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P69910

- DCEB_ECOLI

UniProt

P69910 - DCEB_ECOLI

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Protein

Glutamate decarboxylase beta

Gene
gadB, b1493, JW1488
Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

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 activityi

L-glutamate = 4-aminobutanoate + CO2.

Cofactori

Pyridoxal phosphate.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei62 – 621Substrate
Binding sitei83 – 831Substrate
Binding sitei212 – 2121Pyridoxal phosphate
Binding sitei275 – 2751Pyridoxal phosphate

GO - Molecular functioni

  1. glutamate decarboxylase activity Source: EcoCyc
  2. pyridoxal phosphate binding Source: InterPro

GO - Biological processi

  1. glutamate metabolic process Source: InterPro
  2. intracellular pH elevation Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Decarboxylase, Lyase

Keywords - Ligandi

Pyridoxal phosphate

Enzyme and pathway databases

BioCyciEcoCyc:GLUTDECARBOXB-MONOMER.
ECOL316407:JW1488-MONOMER.
MetaCyc:GLUTDECARBOXB-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Glutamate decarboxylase beta (EC:4.1.1.15)
Short name:
GAD-beta
Gene namesi
Name:gadB
Ordered Locus Names:b1493, JW1488
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

Organism-specific databases

EcoGeneiEG11490. gadB.

Subcellular locationi

Cytoplasm. Membrane
Note: Localized exclusively in the cytoplasm at neutral pH, but is recruited to the membrane when the pH falls.1 Publication

GO - Cellular componenti

  1. cytosol Source: UniProtKB
  2. membrane Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Membrane

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi276 – 2761K → A: Strongly reduces pyridoxal phosphate binding and increases stability of the polypeptide. 1 Publication
Mutagenesisi276 – 2761K → H: Abolishes pyridoxal phosphate binding. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 466466Glutamate decarboxylase betaPRO_0000146982Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei276 – 2761N6-(pyridoxal phosphate)lysine
Modified residuei446 – 4461N6-acetyllysine1 Publication
Modified residuei453 – 4531N6-acetyllysine1 Publication
Modified residuei464 – 4641N6-acetyllysine1 Publication

Keywords - PTMi

Acetylation

Proteomic databases

PaxDbiP69910.
PRIDEiP69910.

Expressioni

Inductioni

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.7 Publications

Gene expression databases

GenevestigatoriP69910.

Interactioni

Subunit structurei

Homohexamer composed of three dimers.1 Publication

Protein-protein interaction databases

DIPiDIP-36202N.
IntActiP69910. 13 interactions.
MINTiMINT-1256225.
STRINGi511145.b1493.

Structurei

Secondary structure

1
466
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi4 – 1411
Turni17 – 193
Helixi21 – 233
Beta strandi25 – 284
Beta strandi29 – 313
Helixi39 – 4911
Helixi50 – 523
Helixi56 – 583
Helixi70 – 789
Turni79 – 813
Turni87 – 893
Helixi91 – 10717
Beta strandi114 – 1163
Beta strandi119 – 1257
Helixi126 – 14722
Beta strandi156 – 1616
Helixi164 – 1729
Beta strandi176 – 1794
Helixi191 – 1977
Beta strandi202 – 2065
Beta strandi208 – 2103
Turni212 – 2143
Helixi220 – 23415
Beta strandi240 – 2434
Helixi247 – 2493
Helixi251 – 2544
Beta strandi267 – 2737
Turni274 – 2785
Beta strandi285 – 2917
Helixi292 – 2943
Helixi297 – 2993
Beta strandi301 – 3033
Beta strandi310 – 3123
Helixi322 – 35837
Beta strandi361 – 3688
Turni371 – 3733
Beta strandi374 – 3829
Helixi392 – 40110
Beta strandi408 – 4103
Helixi413 – 4153
Beta strandi419 – 4246
Helixi431 – 45020
Helixi452 – 4543

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1PMMX-ray2.00A/B/C/D/E/F1-466[»]
1PMOX-ray2.30A/B/C/D/E/F1-466[»]
2DGKX-ray1.90A/B/C/D/E/F15-466[»]
2DGLX-ray3.15A/B/C/D/E/F1-466[»]
2DGMX-ray1.95A/B/C/D/E/F1-466[»]
3FZ6X-ray2.82A/B/C/D/E/F1-466[»]
3FZ7X-ray2.50A/B/C/D/E/F1-466[»]
3FZ8X-ray3.00A/B/C/D/E/F1-466[»]
ProteinModelPortaliP69910.
SMRiP69910. Positions 3-456.

Miscellaneous databases

EvolutionaryTraceiP69910.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni126 – 1272Pyridoxal phosphate binding

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0076.
HOGENOMiHOG000070228.
KOiK01580.
OMAiPTFQINF.
OrthoDBiEOG6TFCPW.
PhylomeDBiP69910.

Family and domain databases

Gene3Di3.40.640.10. 1 hit.
InterProiIPR010107. Glutamate_decarboxylase.
IPR002129. PyrdxlP-dep_de-COase.
IPR015424. PyrdxlP-dep_Trfase.
IPR015421. PyrdxlP-dep_Trfase_major_sub1.
IPR021115. Pyridoxal-P_BS.
[Graphical view]
PfamiPF00282. Pyridoxal_deC. 1 hit.
[Graphical view]
SUPFAMiSSF53383. SSF53383. 1 hit.
TIGRFAMsiTIGR01788. Glu-decarb-GAD. 1 hit.
PROSITEiPS00392. DDC_GAD_HDC_YDC. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P69910-1 [UniParc]FASTAAdd to Basket

« Hide

MDKKQVTDLR SELLDSRFGA KSISTIAESK RFPLHEMRDD VAFQIINDEL    50
YLDGNARQNL ATFCQTWDDE NVHKLMDLSI NKNWIDKEEY PQSAAIDLRC 100
VNMVADLWHA PAPKNGQAVG TNTIGSSEAC MLGGMAMKWR WRKRMEAAGK 150
PTDKPNLVCG PVQICWHKFA RYWDVELREI PMRPGQLFMD PKRMIEACDE 200
NTIGVVPTFG VTYTGNYEFP QPLHDALDKF QADTGIDIDM HIDAASGGFL 250
APFVAPDIVW DFRLPRVKSI SASGHKFGLA PLGCGWVIWR DEEALPQELV 300
FNVDYLGGQI GTFAINFSRP AGQVIAQYYE FLRLGREGYT KVQNASYQVA 350
AYLADEIAKL GPYEFICTGR PDEGIPAVCF KLKDGEDPGY TLYDLSERLR 400
LRGWQVPAFT LGGEATDIVV MRIMCRRGFE MDFAELLLED YKASLKYLSD 450
HPKLQGIAQQ NSFKHT 466
Length:466
Mass (Da):52,668
Last modified:January 4, 2005 - v1
Checksum:i8E653330A3C5B4ED
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
M84025 Genomic DNA. Translation: AAA23834.1.
U00096 Genomic DNA. Translation: AAC74566.1.
AP009048 Genomic DNA. Translation: BAA15163.1.
X71917 Genomic DNA. Translation: CAA50736.1. Sequence problems.
PIRiB43332.
RefSeqiNP_416010.1. NC_000913.3.
YP_489758.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC74566; AAC74566; b1493.
BAA15163; BAA15163; BAA15163.
GeneIDi12931794.
946058.
KEGGiecj:Y75_p1469.
eco:b1493.
PATRICi32118280. VBIEscCol129921_1560.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
M84025 Genomic DNA. Translation: AAA23834.1 .
U00096 Genomic DNA. Translation: AAC74566.1 .
AP009048 Genomic DNA. Translation: BAA15163.1 .
X71917 Genomic DNA. Translation: CAA50736.1 . Sequence problems.
PIRi B43332.
RefSeqi NP_416010.1. NC_000913.3.
YP_489758.1. NC_007779.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1PMM X-ray 2.00 A/B/C/D/E/F 1-466 [» ]
1PMO X-ray 2.30 A/B/C/D/E/F 1-466 [» ]
2DGK X-ray 1.90 A/B/C/D/E/F 15-466 [» ]
2DGL X-ray 3.15 A/B/C/D/E/F 1-466 [» ]
2DGM X-ray 1.95 A/B/C/D/E/F 1-466 [» ]
3FZ6 X-ray 2.82 A/B/C/D/E/F 1-466 [» ]
3FZ7 X-ray 2.50 A/B/C/D/E/F 1-466 [» ]
3FZ8 X-ray 3.00 A/B/C/D/E/F 1-466 [» ]
ProteinModelPortali P69910.
SMRi P69910. Positions 3-456.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

DIPi DIP-36202N.
IntActi P69910. 13 interactions.
MINTi MINT-1256225.
STRINGi 511145.b1493.

Proteomic databases

PaxDbi P69910.
PRIDEi P69910.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAC74566 ; AAC74566 ; b1493 .
BAA15163 ; BAA15163 ; BAA15163 .
GeneIDi 12931794.
946058.
KEGGi ecj:Y75_p1469.
eco:b1493.
PATRICi 32118280. VBIEscCol129921_1560.

Organism-specific databases

EchoBASEi EB1453.
EcoGenei EG11490. gadB.

Phylogenomic databases

eggNOGi COG0076.
HOGENOMi HOG000070228.
KOi K01580.
OMAi PTFQINF.
OrthoDBi EOG6TFCPW.
PhylomeDBi P69910.

Enzyme and pathway databases

BioCyci EcoCyc:GLUTDECARBOXB-MONOMER.
ECOL316407:JW1488-MONOMER.
MetaCyc:GLUTDECARBOXB-MONOMER.

Miscellaneous databases

EvolutionaryTracei P69910.
PROi P69910.

Gene expression databases

Genevestigatori P69910.

Family and domain databases

Gene3Di 3.40.640.10. 1 hit.
InterProi IPR010107. Glutamate_decarboxylase.
IPR002129. PyrdxlP-dep_de-COase.
IPR015424. PyrdxlP-dep_Trfase.
IPR015421. PyrdxlP-dep_Trfase_major_sub1.
IPR021115. Pyridoxal-P_BS.
[Graphical view ]
Pfami PF00282. Pyridoxal_deC. 1 hit.
[Graphical view ]
SUPFAMi SSF53383. SSF53383. 1 hit.
TIGRFAMsi TIGR01788. Glu-decarb-GAD. 1 hit.
PROSITEi PS00392. DDC_GAD_HDC_YDC. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Escherichia coli has two homologous glutamate decarboxylase genes that map to distinct loci."
    Smith D.K., Kassam T., Singh B., Elliott J.F.
    J. Bacteriol. 174:5820-5826(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: K12.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  4. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  5. "Sequence and functional analysis of an Escherichia coli DNA fragment able to complement pqqE and pqqF mutants from Methylobacterium organophilum."
    Turlin E., Gasser F., Biville F.
    Biochimie 78:823-831(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-318.
    Strain: K12.
  6. "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."
    Yoshida T., Ueguchi C., Yamada H., Mizuno T.
    Mol. Gen. Genet. 237:113-122(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 1-15.
    Strain: K12.
  7. "The response to stationary-phase stress conditions in Escherichia coli: role and regulation of the glutamic acid decarboxylase system."
    De Biase D., Tramonti A., Bossa F., Visca P.
    Mol. Microbiol. 32:1198-1211(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: TRANSCRIPTIONAL REGULATION.
    Strain: ATCC 11246.
  8. "Contribution of Lys276 to the conformational flexibility of the active site of glutamate decarboxylase from Escherichia coli."
    Tramonti A., John R.A., Bossa F., De Biase D.
    Eur. J. Biochem. 269:4913-4920(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF LYS-276.
    Strain: K12 / JM109 / ATCC 53323.
  9. "Functional characterization and regulation of gadX, a gene encoding an AraC/XylS-like transcriptional activator of the Escherichia coli glutamic acid decarboxylase system."
    Tramonti A., Visca P., De Canio M., Falconi M., De Biase D.
    J. Bacteriol. 184:2603-2613(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: TRANSCRIPTIONAL REGULATION.
    Strain: ATCC 11246.
  10. "Escherichia coli gene expression responsive to levels of the response regulator EvgA."
    Masuda N., Church G.M.
    J. Bacteriol. 184:6225-6234(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: TRANSCRIPTIONAL REGULATION.
    Strain: K12 / MG1655 / ATCC 47076.
  11. "Collaborative regulation of Escherichia coli glutamate-dependent acid resistance by two AraC-like regulators, GadX and GadW (YhiW)."
    Ma Z., Richard H., Tucker D.L., Conway T., Foster J.W.
    J. Bacteriol. 184:7001-7012(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: TRANSCRIPTIONAL REGULATION.
    Strain: K12.
  12. "Transcriptional expression of Escherichia coli glutamate-dependent acid resistance genes gadA and gadBC in an hns rpoS mutant."
    Waterman S.R., Small P.L.C.
    J. Bacteriol. 185:4644-4647(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: TRANSCRIPTIONAL REGULATION.
  13. "Regulatory network of acid resistance genes in Escherichia coli."
    Masuda N., Church G.M.
    Mol. Microbiol. 48:699-712(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: TRANSCRIPTIONAL REGULATION.
    Strain: K12 / MG1655 / ATCC 47076.
  14. "GadE (YhiE) activates glutamate decarboxylase-dependent acid resistance in Escherichia coli K-12."
    Ma Z., Gong S., Richard H., Tucker D.L., Conway T., Foster J.W.
    Mol. Microbiol. 49:1309-1320(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: TRANSCRIPTIONAL REGULATION.
    Strain: K12.
  15. "Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli."
    Zhang J., Sprung R., Pei J., Tan X., Kim S., Zhu H., Liu C.F., Grishin N.V., Zhao Y.
    Mol. Cell. Proteomics 8:215-225(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-446; LYS-453 AND LYS-464, IDENTIFICATION BY MASS SPECTROMETRY.
    Strain: K12 / JW1106 and K12 / MG1655 / ATCC 47076.
  16. "Crystal structure and functional analysis of Escherichia coli glutamate decarboxylase."
    Capitani G., De Biase D., Aurizi C., Gut H., Bossa F., Gruetter M.G.
    EMBO J. 22:4027-4037(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS), SUBUNIT, SUBCELLULAR LOCATION.

Entry informationi

Entry nameiDCEB_ECOLI
AccessioniPrimary (citable) accession number: P69910
Secondary accession number(s): P28302, P76873
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 4, 2005
Last sequence update: January 4, 2005
Last modified: June 11, 2014
This is version 94 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

Changing Lys-276 to Ala increases thermal stability and protease resistance. The unfolding temperature is increased by 11 degrees Celsius.

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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