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P69908

- DCEA_ECOLI

UniProt

P69908 - DCEA_ECOLI

Protein

Glutamate decarboxylase alpha

Gene

gadA

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 89 (01 Oct 2014)
      Sequence version 1 (04 Jan 2005)
      Previous versions | rss
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    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

    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

    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.
    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

    MDQKLLTDFR SELLDSRFGA KAISTIAESK 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):52,685
    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.
    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

    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 1, 2014
    This is version 89 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