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Protein

Glucarate dehydratase

Gene

gudD

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

Functioni

Catalyzes the dehydration of glucarate to 5-keto-4-deoxy-D-glucarate (5-kdGluc). Also acts on L-idarate.

Catalytic activityi

D-glucarate = 5-dehydro-4-deoxy-D-glucarate + H2O.

Cofactori

Mg2+1 Publication

Kineticsi

  1. KM=16 µM for idarate1 Publication
  2. KM=60 µM for glucarate1 Publication

    Pathway: D-glucarate degradation

    This protein is involved in step 1 of the subpathway that synthesizes 2,5-dioxopentanoate from D-glucarate.
    Proteins known to be involved in the 2 steps of the subpathway in this organism are:
    1. Glucarate dehydratase (gudD)
    2. no protein annotated in this organism
    This subpathway is part of the pathway D-glucarate degradation, which is itself part of Carbohydrate acid metabolism.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes 2,5-dioxopentanoate from D-glucarate, the pathway D-glucarate degradation and in Carbohydrate acid metabolism.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei32 – 321Substrate
    Binding sitei103 – 1031Substrate
    Binding sitei150 – 1501Substrate
    Binding sitei205 – 2051Substrate
    Active sitei207 – 2071Proton acceptor
    Metal bindingi235 – 2351Magnesium
    Metal bindingi266 – 2661Magnesium
    Metal bindingi289 – 2891Magnesium
    Binding sitei289 – 2891Substrate
    Active sitei339 – 3391Proton acceptor
    Binding sitei368 – 3681Substrate
    Binding sitei422 – 4221Substrate

    GO - Molecular functioni

    • glucarate dehydratase activity Source: UniProtKB
    • magnesium ion binding Source: UniProtKB

    GO - Biological processi

    • D-glucarate catabolic process Source: UniProtKB
    Complete GO annotation...

    Keywords - Molecular functioni

    Lyase

    Keywords - Ligandi

    Magnesium, Metal-binding

    Enzyme and pathway databases

    BioCyciEcoCyc:GLUCARDEHYDRA-MONOMER.
    ECOL316407:JW2758-MONOMER.
    MetaCyc:GLUCARDEHYDRA-MONOMER.
    BRENDAi4.2.1.40. 2026.
    SABIO-RKP0AES2.
    UniPathwayiUPA00564; UER00627.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Glucarate dehydratase (EC:4.2.1.40)
    Short name:
    GDH
    Short name:
    GlucD
    Gene namesi
    Name:gudD
    Synonyms:ygcX
    Ordered Locus Names:b2787, JW2758
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318 Componenti: Chromosome UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG13167. gudD.

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi150 – 1501Y → F: Reduces activity 100-fold. 1 Publication
    Mutagenesisi207 – 2071K → Q: Reduces activity 1000-fold. 1 Publication
    Mutagenesisi207 – 2071K → R: Reduces activity 10000-fold. 1 Publication
    Mutagenesisi339 – 3391H → A: Loss of activity. 1 Publication
    Mutagenesisi339 – 3391H → N: Reduces activity 10000-fold. 1 Publication
    Mutagenesisi339 – 3391H → Q: Reduces activity 1000-fold. 1 Publication
    Mutagenesisi366 – 3661D → A or N: Reduces activity over 100-fold. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed1 Publication
    Chaini2 – 446445Glucarate dehydratasePRO_0000171264Add
    BLAST

    Proteomic databases

    PaxDbiP0AES2.
    PRIDEiP0AES2.

    Interactioni

    Subunit structurei

    Homodimer.2 Publications

    Protein-protein interaction databases

    IntActiP0AES2. 3 interactions.
    STRINGi511145.b2787.

    Structurei

    Secondary structure

    1
    446
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi9 – 2113Combined sources
    Beta strandi25 – 273Combined sources
    Beta strandi34 – 4512Combined sources
    Beta strandi50 – 567Combined sources
    Helixi59 – 7214Combined sources
    Helixi77 – 793Combined sources
    Helixi80 – 9011Combined sources
    Helixi92 – 954Combined sources
    Turni96 – 994Combined sources
    Beta strandi101 – 1044Combined sources
    Helixi109 – 12820Combined sources
    Beta strandi130 – 1323Combined sources
    Helixi133 – 1353Combined sources
    Beta strandi143 – 1475Combined sources
    Beta strandi149 – 1524Combined sources
    Helixi157 – 1593Combined sources
    Beta strandi160 – 1623Combined sources
    Helixi173 – 1775Combined sources
    Helixi185 – 19915Combined sources
    Beta strandi202 – 2076Combined sources
    Beta strandi209 – 2113Combined sources
    Helixi213 – 22614Combined sources
    Beta strandi230 – 2356Combined sources
    Helixi242 – 25110Combined sources
    Turni252 – 2554Combined sources
    Beta strandi256 – 2616Combined sources
    Helixi271 – 28212Combined sources
    Beta strandi286 – 2916Combined sources
    Helixi295 – 30410Combined sources
    Beta strandi308 – 3114Combined sources
    Helixi314 – 3174Combined sources
    Helixi319 – 33113Combined sources
    Helixi345 – 35612Combined sources
    Helixi369 – 3724Combined sources
    Turni373 – 3753Combined sources
    Beta strandi378 – 3814Combined sources
    Beta strandi389 – 3913Combined sources
    Beta strandi395 – 3973Combined sources
    Helixi404 – 41613Combined sources
    Helixi425 – 4295Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1EC7X-ray1.90A/B/C/D1-446[»]
    1EC8X-ray1.90A/B/C/D1-446[»]
    1EC9X-ray2.00A/B/C/D1-446[»]
    1ECQX-ray2.00A/B/C/D1-446[»]
    1JCTX-ray2.75A/B1-446[»]
    1JDFX-ray2.00A/B/C/D1-446[»]
    3PWGX-ray2.00A/B/C/D1-446[»]
    3PWIX-ray2.23A/B1-446[»]
    4GYPX-ray2.10A/B1-446[»]
    ProteinModelPortaliP0AES2.
    SMRiP0AES2. Positions 5-446.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP0AES2.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni235 – 2373Substrate binding
    Regioni339 – 3413Substrate binding

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiCOG4948.
    HOGENOMiHOG000238021.
    InParanoidiP0AES2.
    KOiK01706.
    OMAiMQYLIPN.
    OrthoDBiEOG6V7BH9.
    PhylomeDBiP0AES2.

    Family and domain databases

    Gene3Di3.20.20.120. 1 hit.
    3.30.390.10. 1 hit.
    InterProiIPR029065. Enolase_C-like.
    IPR029017. Enolase_N_like.
    IPR017653. Glucarate_dehydratase.
    IPR013342. Mandelate_racemase_C.
    IPR001354. MR/MLE/MAL.
    [Graphical view]
    PANTHERiPTHR13794. PTHR13794. 1 hit.
    PfamiPF01188. MR_MLE. 1 hit.
    [Graphical view]
    SMARTiSM00922. MR_MLE. 1 hit.
    [Graphical view]
    SUPFAMiSSF51604. SSF51604. 1 hit.
    SSF54826. SSF54826. 1 hit.
    TIGRFAMsiTIGR03247. glucar-dehydr. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    P0AES2-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MSSQFTTPVV TEMQVIPVAG HDSMLMNLSG AHAPFFTRNI VIIKDNSGHT
    60 70 80 90 100
    GVGEIPGGEK IRKTLEDAIP LVVGKTLGEY KNVLTLVRNT FADRDAGGRG
    110 120 130 140 150
    LQTFDLRTTI HVVTGIEAAM LDLLGQHLGV NVASLLGDGQ QRSEVEMLGY
    160 170 180 190 200
    LFFVGNRKAT PLPYQSQPDD SCDWYRLRHE EAMTPDAVVR LAEAAYEKYG
    210 220 230 240 250
    FNDFKLKGGV LAGEEEAESI VALAQRFPQA RITLDPNGAW SLNEAIKIGK
    260 270 280 290 300
    YLKGSLAYAE DPCGAEQGFS GREVMAEFRR ATGLPTATNM IATDWRQMGH
    310 320 330 340 350
    TLSLQSVDIP LADPHFWTMQ GSVRVAQMCH EFGLTWGSHS NNHFDISLAM
    360 370 380 390 400
    FTHVAAAAPG KITAIDTHWI WQEGNQRLTK EPFEIKGGLV QVPEKPGLGV
    410 420 430 440
    EIDMDQVMKA HELYQKHGLG ARDDAMGMQY LIPGWTFDNK RPCMVR
    Length:446
    Mass (Da):49,141
    Last modified:January 23, 2007 - v2
    Checksum:iDFB07C9CA33F542C
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti310 – 3134PLAD → RWRI in AAB40437 (PubMed:9278503).Curated

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U00096 Genomic DNA. Translation: AAC75829.1.
    U29581 Genomic DNA. Translation: AAB40437.1.
    AP009048 Genomic DNA. Translation: BAA16572.2.
    PIRiG65060.
    RefSeqiNP_417267.1. NC_000913.3.

    Genome annotation databases

    EnsemblBacteriaiAAC75829; AAC75829; b2787.
    BAA16572; BAA16572; BAA16572.
    GeneIDi947258.
    KEGGiecj:Y75_p2724.
    eco:b2787.
    PATRICi32120990. VBIEscCol129921_2887.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U00096 Genomic DNA. Translation: AAC75829.1.
    U29581 Genomic DNA. Translation: AAB40437.1.
    AP009048 Genomic DNA. Translation: BAA16572.2.
    PIRiG65060.
    RefSeqiNP_417267.1. NC_000913.3.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1EC7X-ray1.90A/B/C/D1-446[»]
    1EC8X-ray1.90A/B/C/D1-446[»]
    1EC9X-ray2.00A/B/C/D1-446[»]
    1ECQX-ray2.00A/B/C/D1-446[»]
    1JCTX-ray2.75A/B1-446[»]
    1JDFX-ray2.00A/B/C/D1-446[»]
    3PWGX-ray2.00A/B/C/D1-446[»]
    3PWIX-ray2.23A/B1-446[»]
    4GYPX-ray2.10A/B1-446[»]
    ProteinModelPortaliP0AES2.
    SMRiP0AES2. Positions 5-446.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    IntActiP0AES2. 3 interactions.
    STRINGi511145.b2787.

    Proteomic databases

    PaxDbiP0AES2.
    PRIDEiP0AES2.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC75829; AAC75829; b2787.
    BAA16572; BAA16572; BAA16572.
    GeneIDi947258.
    KEGGiecj:Y75_p2724.
    eco:b2787.
    PATRICi32120990. VBIEscCol129921_2887.

    Organism-specific databases

    EchoBASEiEB2959.
    EcoGeneiEG13167. gudD.

    Phylogenomic databases

    eggNOGiCOG4948.
    HOGENOMiHOG000238021.
    InParanoidiP0AES2.
    KOiK01706.
    OMAiMQYLIPN.
    OrthoDBiEOG6V7BH9.
    PhylomeDBiP0AES2.

    Enzyme and pathway databases

    UniPathwayiUPA00564; UER00627.
    BioCyciEcoCyc:GLUCARDEHYDRA-MONOMER.
    ECOL316407:JW2758-MONOMER.
    MetaCyc:GLUCARDEHYDRA-MONOMER.
    BRENDAi4.2.1.40. 2026.
    SABIO-RKP0AES2.

    Miscellaneous databases

    EvolutionaryTraceiP0AES2.
    PROiP0AES2.

    Family and domain databases

    Gene3Di3.20.20.120. 1 hit.
    3.30.390.10. 1 hit.
    InterProiIPR029065. Enolase_C-like.
    IPR029017. Enolase_N_like.
    IPR017653. Glucarate_dehydratase.
    IPR013342. Mandelate_racemase_C.
    IPR001354. MR/MLE/MAL.
    [Graphical view]
    PANTHERiPTHR13794. PTHR13794. 1 hit.
    PfamiPF01188. MR_MLE. 1 hit.
    [Graphical view]
    SMARTiSM00922. MR_MLE. 1 hit.
    [Graphical view]
    SUPFAMiSSF51604. SSF51604. 1 hit.
    SSF54826. SSF54826. 1 hit.
    TIGRFAMsiTIGR03247. glucar-dehydr. 1 hit.
    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. "Construction of a contiguous 874-kb sequence of the Escherichia coli-K12 genome corresponding to 50.0-68.8 min on the linkage map and analysis of its sequence features."
      Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T., Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K., Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T.
      , Oyama S., Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H., Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T.
      DNA Res. 4:91-113(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA] OF 315-446.
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    4. "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 2-15, BIOPHYSICOCHEMICAL PROPERTIES.
    5. "Evolution of enzymatic activities in the enolase superfamily: crystallographic and mutagenesis studies of the reaction catalyzed by D-glucarate dehydratase from Escherichia coli."
      Gulick A.M., Hubbard B.K., Gerlt J.A., Rayment I.
      Biochemistry 39:4590-4602(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS AND MAGNESIUM IONS, MUTAGENESIS OF TYR-150; LYS-207; HIS-339 AND ASP-366, COFACTOR, SUBUNIT.
    6. "Evolution of enzymatic activities in the enolase superfamily: identification of the general acid catalyst in the active site of D-glucarate dehydratase from Escherichia coli."
      Gulick A.M., Hubbard B.K., Gerlt J.A., Rayment I.
      Biochemistry 40:10054-10062(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.75 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS AND MAGNESIUM IONS, SUBUNIT.

    Entry informationi

    Entry nameiGUDD_ECOLI
    AccessioniPrimary (citable) accession number: P0AES2
    Secondary accession number(s): P76637, P78217, Q46914
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: December 20, 2005
    Last sequence update: January 23, 2007
    Last modified: June 24, 2015
    This is version 85 of the entry and version 2 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. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. 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.