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P36234

- DHGY_HYPME

UniProt

P36234 - DHGY_HYPME

Protein

Glycerate dehydrogenase

Gene
N/A
Organism
Hyphomicrobium methylovorum
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 92 (01 Oct 2014)
      Sequence version 2 (23 Jan 2007)
      Previous versions | rss
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    • Comment

    Functioni

    Active on hydroxypyruvate and glyoxylate.

    Catalytic activityi

    D-glycerate + NAD+ = hydroxypyruvate + NADH.

    pH dependencei

    Optimum pH is 6.8.

    Temperature dependencei

    Optimum temperature is 45 degrees Celsius.

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei178 – 1781NADBy similarity
    Active sitei241 – 2411
    Binding sitei265 – 2651NADBy similarity
    Active sitei270 – 2701
    Active sitei288 – 2881Proton donor

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi158 – 1592NADBy similarity
    Nucleotide bindingi239 – 2413NADBy similarity
    Nucleotide bindingi288 – 2914NADBy similarity

    GO - Molecular functioni

    1. glycerate dehydrogenase activity Source: UniProtKB-EC
    2. NAD binding Source: InterPro

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Ligandi

    NAD

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-4245.
    UniPathwayiUPA00927.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Glycerate dehydrogenase (EC:1.1.1.29)
    Short name:
    GDH
    Alternative name(s):
    Glyoxylate reductase
    Hydroxypyruvate dehydrogenase
    NADH-dependent hydroxypyruvate reductase
    Short name:
    HPR
    OrganismiHyphomicrobium methylovorum
    Taxonomic identifieri84 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesHyphomicrobiaceaeHyphomicrobium

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed
    Chaini2 – 322321Glycerate dehydrogenasePRO_0000075942Add
    BLAST

    Expressioni

    Inductioni

    By methanol.

    Interactioni

    Subunit structurei

    Homodimer.

    Structurei

    Secondary structure

    1
    322
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi5 – 106
    Helixi14 – 218
    Beta strandi24 – 285
    Helixi37 – 448
    Beta strandi48 – 536
    Helixi60 – 656
    Beta strandi72 – 787
    Helixi85 – 906
    Beta strandi94 – 963
    Helixi103 – 11816
    Helixi121 – 1299
    Turni138 – 1414
    Beta strandi150 – 1545
    Helixi158 – 16811
    Turni169 – 1713
    Beta strandi173 – 1775
    Helixi184 – 1896
    Helixi198 – 2047
    Beta strandi206 – 2105
    Turni216 – 2205
    Helixi224 – 2274
    Beta strandi234 – 2385
    Helixi242 – 2443
    Helixi247 – 2559
    Beta strandi258 – 2658
    Turni268 – 2714
    Helixi277 – 2793
    Beta strandi283 – 2853
    Helixi294 – 31219
    Beta strandi320 – 3223

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1GDHX-ray2.40A/B3-322[»]
    ProteinModelPortaliP36234.
    SMRiP36234. Positions 3-322.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP36234.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni2 – 10099CatalyticAdd
    BLAST
    Regioni101 – 291191Coenzyme-bindingAdd
    BLAST
    Regioni292 – 32231CatalyticAdd
    BLAST

    Sequence similaritiesi

    Family and domain databases

    Gene3Di3.40.50.720. 2 hits.
    InterProiIPR006139. D-isomer_2_OHA_DH_cat_dom.
    IPR006140. D-isomer_DH_NAD-bd.
    IPR016040. NAD(P)-bd_dom.
    [Graphical view]
    PfamiPF00389. 2-Hacid_dh. 1 hit.
    PF02826. 2-Hacid_dh_C. 1 hit.
    [Graphical view]
    PROSITEiPS00065. D_2_HYDROXYACID_DH_1. 1 hit.
    PS00670. D_2_HYDROXYACID_DH_2. 1 hit.
    PS00671. D_2_HYDROXYACID_DH_3. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

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

    P36234-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSKKKILITW PLPEAAMARA RESYDVIAHG DDPKITIDEM IETAKSVDAL    50
    LITLNEKCRK EVIDRIPENI KCISTYSIGF DHIDLDACKA RGIKVGNAPH 100
    GVTVATAEIA MLLLLGSARR AGEGEKMIRT RSWPGWEPLE LVGEKLDNKT 150
    LGIYGFGSIG QALAKRAQGF DMDIDYFDTH RASSSDEASY QATFHDSLDS 200
    LLSVSQFFSL NAPSTPETRY FFNKATIKSL PQGAIVVNTA RGDLVDNELV 250
    VAALEAGRLA YAGFDVFAGE PNINEGYYDL PNTFLFPHIG SAATQAREDM 300
    AHQANDLIDA LFGGADMSYA LA 322
    Length:322
    Mass (Da):35,115
    Last modified:January 23, 2007 - v2
    Checksum:iCA5E39C1617AF2FE
    GO

    Cross-referencesi

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1GDH X-ray 2.40 A/B 3-322 [» ]
    ProteinModelPortali P36234.
    SMRi P36234. Positions 3-322.
    ModBasei Search...
    MobiDBi Search...

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Enzyme and pathway databases

    UniPathwayi UPA00927 .
    BioCyci MetaCyc:MONOMER-4245.

    Miscellaneous databases

    EvolutionaryTracei P36234.

    Family and domain databases

    Gene3Di 3.40.50.720. 2 hits.
    InterProi IPR006139. D-isomer_2_OHA_DH_cat_dom.
    IPR006140. D-isomer_DH_NAD-bd.
    IPR016040. NAD(P)-bd_dom.
    [Graphical view ]
    Pfami PF00389. 2-Hacid_dh. 1 hit.
    PF02826. 2-Hacid_dh_C. 1 hit.
    [Graphical view ]
    PROSITEi PS00065. D_2_HYDROXYACID_DH_1. 1 hit.
    PS00670. D_2_HYDROXYACID_DH_2. 1 hit.
    PS00671. D_2_HYDROXYACID_DH_3. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Crystal structure of a NAD-dependent D-glycerate dehydrogenase at 2.4-A resolution."
      Goldberg J.D., Yoshida T., Brick P.
      J. Mol. Biol. 236:1123-1140(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS).
    2. "Purification and characterization of hydroxypyruvate reductase from a serine-producing methylotroph, Hyphomicrobium methylovorum GM2."
      Izumi Y., Yoshida T., Kanzaki H., Toki S., Miyazaki S.S., Yamada H.
      Eur. J. Biochem. 190:279-284(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: CHARACTERIZATION.
      Strain: KM146 / GM2.

    Entry informationi

    Entry nameiDHGY_HYPME
    AccessioniPrimary (citable) accession number: P36234
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: June 1, 1994
    Last sequence update: January 23, 2007
    Last modified: October 1, 2014
    This is version 92 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

    Documents

    1. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    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