Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

2-(hydroxymethyl)glutarate dehydrogenase

Gene

Hgd

Organism
Eubacterium barkeri (Clostridium barkeri)
Status
Reviewed-Annotation score: -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)DescriptionActionsGraphical viewLength
    Binding sitei99NADBy similarity1
    Active sitei174By similarity1
    Binding sitei243NADBy similarity1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi8 – 22NADBy similarityAdd BLAST15

    GO - Molecular functioni

    GO - Biological processi

    • cofactor catabolic process Source: UniProtKB

    Keywordsi

    Molecular functionOxidoreductase
    LigandNAD

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-13674
    SABIO-RKiQ0QLF5
    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)DescriptionActionsGraphical viewLength
    ChainiPRO_00004039741 – 3012-(hydroxymethyl)glutarate dehydrogenaseAdd BLAST301

    Interactioni

    Subunit structurei

    Homotetramer.2 Publications

    Structurei

    Secondary structure

    1301
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi6 – 10Combined sources5
    Helixi16 – 25Combined sources10
    Beta strandi29 – 33Combined sources5
    Helixi37 – 44Combined sources8
    Turni45 – 47Combined sources3
    Helixi54 – 60Combined sources7
    Beta strandi62 – 66Combined sources5
    Helixi71 – 79Combined sources9
    Helixi84 – 87Combined sources4
    Beta strandi93 – 96Combined sources4
    Helixi102 – 114Combined sources13
    Beta strandi118 – 121Combined sources4
    Beta strandi124 – 126Combined sources3
    Helixi127 – 132Combined sources6
    Beta strandi136 – 142Combined sources7
    Helixi144 – 157Combined sources14
    Beta strandi158 – 166Combined sources9
    Helixi169 – 197Combined sources29
    Helixi202 – 210Combined sources9
    Helixi217 – 222Combined sources6
    Helixi223 – 228Combined sources6
    Beta strandi233 – 237Combined sources5
    Helixi238 – 255Combined sources18
    Helixi260 – 274Combined sources15
    Helixi282 – 285Combined sources4
    Helixi286 – 293Combined sources8

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    3CKYX-ray2.30A/B/C/D1-301[»]
    ProteinModelPortaliQ0QLF5
    SMRiQ0QLF5
    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
    InterProiView protein in InterPro
    IPR002204 3-OH-isobutyrate_DH-rel_CS
    IPR008927 6-PGluconate_DH-like_C_sf
    IPR013328 6PGD_dom2
    IPR006115 6PGDH_NADP-bd
    IPR015815 HIBADH-related
    IPR036291 NAD(P)-bd_dom_sf
    IPR029154 NADP-bd
    PfamiView protein in Pfam
    PF14833 NAD_binding_11, 1 hit
    PF03446 NAD_binding_2, 1 hit
    PIRSFiPIRSF000103 HIBADH, 1 hit
    SUPFAMiSSF48179 SSF48179, 1 hit
    SSF51735 SSF51735, 1 hit
    PROSITEiView protein in PROSITE
    PS00895 3_HYDROXYISOBUT_DH, 1 hit

    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

    Similar proteinsi

    Entry informationi

    Entry nameiHMGD_EUBBA
    AccessioniPrimary (citable) accession number: Q0QLF5
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 8, 2011
    Last sequence update: September 5, 2006
    Last modified: March 28, 2018
    This is version 54 of the entry and version 1 of the sequence. See complete history.
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure
    UniProt is an ELIXIR core data resource
    Main funding by: National Institutes of Health