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Protein

Glucarate dehydratase-related protein

Gene

gudX

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Does not seem to have an in-vivo activity on glucarate or idarate. Its real substrate is unknown.

Cofactori

Kineticsi

  1. KM=170 µM for idarate1 Publication
  2. KM=320 µM for glucarate1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei31 – 311SubstrateBy similarity
    Binding sitei104 – 1041SubstrateBy similarity
    Binding sitei149 – 1491SubstrateBy similarity
    Binding sitei204 – 2041SubstrateBy similarity
    Active sitei206 – 2061Proton acceptorSequence Analysis
    Metal bindingi234 – 2341MagnesiumSequence Analysis
    Metal bindingi265 – 2651MagnesiumSequence Analysis
    Metal bindingi288 – 2881MagnesiumSequence Analysis
    Binding sitei288 – 2881SubstrateBy similarity
    Active sitei338 – 3381Proton acceptorSequence Analysis
    Binding sitei367 – 3671SubstrateBy similarity
    Binding sitei421 – 4211SubstrateBy similarity

    GO - Molecular functioni

    GO - Biological processi

    • cellular amino acid catabolic process Source: InterPro
    • cellular catabolic process Source: EcoCyc
    Complete GO annotation...

    Keywords - Molecular functioni

    Lyase

    Keywords - Ligandi

    Magnesium, Metal-binding

    Enzyme and pathway databases

    BioCyciEcoCyc:G7446-MONOMER.
    ECOL316407:JW2759-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Glucarate dehydratase-related protein (EC:4.2.1.-)
    Short name:
    GDH-RP
    Short name:
    GlucDRP
    Gene namesi
    Name:gudX
    Synonyms:ygcY
    Ordered Locus Names:b2788, JW2759
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318 Componenti: Chromosome UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG13168. gudX.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 446446Glucarate dehydratase-related proteinPRO_0000171266Add
    BLAST

    Proteomic databases

    PRIDEiQ46915.

    Interactioni

    Protein-protein interaction databases

    IntActiQ46915. 3 interactions.
    STRINGi511145.b2788.

    Structurei

    Secondary structure

    1
    446
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi8 – 2013Combined sources
    Beta strandi24 – 263Combined sources
    Beta strandi33 – 4412Combined sources
    Beta strandi49 – 557Combined sources
    Helixi58 – 669Combined sources
    Helixi68 – 714Combined sources
    Helixi76 – 783Combined sources
    Helixi79 – 9012Combined sources
    Helixi92 – 998Combined sources
    Helixi104 – 1063Combined sources
    Helixi107 – 12721Combined sources
    Helixi131 – 1344Combined sources
    Beta strandi142 – 1465Combined sources
    Beta strandi148 – 1503Combined sources
    Helixi156 – 1583Combined sources
    Beta strandi169 – 1713Combined sources
    Helixi173 – 1764Combined sources
    Helixi184 – 19815Combined sources
    Beta strandi201 – 2066Combined sources
    Beta strandi208 – 2103Combined sources
    Helixi212 – 22514Combined sources
    Beta strandi229 – 2346Combined sources
    Helixi241 – 2477Combined sources
    Turni248 – 2503Combined sources
    Turni252 – 2543Combined sources
    Beta strandi256 – 2605Combined sources
    Helixi270 – 28112Combined sources
    Beta strandi285 – 2906Combined sources
    Helixi294 – 3029Combined sources
    Beta strandi307 – 3104Combined sources
    Helixi313 – 3164Combined sources
    Helixi318 – 33013Combined sources
    Helixi344 – 35512Combined sources
    Helixi368 – 3714Combined sources
    Turni372 – 3743Combined sources
    Beta strandi378 – 3803Combined sources
    Beta strandi388 – 3903Combined sources
    Beta strandi394 – 3963Combined sources
    Helixi403 – 41412Combined sources
    Helixi424 – 4307Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4GYPX-ray2.10C/D2-446[»]
    4IL0X-ray2.80A/B/C/D/E/F/G/H1-446[»]
    ProteinModelPortaliQ46915.
    SMRiQ46915. Positions 6-445.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni234 – 2363Substrate bindingBy similarity
    Regioni338 – 3403Substrate bindingBy similarity

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiCOG4948.
    HOGENOMiHOG000238021.
    InParanoidiQ46915.
    KOiK13918.
    OMAiREMNHAL.
    OrthoDBiEOG6V7BH9.
    PhylomeDBiQ46915.

    Family and domain databases

    Gene3Di3.20.20.120. 1 hit.
    3.30.390.10. 1 hit.
    InterProiIPR029065. Enolase_C-like.
    IPR029017. Enolase_N-like.
    IPR018110. Mandel_Rmase/mucon_lact_enz_CS.
    IPR013342. Mandelate_racemase_C.
    IPR013341. Mandelate_racemase_N_dom.
    IPR001354. MR/MLE/MAL.
    [Graphical view]
    PANTHERiPTHR13794. PTHR13794. 1 hit.
    PfamiPF01188. MR_MLE. 1 hit.
    PF02746. MR_MLE_N. 1 hit.
    [Graphical view]
    SMARTiSM00922. MR_MLE. 1 hit.
    [Graphical view]
    SUPFAMiSSF51604. SSF51604. 1 hit.
    SSF54826. SSF54826. 1 hit.
    PROSITEiPS00908. MR_MLE_1. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Q46915-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MATQSSPVIT DMKVIPVAGH DSMLLNIGGA HNAYFTRNIV VLTDNAGHTG
    60 70 80 90 100
    IGEAPGGDVI YQTLVDAIPM VLGQEVARLN KVVQQVHKGN QAADFDTFGK
    110 120 130 140 150
    GAWTFELRVN AVAALEAALL DLLGKALNVP VCELLGPGKQ REAITVLGYL
    160 170 180 190 200
    FYIGDRTKTD LPYVENTPGN HEWYQLRHQK AMNSEAVVRL AEASQDRYGF
    210 220 230 240 250
    KDFKLKGGVL PGEQEIDTVR ALKKRFPDAR ITVDPNGAWL LDEAISLCKG
    260 270 280 290 300
    LNDVLTYAED PCGAEQGFSG REVMAEFRRA TGLPVATNMI ATNWREMGHA
    310 320 330 340 350
    VMLNAVDIPL ADPHFWTLSG AVRVAQLCDD WGLTWGCHSN NHFDISLAMF
    360 370 380 390 400
    THVGAAAPGN PTAIDTHWIW QEGDCRLTQN PLEIKNGKIA VPDAPGLGVE
    410 420 430 440
    LDWEQVQKAH EAYKRLPGGA RNDAGPMQYL IPGWTFDRKR PVFGRH
    Length:446
    Mass (Da):48,850
    Last modified:November 1, 1996 - v1
    Checksum:i9010C7FAAE4FBE49
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U29581 Genomic DNA. Translation: AAB40438.1.
    U00096 Genomic DNA. Translation: AAC75830.1.
    AP009048 Genomic DNA. Translation: BAE76860.1.
    PIRiH65060.
    RefSeqiNP_417268.1. NC_000913.3.
    WP_000235391.1. NZ_CP010445.1.

    Genome annotation databases

    EnsemblBacteriaiAAC75830; AAC75830; b2788.
    BAE76860; BAE76860; BAE76860.
    GeneIDi947261.
    KEGGieco:b2788.
    PATRICi32120992. VBIEscCol129921_2888.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U29581 Genomic DNA. Translation: AAB40438.1.
    U00096 Genomic DNA. Translation: AAC75830.1.
    AP009048 Genomic DNA. Translation: BAE76860.1.
    PIRiH65060.
    RefSeqiNP_417268.1. NC_000913.3.
    WP_000235391.1. NZ_CP010445.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4GYPX-ray2.10C/D2-446[»]
    4IL0X-ray2.80A/B/C/D/E/F/G/H1-446[»]
    ProteinModelPortaliQ46915.
    SMRiQ46915. Positions 6-445.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    IntActiQ46915. 3 interactions.
    STRINGi511145.b2788.

    Proteomic databases

    PRIDEiQ46915.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC75830; AAC75830; b2788.
    BAE76860; BAE76860; BAE76860.
    GeneIDi947261.
    KEGGieco:b2788.
    PATRICi32120992. VBIEscCol129921_2888.

    Organism-specific databases

    EchoBASEiEB2960.
    EcoGeneiEG13168. gudX.

    Phylogenomic databases

    eggNOGiCOG4948.
    HOGENOMiHOG000238021.
    InParanoidiQ46915.
    KOiK13918.
    OMAiREMNHAL.
    OrthoDBiEOG6V7BH9.
    PhylomeDBiQ46915.

    Enzyme and pathway databases

    BioCyciEcoCyc:G7446-MONOMER.
    ECOL316407:JW2759-MONOMER.

    Miscellaneous databases

    PROiQ46915.

    Family and domain databases

    Gene3Di3.20.20.120. 1 hit.
    3.30.390.10. 1 hit.
    InterProiIPR029065. Enolase_C-like.
    IPR029017. Enolase_N-like.
    IPR018110. Mandel_Rmase/mucon_lact_enz_CS.
    IPR013342. Mandelate_racemase_C.
    IPR013341. Mandelate_racemase_N_dom.
    IPR001354. MR/MLE/MAL.
    [Graphical view]
    PANTHERiPTHR13794. PTHR13794. 1 hit.
    PfamiPF01188. MR_MLE. 1 hit.
    PF02746. MR_MLE_N. 1 hit.
    [Graphical view]
    SMARTiSM00922. MR_MLE. 1 hit.
    [Graphical view]
    SUPFAMiSSF51604. SSF51604. 1 hit.
    SSF54826. SSF54826. 1 hit.
    PROSITEiPS00908. MR_MLE_1. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    2. "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.
    3. "Evolution of enzymatic activities in the enolase superfamily: characterization of the (D)-glucarate/galactarate catabolic pathway in Escherichia coli."
      Hubbard B.K., Koch M., Palmer D.R., Babbitt P.C., Gerlt J.A.
      Biochemistry 37:14369-14375(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 1-15, BIOPHYSICOCHEMICAL PROPERTIES.

    Entry informationi

    Entry nameiGUDX_ECOLI
    AccessioniPrimary (citable) accession number: Q46915
    Secondary accession number(s): Q2MA46
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1997
    Last sequence update: November 1, 1996
    Last modified: July 22, 2015
    This is version 102 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

    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.