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Protein

2,3-dimethylmalate lyase

Gene

Dml

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

Functioni

Catalyzes the formation of proponate and pyruvate from (2R,3S)-2,3-dimethylmalate. Has no activity toward dimethylmaleate, malate, citramalate, isocitrate and citrate.1 Publication

Catalytic activityi

(2R,3S)-2,3-dimethylmalate = propanoate + pyruvate.2 Publications

Cofactori

Mg2+1 Publication

Enzyme regulationi

Completely inhibited by propionic anhydride and by cystamine. Irreversibly inhibited by the mercapto reagents iodoacetate and iodoacetamide. Unaffected by hydroxylamine.1 Publication

Kineticsi

  1. KM=0.66 mM for 2,3-dimethylmalate1 Publication

    Pathwayi: nicotinate degradation

    This protein is involved in step 8 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.

    GO - Molecular functioni

    • 2,3-dimethylmalate lyase activity Source: UniProtKB
    • metal ion binding Source: UniProtKB-KW

    GO - Biological processi

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

    Keywords - Molecular functioni

    Lyase

    Keywords - Ligandi

    Magnesium, Metal-binding

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-11714.
    UniPathwayiUPA01010; UER01019.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    2,3-dimethylmalate lyaseImported (EC:4.1.3.32)
    Gene namesi
    Name:DmlImported
    OrganismiEubacterium barkeri (Clostridium barkeri)
    Taxonomic identifieri1528 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesClostridiaClostridialesEubacteriaceaeEubacterium

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00004039961 – 2892,3-dimethylmalate lyaseAdd BLAST289

    Interactioni

    Subunit structurei

    Homotetramer.1 Publication

    Structurei

    3D structure databases

    ProteinModelPortaliQ0QLE4.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the isocitrate lyase/PEP mutase superfamily.Sequence analysis

    Phylogenomic databases

    KOiK20454.

    Family and domain databases

    Gene3Di3.20.20.60. 1 hit.
    InterProiIPR018523. Isocitrate_lyase_ph_CS.
    IPR015813. Pyrv/PenolPyrv_Kinase-like_dom.
    [Graphical view]
    SUPFAMiSSF51621. SSF51621. 1 hit.
    PROSITEiPS00161. ISOCITRATE_LYASE. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Q0QLE4-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MNTAAKMREL LSTKKMVVAP GAHDAMTAKV IGRLGFDAVY MTGYGQSASH
    60 70 80 90 100
    LGQPDVGLLT MTEMVARANA IVEAAGVPVI ADADTGFGNA VNVMRTVREY
    110 120 130 140 150
    EKAGVAVIQL EDQVMPKKCG HMVGREIVSK EEMVGKIKAA VDTRVNPDFM
    160 170 180 190 200
    IMARTDARTT KGIDEALERG LAYKEAGADI IFIESPEGEE EMKRINETIP
    210 220 230 240 250
    GYTLANMVEG GRTPLLKNAE LEALGYNITI YPTASIYVAT KAMVDLWTAL
    260 270 280
    KNDDTTAGVM DTMVTFSEFN DLMGLEKIRE VEHNYATGR
    Length:289
    Mass (Da):31,379
    Last modified:September 5, 2006 - v1
    Checksum:iC155BC9C580389F3
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    DQ310789 Genomic DNA. Translation: ABC88406.1.

    Genome annotation databases

    KEGGiag:ABC88406.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    DQ310789 Genomic DNA. Translation: ABC88406.1.

    3D structure databases

    ProteinModelPortaliQ0QLE4.
    ModBaseiSearch...
    MobiDBiSearch...

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    KEGGiag:ABC88406.

    Phylogenomic databases

    KOiK20454.

    Enzyme and pathway databases

    UniPathwayiUPA01010; UER01019.
    BioCyciMetaCyc:MONOMER-11714.

    Family and domain databases

    Gene3Di3.20.20.60. 1 hit.
    InterProiIPR018523. Isocitrate_lyase_ph_CS.
    IPR015813. Pyrv/PenolPyrv_Kinase-like_dom.
    [Graphical view]
    SUPFAMiSSF51621. SSF51621. 1 hit.
    PROSITEiPS00161. ISOCITRATE_LYASE. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiDML_EUBBA
    AccessioniPrimary (citable) accession number: Q0QLE4
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 8, 2011
    Last sequence update: September 5, 2006
    Last modified: October 5, 2016
    This is version 42 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Documents

    1. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. 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.