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Protein

Glutamate decarboxylase beta

Gene

gadB

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: 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

Sites

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

GO - Molecular functioni

  • glutamate decarboxylase activity Source: EcoCyc
  • pyridoxal phosphate binding Source: InterPro

GO - Biological processi

  • glutamate metabolic process Source: InterPro
  • 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.
BRENDAi4.1.1.15. 2026.

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 Componenti: Chromosome UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11490. gadB.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: UniProtKB
  • 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

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

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP69910.

Family & Domainsi

Region

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

Sequence similaritiesi

Belongs to the group II decarboxylase family.Curated

Phylogenomic databases

eggNOGiCOG0076.
HOGENOMiHOG000070228.
InParanoidiP69910.
KOiK01580.
OMAiFVGTWMD.
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

        10         20         30         40         50
MDKKQVTDLR SELLDSRFGA KSISTIAESK RFPLHEMRDD VAFQIINDEL
60 70 80 90 100
YLDGNARQNL ATFCQTWDDE NVHKLMDLSI NKNWIDKEEY PQSAAIDLRC
110 120 130 140 150
VNMVADLWHA PAPKNGQAVG TNTIGSSEAC MLGGMAMKWR WRKRMEAAGK
160 170 180 190 200
PTDKPNLVCG PVQICWHKFA RYWDVELREI PMRPGQLFMD PKRMIEACDE
210 220 230 240 250
NTIGVVPTFG VTYTGNYEFP QPLHDALDKF QADTGIDIDM HIDAASGGFL
260 270 280 290 300
APFVAPDIVW DFRLPRVKSI SASGHKFGLA PLGCGWVIWR DEEALPQELV
310 320 330 340 350
FNVDYLGGQI GTFAINFSRP AGQVIAQYYE FLRLGREGYT KVQNASYQVA
360 370 380 390 400
AYLADEIAKL GPYEFICTGR PDEGIPAVCF KLKDGEDPGY TLYDLSERLR
410 420 430 440 450
LRGWQVPAFT LGGEATDIVV MRIMCRRGFE MDFAELLLED YKASLKYLSD
460
HPKLQGIAQQ NSFKHT
Length:466
Mass (Da):52,668
Last modified:January 4, 2005 - v1
Checksum:i8E653330A3C5B4ED
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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.

Genome annotation databases

EnsemblBacteriaiAAC74566; AAC74566; b1493.
BAA15163; BAA15163; BAA15163.
GeneIDi946058.
KEGGiecj:Y75_p1469.
eco:b1493.
PATRICi32118280. VBIEscCol129921_1560.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

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

Proteomic databases

PaxDbiP69910.
PRIDEiP69910.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC74566; AAC74566; b1493.
BAA15163; BAA15163; BAA15163.
GeneIDi946058.
KEGGiecj:Y75_p1469.
eco:b1493.
PATRICi32118280. VBIEscCol129921_1560.

Organism-specific databases

EchoBASEiEB1453.
EcoGeneiEG11490. gadB.

Phylogenomic databases

eggNOGiCOG0076.
HOGENOMiHOG000070228.
InParanoidiP69910.
KOiK01580.
OMAiFVGTWMD.
OrthoDBiEOG6TFCPW.
PhylomeDBiP69910.

Enzyme and pathway databases

BioCyciEcoCyc:GLUTDECARBOXB-MONOMER.
ECOL316407:JW1488-MONOMER.
MetaCyc:GLUTDECARBOXB-MONOMER.
BRENDAi4.1.1.15. 2026.

Miscellaneous databases

EvolutionaryTraceiP69910.
PROiP69910.

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]
ProtoNetiSearch...

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 24, 2015
This is version 101 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.