NCB5R_YEAST
ID NCB5R_YEAST Reviewed; 284 AA.
AC P38626; D6VVN9;
DT 01-OCT-1994, integrated into UniProtKB/Swiss-Prot.
DT 29-APR-2008, sequence version 2.
DT 03-AUG-2022, entry version 178.
DE RecName: Full=NADH-cytochrome b5 reductase 1 {ECO:0000303|PubMed:14930};
DE EC=1.6.2.2 {ECO:0000269|PubMed:14930};
DE AltName: Full=Microsomal cytochrome b reductase {ECO:0000303|PubMed:14930};
DE AltName: Full=P35 {ECO:0000303|PubMed:14930};
GN Name=CBR1; Synonyms=CBR, CBR5; OrderedLocusNames=YIL043C;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=842;
RX PubMed=8307010; DOI=10.1111/j.1432-1033.1994.tb19957.x;
RA Csukai M., Murray M., Orr E.;
RT "Isolation and complete sequence of CBR, a gene encoding a putative
RT cytochrome b reductase in Saccharomyces cerevisiae.";
RL Eur. J. Biochem. 219:441-448(1994).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169870;
RA Churcher C.M., Bowman S., Badcock K., Bankier A.T., Brown D.,
RA Chillingworth T., Connor R., Devlin K., Gentles S., Hamlin N., Harris D.E.,
RA Horsnell T., Hunt S., Jagels K., Jones M., Lye G., Moule S., Odell C.,
RA Pearson D., Rajandream M.A., Rice P., Rowley N., Skelton J., Smith V.,
RA Walsh S.V., Whitehead S., Barrell B.G.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome IX.";
RL Nature 387:84-87(1997).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [4]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, ACTIVITY
RP REGULATION, AND SUBUNIT.
RX PubMed=14930; DOI=10.1093/oxfordjournals.jbchem.a131434;
RA Kubota S., Yoshida Y., Kumaoka H.;
RT "Studies on the microsomal electron-transport system of anaerobically grown
RT yeast. IV. Purification and characterization of NADH-cytochrome b5
RT reductase.";
RL J. Biochem. 81:187-195(1977).
RN [5]
RP INDUCTION, AND ACTIVITY REGULATION.
RX PubMed=6442167; DOI=10.1016/0300-9084(84)90155-x;
RA Bertrand J.-C., Mattei G., Parra C., Giordani R., Gilewicz M.;
RT "Influence of oxygen on the microsomal electron transport system in
RT Saccharomyces cerevisiae.";
RL Biochimie 66:583-588(1984).
RN [6]
RP FUNCTION.
RX PubMed=10622712; DOI=10.1016/s0014-5793(99)01548-3;
RA Lamb D.C., Kelly D.E., Manning N.J., Kaderbhai M.A., Kelly S.L.;
RT "Biodiversity of the P450 catalytic cycle: yeast cytochrome b5/NADH
RT cytochrome b5 reductase complex efficiently drives the entire sterol 14-
RT demethylation (CYP51) reaction.";
RL FEBS Lett. 462:283-288(1999).
RN [7]
RP IDENTIFICATION OF PROBABLE INITIATION SITE.
RX PubMed=12748633; DOI=10.1038/nature01644;
RA Kellis M., Patterson N., Endrizzi M., Birren B.W., Lander E.S.;
RT "Sequencing and comparison of yeast species to identify genes and
RT regulatory elements.";
RL Nature 423:241-254(2003).
RN [8]
RP SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RX PubMed=14562095; DOI=10.1038/nature02026;
RA Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
RA Weissman J.S., O'Shea E.K.;
RT "Global analysis of protein localization in budding yeast.";
RL Nature 425:686-691(2003).
RN [9]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
RN [10]
RP IDENTIFICATION OF PROBABLE INITIATION SITE.
RX PubMed=15905473; DOI=10.1093/nar/gki583;
RA Zhang Z., Dietrich F.S.;
RT "Mapping of transcription start sites in Saccharomyces cerevisiae using 5'
RT SAGE.";
RL Nucleic Acids Res. 33:2838-2851(2005).
RN [11]
RP SUBCELLULAR LOCATION, AND IDENTIFICATION BY MASS SPECTROMETRY.
RX PubMed=16407407; DOI=10.1091/mbc.e05-08-0740;
RA Zahedi R.P., Sickmann A., Boehm A.M., Winkler C., Zufall N.,
RA Schoenfisch B., Guiard B., Pfanner N., Meisinger C.;
RT "Proteomic analysis of the yeast mitochondrial outer membrane reveals
RT accumulation of a subclass of preproteins.";
RL Mol. Biol. Cell 17:1436-1450(2006).
RN [12]
RP FUNCTION, AND INTERACTION WITH STE20.
RX PubMed=17895367; DOI=10.1242/jcs.009860;
RA Tiedje C., Holland D.G., Just U., Hofken T.;
RT "Proteins involved in sterol synthesis interact with Ste20 and regulate
RT cell polarity.";
RL J. Cell Sci. 120:3613-3624(2007).
RN [13]
RP FUNCTION, IDENTIFICATION IN THE 2-(3-AMINO-3-CARBOXYPROPYL)HISTIDINE
RP SYNTHASE COMPLEX, INTERACTION WITH KTI11, AND DISRUPTION PHENOTYPE.
RX PubMed=27694803; DOI=10.1038/nchembio.2190;
RA Lin Z., Dong M., Zhang Y., Lee E.A., Lin H.;
RT "Cbr1 is a Dph3 reductase required for the tRNA wobble uridine
RT modification.";
RL Nat. Chem. Biol. 12:995-997(2016).
RN [14]
RP FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=31463593; DOI=10.1007/s00775-019-01702-0;
RA Dong M., Dando E.E., Kotliar I., Su X., Dzikovski B., Freed J.H., Lin H.;
RT "The asymmetric function of Dph1-Dph2 heterodimer in diphthamide
RT biosynthesis.";
RL J. Biol. Inorg. Chem. 24:777-782(2019).
RN [15]
RP FUNCTION, CATALYTIC ACTIVITY, AND PATHWAY.
RX PubMed=34154323; DOI=10.1021/jacs.1c03956;
RA Zhang Y., Su D., Dzikovski B., Majer S.H., Coleman R., Chandrasekaran S.,
RA Fenwick M.K., Crane B.R., Lancaster K.M., Freed J.H., Lin H.;
RT "Dph3 Enables Aerobic Diphthamide Biosynthesis by Donating One Iron Atom to
RT Transform a [3Fe-4S] to a [4Fe-4S] Cluster in Dph1-Dph2.";
RL J. Am. Chem. Soc. 143:9314-9319(2021).
CC -!- FUNCTION: NADH-dependent reductase for KTI11/DPH3 and cytochrome b5
CC (PubMed:14930, PubMed:10622712, PubMed:27694803, PubMed:31463593,
CC PubMed:34154323). Required for the first step of diphthamide
CC biosynthesis, a post-translational modification of histidine which
CC occurs in elongation factor 2 (PubMed:31463593, PubMed:34154323,
CC PubMed:27694803). DPH1 and DPH2 transfer a 3-amino-3-carboxypropyl
CC (ACP) group from S-adenosyl-L-methionine (SAM) to a histidine residue,
CC the reaction is assisted by a reduction system comprising KTI11/DPH3
CC and a NADH-dependent reductase, predominantly CBR1 (PubMed:31463593,
CC PubMed:34154323). By reducing KTI11/DPH3, also involved in the
CC formation of the tRNA wobble base modification mcm5s 2U (5-
CC methoxycarbonylmethyl-2-thiouridine), mediated by the elongator complex
CC (PubMed:27694803). The cytochrome b5/NADH cytochrome b5 reductase
CC electron transfer system supports the catalytic activity of several
CC sterol biosynthetic enzymes (PubMed:10622712). Plays a role in bud
CC morphology (PubMed:17895367). {ECO:0000269|PubMed:10622712,
CC ECO:0000269|PubMed:14930, ECO:0000269|PubMed:17895367,
CC ECO:0000269|PubMed:27694803, ECO:0000269|PubMed:31463593,
CC ECO:0000269|PubMed:34154323}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2 Fe(III)-[cytochrome b5] + NADH = 2 Fe(II)-[cytochrome b5] +
CC H(+) + NAD(+); Xref=Rhea:RHEA:46680, Rhea:RHEA-COMP:10438, Rhea:RHEA-
CC COMP:10439, ChEBI:CHEBI:15378, ChEBI:CHEBI:29033, ChEBI:CHEBI:29034,
CC ChEBI:CHEBI:57540, ChEBI:CHEBI:57945; EC=1.6.2.2;
CC Evidence={ECO:0000269|PubMed:14930};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2 Fe(3+)-[Dph3] + NADH = 2 Fe(2+)-[Dph3] + H(+) + NAD(+);
CC Xref=Rhea:RHEA:71231, Rhea:RHEA-COMP:18002, Rhea:RHEA-COMP:18003,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:29033, ChEBI:CHEBI:29034,
CC ChEBI:CHEBI:57540, ChEBI:CHEBI:57945, ChEBI:CHEBI:83228;
CC Evidence={ECO:0000269|PubMed:27694803};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:71232;
CC Evidence={ECO:0000269|PubMed:27694803};
CC -!- COFACTOR:
CC Name=FAD; Xref=ChEBI:CHEBI:57692; Evidence={ECO:0000255};
CC -!- ACTIVITY REGULATION: Competitively inhibited by NAD(+). Inhibited by
CC mercurials such as p-chloromercuribenzoate (PCMB) and HgCl(2).
CC Enzymatic activity increases under anaerobic conditions.
CC {ECO:0000269|PubMed:14930, ECO:0000269|PubMed:6442167}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=6.3 uM for NADH {ECO:0000269|PubMed:14930};
CC KM=0.8 uM for cytochrome b5 {ECO:0000269|PubMed:14930};
CC pH dependence:
CC Optimum pH is 5.6. Active from pH 5 to 7.5.
CC {ECO:0000269|PubMed:14930};
CC -!- PATHWAY: Protein modification; peptidyl-diphthamide biosynthesis.
CC {ECO:0000269|PubMed:34154323}.
CC -!- SUBUNIT: Monomer (PubMed:14930). Component of the 2-(3-amino-3-
CC carboxypropyl)histidine synthase complex composed of DPH1, DPH2,
CC KTI11/DPH3 and a NADH-dependent reductase, predominantly CBR1
CC (PubMed:27694803). Interacts with KTI11/DPH3 (PubMed:27694803).
CC Interacts with STE20 (PubMed:17895367). {ECO:0000269|PubMed:14930,
CC ECO:0000269|PubMed:17895367, ECO:0000269|PubMed:27694803}.
CC -!- SUBCELLULAR LOCATION: Mitochondrion outer membrane
CC {ECO:0000269|PubMed:16407407}; Single-pass membrane protein
CC {ECO:0000255}.
CC -!- INDUCTION: Protein levels are highest during exponential growth phase
CC and lowest in stationary phase. {ECO:0000269|PubMed:6442167}.
CC -!- DISRUPTION PHENOTYPE: Simultaneous disruption of MCR1 results in
CC resistance to diphtheria toxin and zymocin.
CC {ECO:0000269|PubMed:27694803}.
CC -!- MISCELLANEOUS: Present with 4820 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the flavoprotein pyridine nucleotide cytochrome
CC reductase family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAA82214.1; Type=Erroneous initiation; Evidence={ECO:0000305};
CC Sequence=CAA86908.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR EMBL; Z28365; CAA82214.1; ALT_INIT; Genomic_DNA.
DR EMBL; Z46861; CAA86908.1; ALT_INIT; Genomic_DNA.
DR EMBL; BK006942; DAA08505.1; -; Genomic_DNA.
DR PIR; S49935; S49935.
DR RefSeq; NP_012221.2; NM_001179393.1.
DR AlphaFoldDB; P38626; -.
DR SMR; P38626; -.
DR BioGRID; 34947; 126.
DR IntAct; P38626; 7.
DR MINT; P38626; -.
DR STRING; 4932.YIL043C; -.
DR iPTMnet; P38626; -.
DR MaxQB; P38626; -.
DR PaxDb; P38626; -.
DR PRIDE; P38626; -.
DR EnsemblFungi; YIL043C_mRNA; YIL043C; YIL043C.
DR GeneID; 854768; -.
DR KEGG; sce:YIL043C; -.
DR SGD; S000001305; CBR1.
DR VEuPathDB; FungiDB:YIL043C; -.
DR eggNOG; KOG0534; Eukaryota.
DR HOGENOM; CLU_003827_9_0_1; -.
DR InParanoid; P38626; -.
DR OMA; KDMRFSF; -.
DR BioCyc; MetaCyc:YIL043C-MON; -.
DR BioCyc; YEAST:YIL043C-MON; -.
DR Reactome; R-SCE-114608; Platelet degranulation.
DR Reactome; R-SCE-196836; Vitamin C (ascorbate) metabolism.
DR Reactome; R-SCE-6798695; Neutrophil degranulation.
DR SABIO-RK; P38626; -.
DR UniPathway; UPA00559; -.
DR PRO; PR:P38626; -.
DR Proteomes; UP000002311; Chromosome IX.
DR RNAct; P38626; protein.
DR GO; GO:0005789; C:endoplasmic reticulum membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
DR GO; GO:0005741; C:mitochondrial outer membrane; HDA:SGD.
DR GO; GO:0005739; C:mitochondrion; HDA:SGD.
DR GO; GO:0005634; C:nucleus; HDA:SGD.
DR GO; GO:0005886; C:plasma membrane; IBA:GO_Central.
DR GO; GO:0004128; F:cytochrome-b5 reductase activity, acting on NAD(P)H; IDA:UniProtKB.
DR GO; GO:0003954; F:NADH dehydrogenase activity; IDA:CACAO.
DR GO; GO:0017183; P:peptidyl-diphthamide biosynthetic process from peptidyl-histidine; IDA:UniProtKB.
DR GO; GO:0002926; P:tRNA wobble base 5-methoxycarbonylmethyl-2-thiouridinylation; IMP:UniProtKB.
DR Gene3D; 3.40.50.80; -; 1.
DR InterPro; IPR001834; CBR-like.
DR InterPro; IPR008333; Cbr1-like_FAD-bd_dom.
DR InterPro; IPR017927; FAD-bd_FR_type.
DR InterPro; IPR001709; Flavoprot_Pyr_Nucl_cyt_Rdtase.
DR InterPro; IPR039261; FNR_nucleotide-bd.
DR InterPro; IPR001433; OxRdtase_FAD/NAD-bd.
DR InterPro; IPR017938; Riboflavin_synthase-like_b-brl.
DR PANTHER; PTHR19370; PTHR19370; 1.
DR Pfam; PF00970; FAD_binding_6; 1.
DR Pfam; PF00175; NAD_binding_1; 1.
DR PRINTS; PR00371; FPNCR.
DR SUPFAM; SSF52343; SSF52343; 1.
DR SUPFAM; SSF63380; SSF63380; 1.
DR PROSITE; PS51384; FAD_FR; 1.
PE 1: Evidence at protein level;
KW FAD; Flavoprotein; Membrane; Mitochondrion; Mitochondrion outer membrane;
KW NAD; Oxidoreductase; Reference proteome; Transferase; Transmembrane;
KW Transmembrane helix.
FT CHAIN 1..284
FT /note="NADH-cytochrome b5 reductase 1"
FT /id="PRO_0000167627"
FT TRANSMEM 7..27
FT /note="Helical"
FT /evidence="ECO:0000255"
FT DOMAIN 38..142
FT /note="FAD-binding FR-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00716"
FT BINDING 122..137
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT BINDING 148..180
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
SQ SEQUENCE 284 AA; 31494 MW; 0E71E7AB083BB623 CRC64;
MAIDAQKLVV VIVIVVVPLL FKFIIGPKTK PVLDPKRNDF QSFPLVEKTI LTHNTSMYKF
GLPHADDVLG LPIGQHIVIK ANINGKDITR SYTPTSLDGD TKGNFELLVK SYPTGNVSKM
IGELKIGDSI QIKGPRGNYH YERNCRSHLG MIAGGTGIAP MYQIMKAIAM DPHDTTKVSL
VFGNVHEEDI LLKKELEALV AMKPSQFKIV YYLDSPDRED WTGGVGYITK DVIKEHLPAA
TMDNVQILIC GPPAMVASVR RSTVDLGFRR SKPLSKMEDQ VFVF
