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Protein

(S)-mandelate dehydrogenase, mitochondrial

Gene
N/A
Organism
Rhodotorula graminis (Yeast)
Status
Reviewed-Annotation score: -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

    Keywordsi

    Molecular functionOxidoreductase
    Biological processAromatic hydrocarbons catabolism, Electron transport, Mandelate pathway, Respiratory chain, Transport
    LigandFlavoprotein, 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

    Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

    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

    Proteomic databases

    PRIDEiP32953

    Interactioni

    Subunit structurei

    Homotetramer.1 Publication

    Structurei

    3D structure databases

    ProteinModelPortaliP32953
    SMRiP32953
    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

    Keywords - Domaini

    Transit peptide

    Family and domain databases

    CDDicd02922 FCB2_FMN, 1 hit
    Gene3Di3.10.120.10, 1 hit
    3.20.20.70, 1 hit
    InterProiView protein in InterPro
    IPR013785 Aldolase_TIM
    IPR001199 Cyt_B5-like_heme/steroid-bd
    IPR036400 Cyt_B5-like_heme/steroid_sf
    IPR018506 Cyt_B5_heme-BS
    IPR000262 FMN-dep_DH
    IPR037396 FMN_HAD
    IPR037458 L-MDH/L-LDH_FMN-bd
    PfamiView protein in Pfam
    PF00173 Cyt-b5, 1 hit
    PF01070 FMN_dh, 1 hit
    SMARTiView protein in SMART
    SM01117 Cyt-b5, 1 hit
    SUPFAMiSSF55856 SSF55856, 1 hit
    PROSITEiView protein in PROSITE
    PS00191 CYTOCHROME_B5_1, 1 hit
    PS50255 CYTOCHROME_B5_2, 1 hit
    PS51349 FMN_HYDROXY_ACID_DH_2, 1 hit

    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

    Similar proteinsi

    Entry informationi

    Entry nameiCYBL_RHOGR
    AccessioniPrimary (citable) accession number: P32953
    Secondary accession number(s): O13510
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 1, 1993
    Last sequence update: July 24, 2013
    Last modified: May 23, 2018
    This is version 90 of the entry and version 2 of the sequence. See complete history.
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Direct protein sequencing

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