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Protein

D-2-hydroxyglutarate dehydrogenase, mitochondrial

Gene

D2HGDH

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the oxidation of D-2-hydroxyglutarate to alpha-ketoglutarate. May be involved in the catabolism of propionyl-CoA derived from beta-oxidation. Involved in degradation of lysine for the supply of carbon and electrons to the ETF/ETFQO complex during dark-induced sugar starvation.3 Publications

Catalytic activityi

(R)-2-hydroxyglutarate + acceptor = 2-oxoglutarate + reduced acceptor.1 Publication

Cofactori

FAD1 PublicationNote: Binds 1 FAD per monomer.1 Publication

Kineticsi

Very low activity toward D-lactate, D-2-hydroxybutyrate and meso-tartrate. Does not efficiently use cytochrome c as electron acceptor and is not able to transfer electrons to NAD or NADP.

  1. KM=584 µM for D-2-hydroxyglutarate (with DCIP as acceptor molecule)1 Publication

    pH dependencei

    Optimum pH is 8.5-9.5.1 Publication

    GO - Molecular functioni

    • (R)-2-hydroxyglutarate dehydrogenase activity Source: TAIR
    • 2-hydroxyglutarate dehydrogenase activity Source: TAIR
    • flavin adenine dinucleotide binding Source: InterPro

    GO - Biological processi

    • nitrogen compound metabolic process Source: TAIR
    • photorespiration Source: TAIR
    Complete GO annotation...

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Ligandi

    FAD, Flavoprotein

    Enzyme and pathway databases

    BioCyciARA:GQT-871-MONOMER.
    ARA:MONOMERQT-4168.
    ReactomeiR-ATH-880009. Interconversion of 2-oxoglutarate and 2-hydroxyglutarate.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    D-2-hydroxyglutarate dehydrogenase, mitochondrial (EC:1.1.99.39)
    Short name:
    AtD-2HGDH
    Gene namesi
    Name:D2HGDH
    Ordered Locus Names:At4g36400
    ORF Names:AP22.14, C7A10.960
    OrganismiArabidopsis thaliana (Mouse-ear cress)
    Taxonomic identifieri3702 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
    Proteomesi
    • UP000006548 Componenti: Chromosome 4

    Organism-specific databases

    TAIRiAT4G36400.

    Subcellular locationi

    GO - Cellular componenti

    • mitochondrion Source: TAIR
    Complete GO annotation...

    Keywords - Cellular componenti

    Mitochondrion

    Pathology & Biotechi

    Disruption phenotypei

    No visible phenotype when grown under standard conditions.2 Publications

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Transit peptidei1 – 6767MitochondrionSequence analysisAdd
    BLAST
    Chaini68 – 559492D-2-hydroxyglutarate dehydrogenase, mitochondrialPRO_0000393389Add
    BLAST

    Proteomic databases

    PaxDbiO23240.
    PRIDEiO23240.

    Expressioni

    Inductioni

    By dark-induced senescence.1 Publication

    Gene expression databases

    GenevisibleiO23240. AT.

    Interactioni

    Subunit structurei

    Homodimer.1 Publication

    Protein-protein interaction databases

    BioGridi15074. 1 interaction.
    STRINGi3702.AT4G36400.1.

    Structurei

    3D structure databases

    ProteinModelPortaliO23240.
    SMRiO23240. Positions 97-309.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini130 – 309180FAD-binding PCMH-typePROSITE-ProRule annotationAdd
    BLAST

    Sequence similaritiesi

    Contains 1 FAD-binding PCMH-type domain.PROSITE-ProRule annotation

    Keywords - Domaini

    Transit peptide

    Phylogenomic databases

    eggNOGiKOG1232. Eukaryota.
    COG0277. LUCA.
    HOGENOMiHOG000230997.
    InParanoidiO23240.
    KOiK18204.
    OMAiNEDWMRK.
    OrthoDBiEOG0936051T.
    PhylomeDBiO23240.

    Family and domain databases

    Gene3Di1.10.45.10. 1 hit.
    3.30.43.10. 1 hit.
    3.30.465.10. 1 hit.
    InterProiIPR016169. CO_DH_flavot_FAD-bd_sub2.
    IPR016166. FAD-bd_2.
    IPR016167. FAD-bd_2_sub1.
    IPR016164. FAD-linked_Oxase-like_C.
    IPR004113. FAD-linked_oxidase_C.
    IPR006094. Oxid_FAD_bind_N.
    IPR016171. Vanillyl_alc_oxidase_C-sub2.
    [Graphical view]
    PfamiPF02913. FAD-oxidase_C. 1 hit.
    PF01565. FAD_binding_4. 1 hit.
    [Graphical view]
    SUPFAMiSSF55103. SSF55103. 1 hit.
    SSF56176. SSF56176. 1 hit.
    PROSITEiPS51387. FAD_PCMH. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

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

    O23240-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MMMQKLRRSG EFIRFGCKSL ISSRPNKDSV SRSVSGFVNH YKSKGKLFEL
    60 70 80 90 100
    SDGNYKTELH HPCISRNVGM LLQQYKCFGS SAASLIQRNP LFSSLDSKDV
    110 120 130 140 150
    SYFKEILGEK NVVEDKERLE TANTDWMHKY KGSSKLMLLP KNTQEVSQIL
    160 170 180 190 200
    EYCDSRRLAV VPQGGNTGLV GGSVPVFDEV IVNVGLMNKI LSFDEVSGVL
    210 220 230 240 250
    VCEAGCILEN LATFLDTKGF IMPLDLGAKG SCHIGGNVST NAGGLRLIRY
    260 270 280 290 300
    GSLHGTVLGL EAVTANGNVL DMLGTLRKDN TGYDLKHLFI GSEGSLGIVT
    310 320 330 340 350
    KVSILTQPKL SSVNLAFIAC KDYLSCQKLL VEAKRNLGEI LSAFEFLDNN
    360 370 380 390 400
    SMDLVLNHLD GVRNPVSSSE NFYILIETTG SDETNDREKL EAFLLKSLEK
    410 420 430 440 450
    GLVSDGVIAQ DINQASSFWR IREGITEALQ KAGAVYKYDL SLPVEEIYNI
    460 470 480 490 500
    VNDLRGRLGD LANVMGYGHL GDGNLHLNIS AAEYNDKLLG LIEPYVYEWT
    510 520 530 540 550
    SKHRGSISAE HGLGVMKANE IFYSKSPETV ALMASIKKLL DPKGILNPYK

    VLPHSLFSN
    Length:559
    Mass (Da):61,445
    Last modified:April 20, 2010 - v3
    Checksum:i53D72B588A7302A9
    GO

    Sequence cautioni

    The sequence AAL24169 differs from that shown.Intron retention.Curated
    The sequence CAB16815 differs from that shown. Reason: Erroneous gene model prediction. Curated
    The sequence CAB80306 differs from that shown. Reason: Erroneous gene model prediction. Curated

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    Z99708 Genomic DNA. Translation: CAB16815.1. Sequence problems.
    AL161589 Genomic DNA. Translation: CAB80306.1. Sequence problems.
    CP002687 Genomic DNA. Translation: AEE86651.1.
    CP002687 Genomic DNA. Translation: AEE86652.1.
    AY058061 mRNA. Translation: AAL24169.1. Sequence problems.
    AY090301 mRNA. Translation: AAL90962.1.
    PIRiF85429.
    RefSeqiNP_568003.2. NM_119803.3.
    NP_974692.1. NM_202963.1.
    UniGeneiAt.26659.

    Genome annotation databases

    EnsemblPlantsiAT4G36400.1; AT4G36400.1; AT4G36400.
    AT4G36400.2; AT4G36400.2; AT4G36400.
    GeneIDi829792.
    GrameneiAT4G36400.1; AT4G36400.1; AT4G36400.
    AT4G36400.2; AT4G36400.2; AT4G36400.
    KEGGiath:AT4G36400.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    Z99708 Genomic DNA. Translation: CAB16815.1. Sequence problems.
    AL161589 Genomic DNA. Translation: CAB80306.1. Sequence problems.
    CP002687 Genomic DNA. Translation: AEE86651.1.
    CP002687 Genomic DNA. Translation: AEE86652.1.
    AY058061 mRNA. Translation: AAL24169.1. Sequence problems.
    AY090301 mRNA. Translation: AAL90962.1.
    PIRiF85429.
    RefSeqiNP_568003.2. NM_119803.3.
    NP_974692.1. NM_202963.1.
    UniGeneiAt.26659.

    3D structure databases

    ProteinModelPortaliO23240.
    SMRiO23240. Positions 97-309.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi15074. 1 interaction.
    STRINGi3702.AT4G36400.1.

    Proteomic databases

    PaxDbiO23240.
    PRIDEiO23240.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblPlantsiAT4G36400.1; AT4G36400.1; AT4G36400.
    AT4G36400.2; AT4G36400.2; AT4G36400.
    GeneIDi829792.
    GrameneiAT4G36400.1; AT4G36400.1; AT4G36400.
    AT4G36400.2; AT4G36400.2; AT4G36400.
    KEGGiath:AT4G36400.

    Organism-specific databases

    TAIRiAT4G36400.

    Phylogenomic databases

    eggNOGiKOG1232. Eukaryota.
    COG0277. LUCA.
    HOGENOMiHOG000230997.
    InParanoidiO23240.
    KOiK18204.
    OMAiNEDWMRK.
    OrthoDBiEOG0936051T.
    PhylomeDBiO23240.

    Enzyme and pathway databases

    BioCyciARA:GQT-871-MONOMER.
    ARA:MONOMERQT-4168.
    ReactomeiR-ATH-880009. Interconversion of 2-oxoglutarate and 2-hydroxyglutarate.

    Miscellaneous databases

    PROiO23240.

    Gene expression databases

    GenevisibleiO23240. AT.

    Family and domain databases

    Gene3Di1.10.45.10. 1 hit.
    3.30.43.10. 1 hit.
    3.30.465.10. 1 hit.
    InterProiIPR016169. CO_DH_flavot_FAD-bd_sub2.
    IPR016166. FAD-bd_2.
    IPR016167. FAD-bd_2_sub1.
    IPR016164. FAD-linked_Oxase-like_C.
    IPR004113. FAD-linked_oxidase_C.
    IPR006094. Oxid_FAD_bind_N.
    IPR016171. Vanillyl_alc_oxidase_C-sub2.
    [Graphical view]
    PfamiPF02913. FAD-oxidase_C. 1 hit.
    PF01565. FAD_binding_4. 1 hit.
    [Graphical view]
    SUPFAMiSSF55103. SSF55103. 1 hit.
    SSF56176. SSF56176. 1 hit.
    PROSITEiPS51387. FAD_PCMH. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiD2HDH_ARATH
    AccessioniPrimary (citable) accession number: O23240
    Secondary accession number(s): Q93Z78
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: April 20, 2010
    Last sequence update: April 20, 2010
    Last modified: September 7, 2016
    This is version 91 of the entry and version 3 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programPlant Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. Arabidopsis thaliana
      Arabidopsis thaliana: entries and gene names
    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.