CYBL_RHOGR
ID CYBL_RHOGR Reviewed; 565 AA.
AC P32953; O13510;
DT 01-OCT-1993, integrated into UniProtKB/Swiss-Prot.
DT 24-JUL-2013, sequence version 2.
DT 03-AUG-2022, entry version 97.
DE RecName: Full=(S)-mandelate dehydrogenase, mitochondrial;
DE EC=1.1.99.31 {ECO:0000269|PubMed:9639569};
DE AltName: Full=Flavocytochrome b;
DE AltName: Full=L(+)-mandelate dehydrogenase;
DE Short=L-MDH;
DE Flags: Precursor;
OS Rhodotorula graminis (Yeast).
OC Eukaryota; Fungi; Dikarya; Basidiomycota; Pucciniomycotina;
OC Microbotryomycetes; Sporidiobolales; Sporidiobolaceae; Rhodotorula.
OX NCBI_TaxID=29898;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, CATALYTIC ACTIVITY, AND
RP BIOPHYSICOCHEMICAL PROPERTIES.
RC STRAIN=GX6000;
RX PubMed=9639569; DOI=10.1042/bj3330107;
RA Illias R.M., Sinclair R., Robertson D., Neu A., Chapman S.K., Reid G.A.;
RT "L-Mandelate dehydrogenase from Phodotorula graminis: cloning, sequencing
RT and kinetic characterization of the recombinant enzyme and its
RT independently expressed flavin domain.";
RL Biochem. J. 333:107-115(1998).
RN [2]
RP PROTEIN SEQUENCE OF 75-105, FUNCTION, COFACTOR, AND SUBUNIT.
RC STRAIN=KGX 39;
RX PubMed=8343125; DOI=10.1042/bj2930455;
RA Yasin M., Fewson C.A.;
RT "L(+)-mandelate dehydrogenase from Rhodotorula graminis: purification,
RT partial characterization and identification as a flavocytochrome b.";
RL Biochem. J. 293:455-460(1993).
CC -!- FUNCTION: Catalyzes the oxidation of (S)-mandelate to benzoylformate
CC and enables utilization of mandelate as substrate for growth.
CC {ECO:0000269|PubMed:8343125, ECO:0000269|PubMed:9639569}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(S)-mandelate + A = AH2 + phenylglyoxylate;
CC Xref=Rhea:RHEA:15749, ChEBI:CHEBI:13193, ChEBI:CHEBI:17499,
CC ChEBI:CHEBI:17756, ChEBI:CHEBI:36656; EC=1.1.99.31;
CC Evidence={ECO:0000269|PubMed:9639569};
CC -!- COFACTOR:
CC Name=FMN; Xref=ChEBI:CHEBI:58210;
CC Evidence={ECO:0000269|PubMed:8343125};
CC Note=Binds 1 FMN per subunit. {ECO:0000269|PubMed:8343125};
CC -!- COFACTOR:
CC Name=heme b; Xref=ChEBI:CHEBI:60344;
CC Evidence={ECO:0000269|PubMed:8343125};
CC Note=Binds 1 heme b group per subunit. {ECO:0000269|PubMed:8343125};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.47 mM for D,L-mandelate (with ferricyanide as electron acceptor)
CC {ECO:0000269|PubMed:9639569};
CC KM=0.53 mM for 2-deuterated D,L-mandelate (with ferricyanide as
CC electron acceptor) {ECO:0000269|PubMed:9639569};
CC KM=0.78 mM for D,L-mandelate (with cytochrome c as electron acceptor)
CC {ECO:0000269|PubMed:9639569};
CC KM=1.33 mM for 2-deuterated D,L-mandelate (with cytochrome c as
CC electron acceptor) {ECO:0000269|PubMed:9639569};
CC -!- PATHWAY: Aromatic compound metabolism; (R)-mandelate degradation;
CC benzoate from (R)-mandelate: step 2/4.
CC -!- SUBUNIT: Homotetramer. {ECO:0000269|PubMed:8343125}.
CC -!- SUBCELLULAR LOCATION: Mitochondrion intermembrane space {ECO:0000250}.
CC -!- SIMILARITY: In the N-terminal section; belongs to the cytochrome b5
CC family. {ECO:0000305}.
CC -!- SIMILARITY: In the C-terminal section; belongs to the FMN-dependent
CC alpha-hydroxy acid dehydrogenase family. {ECO:0000305}.
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DR EMBL; AJ001430; CAA04758.1; -; Genomic_DNA.
DR PIR; S35053; S35053.
DR AlphaFoldDB; P32953; -.
DR SMR; P32953; -.
DR PRIDE; P32953; -.
DR UniPathway; UPA00873; UER00853.
DR GO; GO:0005758; C:mitochondrial intermembrane space; IEA:UniProtKB-SubCell.
DR GO; GO:0070469; C:respirasome; IEA:UniProtKB-KW.
DR GO; GO:0033720; F:(S)-mandelate dehydrogenase activity; IEA:UniProtKB-EC.
DR GO; GO:0020037; F:heme binding; IEA:InterPro.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0019596; P:mandelate catabolic process; IEA:UniProtKB-UniPathway.
DR CDD; cd02922; FCB2_FMN; 1.
DR Gene3D; 3.10.120.10; -; 1.
DR Gene3D; 3.20.20.70; -; 1.
DR InterPro; IPR013785; Aldolase_TIM.
DR InterPro; IPR001199; Cyt_B5-like_heme/steroid-bd.
DR InterPro; IPR036400; Cyt_B5-like_heme/steroid_sf.
DR InterPro; IPR018506; Cyt_B5_heme-BS.
DR InterPro; IPR000262; FMN-dep_DH.
DR InterPro; IPR037396; FMN_HAD.
DR InterPro; IPR037458; L-MDH/L-LDH_FMN-bd.
DR Pfam; PF00173; Cyt-b5; 1.
DR Pfam; PF01070; FMN_dh; 1.
DR SMART; SM01117; Cyt-b5; 1.
DR SUPFAM; SSF55856; SSF55856; 1.
DR PROSITE; PS00191; CYTOCHROME_B5_1; 1.
DR PROSITE; PS50255; CYTOCHROME_B5_2; 1.
DR PROSITE; PS51349; FMN_HYDROXY_ACID_DH_2; 1.
PE 1: Evidence at protein level;
KW Aromatic hydrocarbons catabolism; Direct protein sequencing;
KW Electron transport; Flavoprotein; FMN; Heme; Iron; Mandelate pathway;
KW Metal-binding; Mitochondrion; Oxidoreductase; Respiratory chain;
KW Transit peptide; Transport.
FT TRANSIT 1..54
FT /note="Mitochondrion"
FT /evidence="ECO:0000255"
FT CHAIN 55..565
FT /note="(S)-mandelate dehydrogenase, mitochondrial"
FT /id="PRO_0000206328"
FT DOMAIN 86..163
FT /note="Cytochrome b5 heme-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00279"
FT DOMAIN 189..559
FT /note="FMN hydroxy acid dehydrogenase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00683"
FT ACT_SITE 451
FT /note="Proton acceptor"
FT /evidence="ECO:0000250|UniProtKB:P00175"
FT BINDING 121
FT /ligand="heme b"
FT /ligand_id="ChEBI:CHEBI:60344"
FT /ligand_part="Fe"
FT /ligand_part_id="ChEBI:CHEBI:18248"
FT /note="axial binding residue"
FT /evidence="ECO:0000250|UniProtKB:P00175"
FT BINDING 144
FT /ligand="heme b"
FT /ligand_id="ChEBI:CHEBI:60344"
FT /ligand_part="Fe"
FT /ligand_part_id="ChEBI:CHEBI:18248"
FT /note="axial binding residue"
FT /evidence="ECO:0000250|UniProtKB:P00175"
FT BINDING 215
FT /ligand="heme b"
FT /ligand_id="ChEBI:CHEBI:60344"
FT /evidence="ECO:0000250|UniProtKB:P00175"
FT BINDING 215
FT /ligand="phenylglyoxylate"
FT /ligand_id="ChEBI:CHEBI:36656"
FT /evidence="ECO:0000250|UniProtKB:P00175"
FT BINDING 267..270
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250|UniProtKB:P00175"
FT BINDING 322
FT /ligand="phenylglyoxylate"
FT /ligand_id="ChEBI:CHEBI:36656"
FT /evidence="ECO:0000250|UniProtKB:P00175"
FT BINDING 364
FT /ligand="heme b"
FT /ligand_id="ChEBI:CHEBI:60344"
FT /evidence="ECO:0000250|UniProtKB:P00175"
FT BINDING 451
FT /ligand="phenylglyoxylate"
FT /ligand_id="ChEBI:CHEBI:36656"
FT /evidence="ECO:0000250|UniProtKB:P00175"
FT BINDING 454
FT /ligand="phenylglyoxylate"
FT /ligand_id="ChEBI:CHEBI:36656"
FT /evidence="ECO:0000250|UniProtKB:P00175"
FT BINDING 485..489
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250|UniProtKB:P00175"
FT BINDING 508..509
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250|UniProtKB:P00175"
SQ SEQUENCE 565 AA; 61974 MW; A16F5BB4CFE418F1 CRC64;
MSFARVRTAL RCQRAAASPA PPKVQARRFA NKAAPHASAS SAGSRAFHLG LAAGAALAVG
GAGLYLFSRS PVLLDAQLPV KQRGRARSIS AAEVAKHNSR DSMWVCIDDE VWDITNFVEL
HPGGAKVLEQ NAGKDVTKVF KSIHPPKTLE KFLTDDNFVG RIDVDEVTKI GGGKNAEDLR
IEQARKELRN VETVVCLDEF EEISQKILSE MAMAYYGTGA ETEQTLRDER EAWQRVRFRP
RVLRKMRHID TNTTFLGIPT PLPIFVAPAG LARLGHPDGE QNIVRGVAKH DILQVVSSGA
SCSIDEIFEV KEPDQNLAWQ FYVHSDKKIA EEKLKRALAL GAKAIFVTVD VPVLGKRERD
LKLKARSQNY EHPIAAQWKA AGSKVEETIA KRGVSDIPDT AHIDANLNWD DIAWIKERAP
GVPIVIKGVG CVEDVELAKQ YGADGVVLST HGARQLDGAR APLDVLIEVR RKNPALLKEI
EVYVDGQARR GTDVLKALCL GARGVGFGRG FLYAQSAYGA DGVDKAIRIL ENEIQNAMRL
LGANTLADLK PEMVECSFPE RWVPE
