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Protein

2-(hydroxymethyl)glutarate dehydrogenase

Gene

Hgd

Organism
Eubacterium barkeri (Clostridium barkeri)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the conversion of 2-formylglutarate to (S)-2-hydroxymethylglutarate. Has very low activity with (S)-3-hydroxyisobutyrate.1 Publication

Catalytic activityi

(S)-2-hydroxymethylglutarate + NAD+ = 2-formylglutarate + NADH.2 Publications

Kineticsi

  1. KM=0.24 mM for (S)-2-hydroxymethylglutarate1 Publication
  2. KM=0.14 mM for NAD+1 Publication
  3. KM=4 mM for (S)-3-hydroxyisobutyrate1 Publication

    Pathwayi: nicotinate degradation

    This protein is involved in step 3 of the subpathway that synthesizes propanoate and pyruvate from 6-hydroxynicotinate.1 Publication
    Proteins known to be involved in the 8 steps of the subpathway in this organism are:
    1. 6-hydroxynicotinate reductase (Hnr)
    2. Enamidase (Ena)
    3. 2-(hydroxymethyl)glutarate dehydrogenase (Hgd)
    4. no protein annotated in this organism
    5. 2-methyleneglutarate mutase (mgm)
    6. 3-methylitaconate isomerase (mii)
    7. 2,3-dimethylmalate dehydratase small subunit (DmdB), 2,3-dimethylmalate dehydratase large subunit (dmdA)
    8. 2,3-dimethylmalate lyase (Dml)
    This subpathway is part of the pathway nicotinate degradation, which is itself part of Cofactor degradation.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes propanoate and pyruvate from 6-hydroxynicotinate, the pathway nicotinate degradation and in Cofactor degradation.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei99 – 991NADBy similarity
    Active sitei174 – 1741By similarity
    Binding sitei243 – 2431NADBy similarity

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi8 – 2215NADBy similarityAdd
    BLAST

    GO - Molecular functioni

    GO - Biological processi

    • cofactor catabolic process Source: UniProtKB
    Complete GO annotation...

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Ligandi

    NAD

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-13674.
    UniPathwayiUPA01010; UER01014.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    2-(hydroxymethyl)glutarate dehydrogenase1 Publication (EC:1.1.1.291)
    Gene namesi
    Name:HgdImported
    OrganismiEubacterium barkeri (Clostridium barkeri)
    Taxonomic identifieri1528 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesClostridiaClostridialesEubacteriaceaeEubacterium

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 3013012-(hydroxymethyl)glutarate dehydrogenasePRO_0000403974Add
    BLAST

    Interactioni

    Subunit structurei

    Homotetramer.2 Publications

    Structurei

    Secondary structure

    1
    301
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi6 – 105Combined sources
    Helixi16 – 2510Combined sources
    Beta strandi29 – 335Combined sources
    Helixi37 – 448Combined sources
    Turni45 – 473Combined sources
    Helixi54 – 607Combined sources
    Beta strandi62 – 665Combined sources
    Helixi71 – 799Combined sources
    Helixi84 – 874Combined sources
    Beta strandi93 – 964Combined sources
    Helixi102 – 11413Combined sources
    Beta strandi118 – 1214Combined sources
    Beta strandi124 – 1263Combined sources
    Helixi127 – 1326Combined sources
    Beta strandi136 – 1427Combined sources
    Helixi144 – 15714Combined sources
    Beta strandi158 – 1669Combined sources
    Helixi169 – 19729Combined sources
    Helixi202 – 2109Combined sources
    Helixi217 – 2226Combined sources
    Helixi223 – 2286Combined sources
    Beta strandi233 – 2375Combined sources
    Helixi238 – 25518Combined sources
    Helixi260 – 27415Combined sources
    Helixi282 – 2854Combined sources
    Helixi286 – 2938Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3CKYX-ray2.30A/B/C/D1-301[»]
    ProteinModelPortaliQ0QLF5.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ0QLF5.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the 3-hydroxyisobutyrate dehydrogenase family.Sequence analysis

    Phylogenomic databases

    KOiK19647.

    Family and domain databases

    Gene3Di1.10.1040.10. 1 hit.
    3.40.50.720. 1 hit.
    InterProiIPR002204. 3-OH-isobutyrate_DH-rel_CS.
    IPR008927. 6-PGluconate_DH_C-like.
    IPR013328. 6PGD_dom_2.
    IPR006115. 6PGDH_NADP-bd.
    IPR015815. HIBADH-related.
    IPR016040. NAD(P)-bd_dom.
    IPR029154. NADP-bd.
    [Graphical view]
    PfamiPF14833. NAD_binding_11. 1 hit.
    PF03446. NAD_binding_2. 1 hit.
    [Graphical view]
    PIRSFiPIRSF000103. HIBADH. 1 hit.
    SUPFAMiSSF48179. SSF48179. 1 hit.
    SSF51735. SSF51735. 1 hit.
    PROSITEiPS00895. 3_HYDROXYISOBUT_DH. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Q0QLF5-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MEKSIKIGFI GLGAMGKPMA INLLKEGVTV YAFDLMEANV AAVVAQGAQA
    60 70 80 90 100
    CENNQKVAAA SDIIFTSLPN AGIVETVMNG PGGVLSACKA GTVIVDMSSV
    110 120 130 140 150
    SPSSTLKMAK VAAEKGIDYV DAPVSGGTKG AEAGTLTIMV GASEAVFEKI
    160 170 180 190 200
    QPVLSVIGKD IYHVGDTGAG DAVKIVNNLL LGCNMASLAE ALVLGVKCGL
    210 220 230 240 250
    KPETMQEIIG KSSGRSYAME AKMEKFIMSG DFAGGFAMDL QHKDLGLALE
    260 270 280 290 300
    AGKEGNVPLP MTAMATQIFE GGRAMGLGRE DMSAVIKVWE QMTGVSVSGG

    Q
    Length:301
    Mass (Da):30,873
    Last modified:September 5, 2006 - v1
    Checksum:i00182B7E309EC11D
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    DQ310789 Genomic DNA. Translation: ABC88394.1.

    Genome annotation databases

    KEGGiag:ABC88394.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    DQ310789 Genomic DNA. Translation: ABC88394.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3CKYX-ray2.30A/B/C/D1-301[»]
    ProteinModelPortaliQ0QLF5.
    ModBaseiSearch...
    MobiDBiSearch...

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    KEGGiag:ABC88394.

    Phylogenomic databases

    KOiK19647.

    Enzyme and pathway databases

    UniPathwayiUPA01010; UER01014.
    BioCyciMetaCyc:MONOMER-13674.

    Miscellaneous databases

    EvolutionaryTraceiQ0QLF5.

    Family and domain databases

    Gene3Di1.10.1040.10. 1 hit.
    3.40.50.720. 1 hit.
    InterProiIPR002204. 3-OH-isobutyrate_DH-rel_CS.
    IPR008927. 6-PGluconate_DH_C-like.
    IPR013328. 6PGD_dom_2.
    IPR006115. 6PGDH_NADP-bd.
    IPR015815. HIBADH-related.
    IPR016040. NAD(P)-bd_dom.
    IPR029154. NADP-bd.
    [Graphical view]
    PfamiPF14833. NAD_binding_11. 1 hit.
    PF03446. NAD_binding_2. 1 hit.
    [Graphical view]
    PIRSFiPIRSF000103. HIBADH. 1 hit.
    SUPFAMiSSF48179. SSF48179. 1 hit.
    SSF51735. SSF51735. 1 hit.
    PROSITEiPS00895. 3_HYDROXYISOBUT_DH. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    1. "Molecular and functional analysis of nicotinate catabolism in Eubacterium barkeri."
      Alhapel A., Darley D.J., Wagener N., Eckel E., Elsner N., Pierik A.J.
      Proc. Natl. Acad. Sci. U.S.A. 103:12341-12346(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], CATALYTIC ACTIVITY, PATHWAY, SUBUNIT.
      Strain: ATCC 25849 / DSM 1223 / JCM 1389 / NCIB 10623Imported.
    2. "Structural and kinetic properties of a beta-hydroxyacid dehydrogenase involved in nicotinate fermentation."
      Reitz S., Alhapel A., Essen L.O., Pierik A.J.
      J. Mol. Biol. 382:802-811(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS), FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT.

    Entry informationi

    Entry nameiHMGD_EUBBA
    AccessioniPrimary (citable) accession number: Q0QLF5
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 8, 2011
    Last sequence update: September 5, 2006
    Last modified: December 9, 2015
    This is version 49 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

    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

    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.