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P69910 (DCEB_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 92. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Glutamate decarboxylase beta

Short name=GAD-beta
EC=4.1.1.15
Gene names
Name:gadB
Ordered Locus Names:b1493, JW1488
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length466 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

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

L-glutamate = 4-aminobutanoate + CO2.

Cofactor

Pyridoxal phosphate.

Subunit structure

Homohexamer composed of three dimers. Ref.16

Subcellular location

Cytoplasm. Membrane. Note: Localized exclusively in the cytoplasm at neutral pH, but is recruited to the membrane when the pH falls. Ref.16

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. Ref.7 Ref.9 Ref.10 Ref.11 Ref.12 Ref.13 Ref.14

Miscellaneous

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

Sequence similarities

Belongs to the group II decarboxylase family.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 466466Glutamate decarboxylase beta
PRO_0000146982

Regions

Region126 – 1272Pyridoxal phosphate binding

Sites

Binding site621Substrate
Binding site831Substrate
Binding site2121Pyridoxal phosphate
Binding site2751Pyridoxal phosphate

Amino acid modifications

Modified residue2761N6-(pyridoxal phosphate)lysine
Modified residue4461N6-acetyllysine Ref.15
Modified residue4531N6-acetyllysine Ref.15
Modified residue4641N6-acetyllysine Ref.15

Experimental info

Mutagenesis2761K → A: Strongly reduces pyridoxal phosphate binding and increases stability of the polypeptide. Ref.8
Mutagenesis2761K → H: Abolishes pyridoxal phosphate binding. Ref.8

Secondary structure

................................................................................ 466
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P69910 [UniParc].

Last modified January 4, 2005. Version 1.
Checksum: 8E653330A3C5B4ED

FASTA46652,668
        10         20         30         40         50         60 
MDKKQVTDLR SELLDSRFGA KSISTIAESK RFPLHEMRDD VAFQIINDEL YLDGNARQNL 

        70         80         90        100        110        120 
ATFCQTWDDE NVHKLMDLSI NKNWIDKEEY PQSAAIDLRC VNMVADLWHA PAPKNGQAVG 

       130        140        150        160        170        180 
TNTIGSSEAC MLGGMAMKWR WRKRMEAAGK PTDKPNLVCG PVQICWHKFA RYWDVELREI 

       190        200        210        220        230        240 
PMRPGQLFMD PKRMIEACDE NTIGVVPTFG VTYTGNYEFP QPLHDALDKF QADTGIDIDM 

       250        260        270        280        290        300 
HIDAASGGFL APFVAPDIVW DFRLPRVKSI SASGHKFGLA PLGCGWVIWR DEEALPQELV 

       310        320        330        340        350        360 
FNVDYLGGQI GTFAINFSRP AGQVIAQYYE FLRLGREGYT KVQNASYQVA AYLADEIAKL 

       370        380        390        400        410        420 
GPYEFICTGR PDEGIPAVCF KLKDGEDPGY TLYDLSERLR LRGWQVPAFT LGGEATDIVV 

       430        440        450        460 
MRIMCRRGFE MDFAELLLED YKASLKYLSD HPKLQGIAQQ NSFKHT 

« Hide

References

« Hide 'large scale' references
[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]"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."
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. expand/collapse author list , 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.
DNA Res. 3:363-377(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[3]"The complete genome sequence of Escherichia coli K-12."
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.
Science 277:1453-1462(1997) [PubMed] [Europe PMC] [Abstract]
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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
PIRB43332.
RefSeqNP_416010.1. NC_000913.3.
YP_489758.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj
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[»]
ProteinModelPortalP69910.
SMRP69910. Positions 3-456.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-36202N.
IntActP69910. 13 interactions.
MINTMINT-1256225.
STRING511145.b1493.

Proteomic databases

PaxDbP69910.
PRIDEP69910.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC74566; AAC74566; b1493.
BAA15163; BAA15163; BAA15163.
GeneID12931794.
946058.
KEGGecj:Y75_p1469.
eco:b1493.
PATRIC32118280. VBIEscCol129921_1560.

Organism-specific databases

EchoBASEEB1453.
EcoGeneEG11490. gadB.

Phylogenomic databases

eggNOGCOG0076.
HOGENOMHOG000070228.
KOK01580.
OMAIADLWNA.
OrthoDBEOG6TFCPW.
PhylomeDBP69910.
ProtClustDBCLSK880040.

Enzyme and pathway databases

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

Gene expression databases

GenevestigatorP69910.

Family and domain databases

Gene3D3.40.640.10. 1 hit.
InterProIPR010107. Glutamate_decarboxylase.
IPR002129. PyrdxlP-dep_de-COase.
IPR015424. PyrdxlP-dep_Trfase.
IPR015421. PyrdxlP-dep_Trfase_major_sub1.
IPR021115. Pyridoxal-P_BS.
[Graphical view]
PANTHERPTHR11999:SF1. PTHR11999:SF1. 1 hit.
PfamPF00282. Pyridoxal_deC. 1 hit.
[Graphical view]
SUPFAMSSF53383. SSF53383. 1 hit.
TIGRFAMsTIGR01788. Glu-decarb-GAD. 1 hit.
PROSITEPS00392. DDC_GAD_HDC_YDC. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP69910.
PROP69910.

Entry information

Entry nameDCEB_ECOLI
AccessionPrimary (citable) accession number: P69910
Secondary accession number(s): P28302, P76873
Entry history
Integrated into UniProtKB/Swiss-Prot: January 4, 2005
Last sequence update: January 4, 2005
Last modified: April 16, 2014
This is version 92 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene