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Protein

(S)-mandelate dehydrogenase, mitochondrial

Gene
N/A
Organism
Rhodotorula graminis (Yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Involved in the reduction of (S)-mandelate to benzoylformate and enables utilization of mandelate as substrate for growth.2 Publications

Catalytic activityi

(S)-2-hydroxy-2-phenylacetate + acceptor = 2-oxo-2-phenylacetate + reduced acceptor.1 Publication

Cofactori

Protein has several cofactor binding sites:
  • FMN1 PublicationNote: Binds 1 FMN per subunit.1 Publication
  • heme1 PublicationNote: Binds 1 heme group per subunit.1 Publication

Kineticsi

  1. KM=0.47 mM for D,L-mandelate (with ferricyanide as electron acceptor)1 Publication
  2. KM=0.53 mM for 2-deuterated D,L-mandelate (with ferricyanide as electron acceptor)1 Publication
  3. KM=0.78 mM for D,L-mandelate (with cytochrome c as electron acceptor)1 Publication
  4. KM=1.33 mM for 2-deuterated D,L-mandelate (with cytochrome c as electron acceptor)1 Publication

    Pathwayi: (R)-mandelate degradation

    This protein is involved in step 2 of the subpathway that synthesizes benzoate from (R)-mandelate.
    Proteins known to be involved in the 4 steps of the subpathway in this organism are:
    1. no protein annotated in this organism
    2. (S)-mandelate dehydrogenase, mitochondrial
    3. no protein annotated in this organism
    4. no protein annotated in this organism
    This subpathway is part of the pathway (R)-mandelate degradation, which is itself part of Aromatic compound metabolism.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes benzoate from (R)-mandelate, the pathway (R)-mandelate degradation and in Aromatic compound metabolism.

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Metal bindingi121Iron (heme axial ligand)PROSITE-ProRule annotation1
    Metal bindingi144Iron (heme axial ligand)PROSITE-ProRule annotation1
    Binding sitei215SubstratePROSITE-ProRule annotation1
    Binding sitei297FMNPROSITE-ProRule annotation1
    Binding sitei320FMNPROSITE-ProRule annotation1
    Binding sitei322SubstratePROSITE-ProRule annotation1
    Binding sitei348FMNPROSITE-ProRule annotation1
    Binding sitei357SubstratePROSITE-ProRule annotation1
    Binding sitei427FMNPROSITE-ProRule annotation1
    Active sitei451Proton acceptorPROSITE-ProRule annotation1
    Binding sitei454SubstratePROSITE-ProRule annotation1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi485 – 509FMNPROSITE-ProRule annotationAdd BLAST25

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    Aromatic hydrocarbons catabolism, Electron transport, Mandelate pathway, Respiratory chain, Transport

    Keywords - Ligandi

    Flavoprotein, FMN, Heme, Iron, Metal-binding

    Enzyme and pathway databases

    UniPathwayiUPA00873; UER00853.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    (S)-mandelate dehydrogenase, mitochondrial (EC:1.1.99.31)
    Alternative name(s):
    Flavocytochrome b
    L(+)-mandelate dehydrogenase
    Short name:
    L-MDH
    OrganismiRhodotorula graminis (Yeast)
    Taxonomic identifieri29898 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaBasidiomycotaPucciniomycotinaMicrobotryomycetesSporidiobolalesSporidiobolaceaeRhodotorula

    Subcellular locationi

    GO - Cellular componenti

    Complete GO annotation...

    Keywords - Cellular componenti

    Mitochondrion

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Transit peptidei1 – 54MitochondrionSequence analysisAdd BLAST54
    ChainiPRO_000020632855 – 565(S)-mandelate dehydrogenase, mitochondrialAdd BLAST511

    Interactioni

    Subunit structurei

    Homotetramer.1 Publication

    Structurei

    3D structure databases

    ProteinModelPortaliP32953.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Domaini86 – 163Cytochrome b5 heme-bindingPROSITE-ProRule annotationAdd BLAST78
    Domaini189 – 559FMN hydroxy acid dehydrogenasePROSITE-ProRule annotationAdd BLAST371

    Sequence similaritiesi

    Belongs to the FMN-dependent alpha-hydroxy acid dehydrogenase family.PROSITE-ProRule annotation
    Contains 1 cytochrome b5 heme-binding domain.PROSITE-ProRule annotation
    Contains 1 FMN hydroxy acid dehydrogenase domain.PROSITE-ProRule annotation

    Keywords - Domaini

    Transit peptide

    Family and domain databases

    Gene3Di3.10.120.10. 1 hit.
    3.20.20.70. 1 hit.
    InterProiIPR013785. Aldolase_TIM.
    IPR012133. Alpha-hydoxy_acid_DH_FMN.
    IPR001199. Cyt_B5-like_heme/steroid-bd.
    IPR018506. Cyt_B5_heme-BS.
    IPR000262. FMN-dep_DH.
    [Graphical view]
    PfamiPF00173. Cyt-b5. 1 hit.
    PF01070. FMN_dh. 1 hit.
    [Graphical view]
    SMARTiSM01117. Cyt-b5. 1 hit.
    [Graphical view]
    SUPFAMiSSF55856. SSF55856. 1 hit.
    PROSITEiPS00191. CYTOCHROME_B5_1. 1 hit.
    PS50255. CYTOCHROME_B5_2. 1 hit.
    PS51349. FMN_HYDROXY_ACID_DH_2. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

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

    P32953-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MSFARVRTAL RCQRAAASPA PPKVQARRFA NKAAPHASAS SAGSRAFHLG
    60 70 80 90 100
    LAAGAALAVG GAGLYLFSRS PVLLDAQLPV KQRGRARSIS AAEVAKHNSR
    110 120 130 140 150
    DSMWVCIDDE VWDITNFVEL HPGGAKVLEQ NAGKDVTKVF KSIHPPKTLE
    160 170 180 190 200
    KFLTDDNFVG RIDVDEVTKI GGGKNAEDLR IEQARKELRN VETVVCLDEF
    210 220 230 240 250
    EEISQKILSE MAMAYYGTGA ETEQTLRDER EAWQRVRFRP RVLRKMRHID
    260 270 280 290 300
    TNTTFLGIPT PLPIFVAPAG LARLGHPDGE QNIVRGVAKH DILQVVSSGA
    310 320 330 340 350
    SCSIDEIFEV KEPDQNLAWQ FYVHSDKKIA EEKLKRALAL GAKAIFVTVD
    360 370 380 390 400
    VPVLGKRERD LKLKARSQNY EHPIAAQWKA AGSKVEETIA KRGVSDIPDT
    410 420 430 440 450
    AHIDANLNWD DIAWIKERAP GVPIVIKGVG CVEDVELAKQ YGADGVVLST
    460 470 480 490 500
    HGARQLDGAR APLDVLIEVR RKNPALLKEI EVYVDGQARR GTDVLKALCL
    510 520 530 540 550
    GARGVGFGRG FLYAQSAYGA DGVDKAIRIL ENEIQNAMRL LGANTLADLK
    560
    PEMVECSFPE RWVPE
    Length:565
    Mass (Da):61,974
    Last modified:July 24, 2013 - v2
    Checksum:iA16F5BB4CFE418F1
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AJ001430 Genomic DNA. Translation: CAA04758.1.
    PIRiS35053.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AJ001430 Genomic DNA. Translation: CAA04758.1.
    PIRiS35053.

    3D structure databases

    ProteinModelPortaliP32953.
    ModBaseiSearch...
    MobiDBiSearch...

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Enzyme and pathway databases

    UniPathwayiUPA00873; UER00853.

    Family and domain databases

    Gene3Di3.10.120.10. 1 hit.
    3.20.20.70. 1 hit.
    InterProiIPR013785. Aldolase_TIM.
    IPR012133. Alpha-hydoxy_acid_DH_FMN.
    IPR001199. Cyt_B5-like_heme/steroid-bd.
    IPR018506. Cyt_B5_heme-BS.
    IPR000262. FMN-dep_DH.
    [Graphical view]
    PfamiPF00173. Cyt-b5. 1 hit.
    PF01070. FMN_dh. 1 hit.
    [Graphical view]
    SMARTiSM01117. Cyt-b5. 1 hit.
    [Graphical view]
    SUPFAMiSSF55856. SSF55856. 1 hit.
    PROSITEiPS00191. CYTOCHROME_B5_1. 1 hit.
    PS50255. CYTOCHROME_B5_2. 1 hit.
    PS51349. FMN_HYDROXY_ACID_DH_2. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiCYBL_RHOGR
    AccessioniPrimary (citable) accession number: P32953
    Secondary accession number(s): O13510
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 1, 1993
    Last sequence update: July 24, 2013
    Last modified: October 5, 2016
    This is version 84 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Direct protein sequencing

    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.