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P69910

- DCEB_ECOLI

UniProt

P69910 - DCEB_ECOLI

Protein

Glutamate decarboxylase beta

Gene

gadB

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 95 (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 – 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

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

    GO - Cellular componenti

    1. cytosol Source: UniProtKB
    2. membrane Source: UniProtKB

    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.
    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.
    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

    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: October 1, 2014
    This is version 95 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