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P0AES2

- GUDD_ECOLI

UniProt

P0AES2 - GUDD_ECOLI

Protein

Glucarate dehydratase

Gene

gudD

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 79 (01 Oct 2014)
      Sequence version 2 (23 Jan 2007)
      Previous versions | rss
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    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

    Magnesium.1 Publication

    Kineticsi

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

    Pathwayi

    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

    1. glucarate dehydratase activity Source: UniProtKB
    2. magnesium ion binding Source: UniProtKB

    GO - Biological processi

    1. D-glucarate catabolic process Source: UniProtKB

    Keywords - Molecular functioni

    Lyase

    Keywords - Ligandi

    Magnesium, Metal-binding

    Enzyme and pathway databases

    BioCyciEcoCyc:GLUCARDEHYDRA-MONOMER.
    ECOL316407:JW2758-MONOMER.
    MetaCyc:GLUCARDEHYDRA-MONOMER.
    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: Chromosome, UP000000625: 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.

    Expressioni

    Gene expression databases

    GenevestigatoriP0AES2.

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

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    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.
    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.
    KOiK01706.
    OMAiAMFTQVA.
    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.
    [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

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    MSSQFTTPVV TEMQVIPVAG HDSMLMNLSG AHAPFFTRNI VIIKDNSGHT    50
    GVGEIPGGEK IRKTLEDAIP LVVGKTLGEY KNVLTLVRNT FADRDAGGRG 100
    LQTFDLRTTI HVVTGIEAAM LDLLGQHLGV NVASLLGDGQ QRSEVEMLGY 150
    LFFVGNRKAT PLPYQSQPDD SCDWYRLRHE EAMTPDAVVR LAEAAYEKYG 200
    FNDFKLKGGV LAGEEEAESI VALAQRFPQA RITLDPNGAW SLNEAIKIGK 250
    YLKGSLAYAE DPCGAEQGFS GREVMAEFRR ATGLPTATNM IATDWRQMGH 300
    TLSLQSVDIP LADPHFWTMQ GSVRVAQMCH EFGLTWGSHS NNHFDISLAM 350
    FTHVAAAAPG KITAIDTHWI WQEGNQRLTK EPFEIKGGLV QVPEKPGLGV 400
    EIDMDQVMKA HELYQKHGLG ARDDAMGMQY LIPGWTFDNK RPCMVR 446
    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:
    EMBL
    GenBank
    DDBJ
    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.
    YP_490995.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC75829; AAC75829; b2787.
    BAA16572; BAA16572; BAA16572.
    GeneIDi12933293.
    947258.
    KEGGiecj:Y75_p2724.
    eco:b2787.
    PATRICi32120990. VBIEscCol129921_2887.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U00096 Genomic DNA. Translation: AAC75829.1 .
    U29581 Genomic DNA. Translation: AAB40437.1 .
    AP009048 Genomic DNA. Translation: BAA16572.2 .
    PIRi G65060.
    RefSeqi NP_417267.1. NC_000913.3.
    YP_490995.1. NC_007779.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1EC7 X-ray 1.90 A/B/C/D 1-446 [» ]
    1EC8 X-ray 1.90 A/B/C/D 1-446 [» ]
    1EC9 X-ray 2.00 A/B/C/D 1-446 [» ]
    1ECQ X-ray 2.00 A/B/C/D 1-446 [» ]
    1JCT X-ray 2.75 A/B 1-446 [» ]
    1JDF X-ray 2.00 A/B/C/D 1-446 [» ]
    3PWG X-ray 2.00 A/B/C/D 1-446 [» ]
    3PWI X-ray 2.23 A/B 1-446 [» ]
    4GYP X-ray 2.10 A/B 1-446 [» ]
    ProteinModelPortali P0AES2.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    IntActi P0AES2. 3 interactions.
    STRINGi 511145.b2787.

    Proteomic databases

    PaxDbi P0AES2.
    PRIDEi P0AES2.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC75829 ; AAC75829 ; b2787 .
    BAA16572 ; BAA16572 ; BAA16572 .
    GeneIDi 12933293.
    947258.
    KEGGi ecj:Y75_p2724.
    eco:b2787.
    PATRICi 32120990. VBIEscCol129921_2887.

    Organism-specific databases

    EchoBASEi EB2959.
    EcoGenei EG13167. gudD.

    Phylogenomic databases

    eggNOGi COG4948.
    HOGENOMi HOG000238021.
    KOi K01706.
    OMAi AMFTQVA.
    OrthoDBi EOG6V7BH9.
    PhylomeDBi P0AES2.

    Enzyme and pathway databases

    UniPathwayi UPA00564 ; UER00627 .
    BioCyci EcoCyc:GLUCARDEHYDRA-MONOMER.
    ECOL316407:JW2758-MONOMER.
    MetaCyc:GLUCARDEHYDRA-MONOMER.
    SABIO-RK P0AES2.

    Miscellaneous databases

    EvolutionaryTracei P0AES2.
    PROi P0AES2.

    Gene expression databases

    Genevestigatori P0AES2.

    Family and domain databases

    Gene3Di 3.20.20.120. 1 hit.
    3.30.390.10. 1 hit.
    InterProi IPR029065. Enolase_C-like.
    IPR029017. Enolase_N_like.
    IPR017653. Glucarate_dehydratase.
    IPR013342. Mandelate_racemase_C.
    IPR001354. MR_MLE.
    [Graphical view ]
    PANTHERi PTHR13794. PTHR13794. 1 hit.
    Pfami PF01188. MR_MLE. 1 hit.
    [Graphical view ]
    SMARTi SM00922. MR_MLE. 1 hit.
    [Graphical view ]
    SUPFAMi SSF51604. SSF51604. 1 hit.
    SSF54826. SSF54826. 1 hit.
    TIGRFAMsi TIGR03247. glucar-dehydr. 1 hit.
    ProtoNeti Search...

    Publicationsi

    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: October 1, 2014
    This is version 79 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