|PDB:2DGK"
FT STRAND 408..410
FT /evidence="ECO:0007829|PDB:2DGK"
FT HELIX 413..415
FT /evidence="ECO:0007829|PDB:2DGM"
FT STRAND 419..424
FT /evidence="ECO:0007829|PDB:2DGK"
FT HELIX 431..450
FT /evidence="ECO:0007829|PDB:2DGK"
FT HELIX 452..454
FT /evidence="ECO:0007829|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
