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P69908

- DCEA_ECOLI

UniProt

P69908 - DCEA_ECOLI

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Protein

Glutamate decarboxylase alpha

Gene

gadA

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 – 621SubstrateBy similarity
Binding sitei83 – 831SubstrateBy similarity
Binding sitei212 – 2121Pyridoxal phosphateBy similarity
Binding sitei275 – 2751Pyridoxal phosphateBy similarity

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:GLUTDECARBOXA-MONOMER.
ECOL316407:JW3485-MONOMER.
MetaCyc:GLUTDECARBOXA-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Glutamate decarboxylase alpha (EC:4.1.1.15)
Short name:
GAD-alpha
Gene namesi
Name:gadA
Synonyms:gadS
Ordered Locus Names:b3517, JW3485
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

Organism-specific databases

EcoGeneiEG50009. gadA.

Subcellular locationi

GO - Cellular componenti

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

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 466466Glutamate decarboxylase alphaPRO_0000146978Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei276 – 2761N6-(pyridoxal phosphate)lysine

Proteomic databases

PRIDEiP69908.

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

GenevestigatoriP69908.

Interactioni

Subunit structurei

Homohexamer.

Protein-protein interaction databases

DIPiDIP-36201N.
IntActiP69908. 14 interactions.
MINTiMINT-1224142.
STRINGi511145.b3517.

Structurei

Secondary structure

1
466
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi6 – 149
Turni17 – 193
Helixi21 – 244
Helixi39 – 4911
Helixi50 – 534
Helixi56 – 583
Helixi70 – 789
Turni79 – 813
Turni87 – 893
Helixi91 – 10717
Beta strandi119 – 1257
Helixi126 – 14722
Beta strandi156 – 1616
Helixi165 – 1728
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 – 3055
Beta strandi308 – 3125
Helixi322 – 35736
Beta strandi360 – 3689
Turni371 – 3733
Beta strandi374 – 3829
Helixi392 – 4009
Turni401 – 4033
Beta strandi408 – 4103
Helixi413 – 4153
Beta strandi419 – 4246
Helixi431 – 44919

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1XEYX-ray2.05A/B1-466[»]
ProteinModelPortaliP69908.
SMRiP69908. Positions 4-452.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP69908.

Family & Domainsi

Region

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

Sequence similaritiesi

Belongs to the group II decarboxylase family.Curated

Phylogenomic databases

HOGENOMiHOG000070228.
InParanoidiP69908.
KOiK01580.
OMAiMIGRLFN.
OrthoDBiEOG6TFCPW.
PhylomeDBiP69908.

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.

P69908-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MDQKLLTDFR SELLDSRFGA KAISTIAESK 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):52,685
Last modified:January 4, 2005 - v1
Checksum:i86F963E710553E22
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti64 – 641C → S AA sequence (PubMed:1740158)Curated
Sequence conflicti73 – 731H → R AA sequence (PubMed:1740158)Curated
Sequence conflicti153 – 1531D → N AA sequence (PubMed:1740158)Curated
Sequence conflicti165 – 1651C → S in CAA44834. (PubMed:1740158)Curated
Sequence conflicti208 – 2081T → N in CAA44834. (PubMed:1740158)Curated
Sequence conflicti295 – 2951L → V in CAA44834. (PubMed:1740158)Curated
Sequence conflicti355 – 3551D → N AA sequence (PubMed:1740158)Curated

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
M84024 Genomic DNA. Translation: AAA23833.1.
X63123 Genomic DNA. Translation: CAA44834.1.
U00039 Genomic DNA. Translation: AAB18493.1.
U00096 Genomic DNA. Translation: AAC76542.1.
AP009048 Genomic DNA. Translation: BAE77777.1.
PIRiS47737. S24234.
RefSeqiNP_417974.1. NC_000913.3.
YP_491918.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC76542; AAC76542; b3517.
BAE77777; BAE77777; BAE77777.
GeneIDi12932603.
948027.
KEGGiecj:Y75_p3660.
eco:b3517.
PATRICi32122496. VBIEscCol129921_3626.

Cross-referencesi

Web resourcesi

Worthington enzyme manual

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
M84024 Genomic DNA. Translation: AAA23833.1 .
X63123 Genomic DNA. Translation: CAA44834.1 .
U00039 Genomic DNA. Translation: AAB18493.1 .
U00096 Genomic DNA. Translation: AAC76542.1 .
AP009048 Genomic DNA. Translation: BAE77777.1 .
PIRi S47737. S24234.
RefSeqi NP_417974.1. NC_000913.3.
YP_491918.1. NC_007779.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1XEY X-ray 2.05 A/B 1-466 [» ]
ProteinModelPortali P69908.
SMRi P69908. Positions 4-452.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

DIPi DIP-36201N.
IntActi P69908. 14 interactions.
MINTi MINT-1224142.
STRINGi 511145.b3517.

Proteomic databases

PRIDEi P69908.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAC76542 ; AAC76542 ; b3517 .
BAE77777 ; BAE77777 ; BAE77777 .
GeneIDi 12932603.
948027.
KEGGi ecj:Y75_p3660.
eco:b3517.
PATRICi 32122496. VBIEscCol129921_3626.

Organism-specific databases

EchoBASEi EB4302.
EcoGenei EG50009. gadA.

Phylogenomic databases

HOGENOMi HOG000070228.
InParanoidi P69908.
KOi K01580.
OMAi MIGRLFN.
OrthoDBi EOG6TFCPW.
PhylomeDBi P69908.

Enzyme and pathway databases

BioCyci EcoCyc:GLUTDECARBOXA-MONOMER.
ECOL316407:JW3485-MONOMER.
MetaCyc:GLUTDECARBOXA-MONOMER.

Miscellaneous databases

EvolutionaryTracei P69908.
PROi P69908.

Gene expression databases

Genevestigatori P69908.

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. "The amino acid sequence of glutamate decarboxylase from Escherichia coli. Evolutionary relationship between mammalian and bacterial enzymes."
    Maras B., Sweeney G., Barra D., Bossa F., John R.A.
    Eur. J. Biochem. 204:93-98(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE, NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 148-466.
    Strain: ATCC 11246.
  3. "Analysis of the Escherichia coli genome. V. DNA sequence of the region from 76.0 to 81.5 minutes."
    Sofia H.J., Burland V., Daniels D.L., Plunkett G. III, Blattner F.R.
    Nucleic Acids Res. 22:2576-2586(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  5. "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.
  6. "Expression of the Escherichia coli dimorphic glutamic acid decarboxylases is regulated by the nucleoid protein H-NS."
    Yoshida T., Yamashino T., Ueguchi C., Mizuno T.
    Biosci. Biotechnol. Biochem. 57:1568-1569(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 1-22.
  7. "Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12."
    Link A.J., Robison K., Church G.M.
    Electrophoresis 18:1259-1313(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 382-392.
    Strain: K12 / EMG2.
  8. "Escherichia coli proteome analysis using the gene-protein database."
    VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.
    Electrophoresis 18:1243-1251(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY 2D-GEL.
  9. "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.
  10. "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.
  11. "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.
  12. "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.
  13. "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.
  14. "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.
  15. "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.
  16. "Structure of the complex of Escherichia coli glutamate decarboxylase (gadA) with glutarate at 2.05 A resolution."
    Dutyshev D.I., Darii E.L., Fomenkova N.P., Pechik I.V., Polyakov K.M., Nikonov S.V., Andreeva N.S., Sukhareva B.S.
    Submitted (SEP-2004) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (2.05 ANGSTROMS).

Entry informationi

Entry nameiDCEA_ECOLI
AccessioniPrimary (citable) accession number: P69908
Secondary accession number(s): P80063, Q2M7H9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 4, 2005
Last sequence update: January 4, 2005
Last modified: October 29, 2014
This is version 90 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

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