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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

    Pathwayi: 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)DescriptionActionsGraphical viewLength
    Binding sitei32Substrate1
    Binding sitei103Substrate1
    Binding sitei150Substrate1
    Binding sitei205Substrate1
    Active sitei207Proton acceptor1
    Metal bindingi235Magnesium1
    Metal bindingi266Magnesium1
    Metal bindingi289Magnesium1
    Binding sitei289Substrate1
    Active sitei339Proton acceptor1
    Binding sitei368Substrate1
    Binding sitei422Substrate1

    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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG13167. gudD.

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi150Y → F: Reduces activity 100-fold. 1 Publication1
    Mutagenesisi207K → Q: Reduces activity 1000-fold. 1 Publication1
    Mutagenesisi207K → R: Reduces activity 10000-fold. 1 Publication1
    Mutagenesisi339H → A: Loss of activity. 1 Publication1
    Mutagenesisi339H → N: Reduces activity 10000-fold. 1 Publication1
    Mutagenesisi339H → Q: Reduces activity 1000-fold. 1 Publication1
    Mutagenesisi366D → A or N: Reduces activity over 100-fold. 1 Publication1

    Chemistry databases

    DrugBankiDB02325. Isopropyl Alcohol.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Initiator methionineiRemoved1 Publication
    ChainiPRO_00001712642 – 446Glucarate dehydrataseAdd BLAST445

    Proteomic databases

    PaxDbiP0AES2.
    PRIDEiP0AES2.

    Interactioni

    Subunit structurei

    Homodimer.2 Publications

    Protein-protein interaction databases

    BioGridi4262287. 12 interactors.
    IntActiP0AES2. 3 interactors.
    STRINGi511145.b2787.

    Structurei

    Secondary structure

    1446
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi9 – 21Combined sources13
    Beta strandi25 – 27Combined sources3
    Beta strandi34 – 45Combined sources12
    Beta strandi50 – 56Combined sources7
    Helixi59 – 72Combined sources14
    Helixi77 – 79Combined sources3
    Helixi80 – 90Combined sources11
    Helixi92 – 95Combined sources4
    Turni96 – 99Combined sources4
    Beta strandi101 – 104Combined sources4
    Helixi109 – 128Combined sources20
    Beta strandi130 – 132Combined sources3
    Helixi133 – 135Combined sources3
    Beta strandi143 – 147Combined sources5
    Beta strandi149 – 152Combined sources4
    Helixi157 – 159Combined sources3
    Beta strandi160 – 162Combined sources3
    Helixi173 – 177Combined sources5
    Helixi185 – 199Combined sources15
    Beta strandi202 – 207Combined sources6
    Beta strandi209 – 211Combined sources3
    Helixi213 – 226Combined sources14
    Beta strandi230 – 235Combined sources6
    Helixi242 – 251Combined sources10
    Turni252 – 255Combined sources4
    Beta strandi256 – 261Combined sources6
    Helixi271 – 282Combined sources12
    Beta strandi286 – 291Combined sources6
    Helixi295 – 304Combined sources10
    Beta strandi308 – 311Combined sources4
    Helixi314 – 317Combined sources4
    Helixi319 – 331Combined sources13
    Helixi345 – 356Combined sources12
    Helixi369 – 372Combined sources4
    Turni373 – 375Combined sources3
    Beta strandi378 – 381Combined sources4
    Beta strandi389 – 391Combined sources3
    Beta strandi395 – 397Combined sources3
    Helixi404 – 416Combined sources13
    Helixi425 – 429Combined sources5

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB 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.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP0AES2.

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni235 – 237Substrate binding3
    Regioni339 – 341Substrate binding3

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiENOG4105EQX. Bacteria.
    COG4948. LUCA.
    HOGENOMiHOG000238021.
    InParanoidiP0AES2.
    KOiK01706.
    OMAiRVAQMCN.
    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. 2 hits.
    PfamiPF13378. MR_MLE_C. 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)DescriptionActionsGraphical viewLength
    Sequence conflicti310 – 313PLAD → RWRI in AAB40437 (PubMed:9278503).Curated4

    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.
    WP_000098255.1. NZ_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAC75829; AAC75829; b2787.
    BAA16572; BAA16572; BAA16572.
    GeneIDi947258.
    KEGGiecj:JW2758.
    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.
    WP_000098255.1. NZ_LN832404.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB 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.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4262287. 12 interactors.
    IntActiP0AES2. 3 interactors.
    STRINGi511145.b2787.

    Chemistry databases

    DrugBankiDB02325. Isopropyl Alcohol.

    Proteomic databases

    PaxDbiP0AES2.
    PRIDEiP0AES2.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC75829; AAC75829; b2787.
    BAA16572; BAA16572; BAA16572.
    GeneIDi947258.
    KEGGiecj:JW2758.
    eco:b2787.
    PATRICi32120990. VBIEscCol129921_2887.

    Organism-specific databases

    EchoBASEiEB2959.
    EcoGeneiEG13167. gudD.

    Phylogenomic databases

    eggNOGiENOG4105EQX. Bacteria.
    COG4948. LUCA.
    HOGENOMiHOG000238021.
    InParanoidiP0AES2.
    KOiK01706.
    OMAiRVAQMCN.
    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. 2 hits.
    PfamiPF13378. MR_MLE_C. 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...

    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: November 2, 2016
    This is version 93 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

    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 one 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.