COX5B_YEAST
ID COX5B_YEAST Reviewed; 151 AA.
AC P00425; D6VVH6;
DT 21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-1992, sequence version 3.
DT 03-AUG-2022, entry version 178.
DE RecName: Full=Cytochrome c oxidase subunit 5B, mitochondrial;
DE AltName: Full=Cytochrome c oxidase polypeptide Vb;
DE Flags: Precursor;
GN Name=COX5B; OrderedLocusNames=YIL111W;
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].
RX PubMed=2824989; DOI=10.1128/mcb.7.10.3511-3519.1987;
RA Cumsky M.G., Trueblood C.E., Ko C., Poyton R.O.;
RT "Structural analysis of two genes encoding divergent forms of yeast
RT cytochrome c oxidase subunit V.";
RL Mol. Cell. Biol. 7:3511-3519(1987).
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 NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-79.
RX PubMed=2548089; DOI=10.1128/mcb.9.6.2765-2770.1989;
RA Hodge M.R., Cumsky M.G.;
RT "Splicing of a yeast intron containing an unusual 5' junction sequence.";
RL Mol. Cell. Biol. 9:2765-2770(1989).
RN [5]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 18-85, AND IDENTIFICATION IN THE
RP CYTOCHROME C OXIDASE COMPLEX.
RX PubMed=2986105; DOI=10.1073/pnas.82.8.2235;
RA Cumsky M.G., Ko C., Trueblood C.E., Poyton R.O.;
RT "Two nonidentical forms of subunit V are functional in yeast cytochrome c
RT oxidase.";
RL Proc. Natl. Acad. Sci. U.S.A. 82:2235-2239(1985).
RN [6]
RP SUBUNIT.
RX PubMed=2546055; DOI=10.1128/mcb.9.5.1958-1964.1989;
RA Hodge M.R., Kim G., Singh K., Cumsky M.G.;
RT "Inverse regulation of the yeast COX5 genes by oxygen and heme.";
RL Mol. Cell. Biol. 9:1958-1964(1989).
RN [7]
RP INDUCTION.
RX PubMed=9169434; DOI=10.1074/jbc.272.23.14705;
RA Burke P.V., Raitt D.C., Allen L.A., Kellogg E.A., Poyton R.O.;
RT "Effects of oxygen concentration on the expression of cytochrome c and
RT cytochrome c oxidase genes in yeast.";
RL J. Biol. Chem. 272:14705-14712(1997).
RN [8]
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).
CC -!- FUNCTION: Component of the cytochrome c oxidase, the last enzyme in the
CC mitochondrial electron transport chain which drives oxidative
CC phosphorylation. The respiratory chain contains 3 multisubunit
CC complexes succinate dehydrogenase (complex II, CII), ubiquinol-
CC cytochrome c oxidoreductase (cytochrome b-c1 complex, complex III,
CC CIII) and cytochrome c oxidase (complex IV, CIV), that cooperate to
CC transfer electrons derived from NADH and succinate to molecular oxygen,
CC creating an electrochemical gradient over the inner membrane that
CC drives transmembrane transport and the ATP synthase. Cytochrome c
CC oxidase is the component of the respiratory chain that catalyzes the
CC reduction of oxygen to water. Electrons originating from reduced
CC cytochrome c in the intermembrane space (IMS) are transferred via the
CC dinuclear copper A center (CU(A)) of COX2 and heme A of COX1 to the
CC active site in COX1, a binuclear center (BNC) formed by heme A3 and
CC copper B (CU(B)). The BNC reduces molecular oxygen to 2 water molecules
CC using 4 electrons from cytochrome c in the IMS and 4 protons from the
CC mitochondrial matrix. {ECO:0000250|UniProtKB:P00424}.
CC -!- PATHWAY: Energy metabolism; oxidative phosphorylation.
CC -!- SUBUNIT: Component of the cytochrome c oxidase (complex IV, CIV), a
CC multisubunit enzyme composed of 12 subunits. The complex is composed of
CC a catalytic core of 3 subunits COX1, COX2 and COX3, encoded in the
CC mitochondrial DNA, and 9 supernumerary subunits COX4, COX5A (or COX5B),
CC COX6, COX7, COX8, COX9, COX12, COX13 and COX26, which are encoded in
CC the nuclear genome (PubMed:2986105). COX5A is the predominant subunit V
CC during aerobic/normoxic growth, it gets replaced by COX5B under
CC anaerobic/hypoxic conditions (PubMed:2546055). The complex exists as a
CC monomer or a dimer and forms supercomplexes (SCs) in the inner
CC mitochondrial membrane with a dimer of ubiquinol-cytochrome c
CC oxidoreductase (cytochrome b-c1 complex, complex III, CIII), resulting
CC in 2 different assemblies (supercomplexes III(2)IV and III(2)IV(2)) (By
CC similarity). {ECO:0000250|UniProtKB:P00424, ECO:0000269|PubMed:2546055,
CC ECO:0000269|PubMed:2986105}.
CC -!- SUBCELLULAR LOCATION: Mitochondrion inner membrane
CC {ECO:0000269|PubMed:2986105}; Single-pass membrane protein
CC {ECO:0000250|UniProtKB:P00424}.
CC -!- INDUCTION: By low oxygen levels (hypoxia) at the level of
CC transcription. Repressed by ROX1 in the presence of oxygen
CC (PubMed:2546055). Not expressed until the oxygen concentration is below
CC 0.5 uM O(2) (PubMed:9169434). {ECO:0000269|PubMed:2546055,
CC ECO:0000269|PubMed:9169434}.
CC -!- MISCELLANEOUS: Present with 2250 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the cytochrome c oxidase IV family.
CC {ECO:0000305}.
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DR EMBL; Z38125; CAA86269.1; -; Genomic_DNA.
DR EMBL; M17799; AAA96310.1; -; Genomic_DNA.
DR EMBL; M11140; AAA34521.1; -; Genomic_DNA.
DR EMBL; BK006942; DAA08442.1; -; Genomic_DNA.
DR PIR; S05755; OTBY5B.
DR RefSeq; NP_012155.1; NM_001179459.1.
DR PDB; 6T0B; EM; 2.80 A; e/r=18-151.
DR PDB; 6T15; EM; 3.29 A; e=18-151.
DR PDBsum; 6T0B; -.
DR PDBsum; 6T15; -.
DR AlphaFoldDB; P00425; -.
DR SMR; P00425; -.
DR BioGRID; 34880; 64.
DR ComplexPortal; CPX-1722; Mitochondrial respiratory chain complex IV, COX5B variant.
DR DIP; DIP-4709N; -.
DR IntAct; P00425; 2.
DR MINT; P00425; -.
DR STRING; 4932.YIL111W; -.
DR TCDB; 3.D.4.8.1; the proton-translocating cytochrome oxidase (cox) superfamily.
DR MaxQB; P00425; -.
DR PaxDb; P00425; -.
DR PRIDE; P00425; -.
DR GeneID; 854695; -.
DR KEGG; sce:YIL111W; -.
DR SGD; S000001373; COX5B.
DR VEuPathDB; FungiDB:YIL111W; -.
DR eggNOG; KOG4075; Eukaryota.
DR HOGENOM; CLU_070101_2_0_1; -.
DR InParanoid; P00425; -.
DR OMA; AFITKGV; -.
DR BioCyc; YEAST:YIL111W-MON; -.
DR UniPathway; UPA00705; -.
DR PRO; PR:P00425; -.
DR Proteomes; UP000002311; Chromosome IX.
DR RNAct; P00425; protein.
DR GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
DR GO; GO:0031966; C:mitochondrial membrane; IDA:ComplexPortal.
DR GO; GO:0005751; C:mitochondrial respiratory chain complex IV; IDA:SGD.
DR GO; GO:0005739; C:mitochondrion; HDA:SGD.
DR GO; GO:0016491; F:oxidoreductase activity; IEA:UniProtKB-KW.
DR GO; GO:0045333; P:cellular respiration; IDA:ComplexPortal.
DR GO; GO:0006123; P:mitochondrial electron transport, cytochrome c to oxygen; IDA:SGD.
DR GO; GO:1902600; P:proton transmembrane transport; IEA:GOC.
DR CDD; cd00922; Cyt_c_Oxidase_IV; 1.
DR Gene3D; 1.10.442.10; -; 1.
DR InterPro; IPR004203; Cyt_c_oxidase_su4_fam.
DR InterPro; IPR036639; Cyt_c_oxidase_su4_sf.
DR PANTHER; PTHR10707; PTHR10707; 1.
DR Pfam; PF02936; COX4; 1.
DR SUPFAM; SSF81406; SSF81406; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Membrane; Mitochondrion; Mitochondrion inner membrane;
KW Oxidoreductase; Reference proteome; Transit peptide; Transmembrane;
KW Transmembrane helix.
FT TRANSIT 1..17
FT /note="Mitochondrion"
FT /evidence="ECO:0000250|UniProtKB:P00424"
FT CHAIN 18..151
FT /note="Cytochrome c oxidase subunit 5B, mitochondrial"
FT /id="PRO_0000006098"
FT TOPO_DOM 18..85
FT /note="Mitochondrial matrix"
FT /evidence="ECO:0000250|UniProtKB:P00424"
FT TRANSMEM 86..108
FT /note="Helical"
FT /evidence="ECO:0000250|UniProtKB:P00424"
FT TOPO_DOM 109..151
FT /note="Mitochondrial intermembrane"
FT /evidence="ECO:0000250|UniProtKB:P00424"
FT HELIX 25..27
FT /evidence="ECO:0007829|PDB:6T0B"
FT HELIX 31..34
FT /evidence="ECO:0007829|PDB:6T0B"
FT STRAND 35..38
FT /evidence="ECO:0007829|PDB:6T0B"
FT HELIX 44..53
FT /evidence="ECO:0007829|PDB:6T0B"
FT HELIX 58..60
FT /evidence="ECO:0007829|PDB:6T15"
FT HELIX 63..74
FT /evidence="ECO:0007829|PDB:6T0B"
FT STRAND 75..77
FT /evidence="ECO:0007829|PDB:6T0B"
FT HELIX 78..80
FT /evidence="ECO:0007829|PDB:6T0B"
FT HELIX 89..110
FT /evidence="ECO:0007829|PDB:6T0B"
FT HELIX 124..136
FT /evidence="ECO:0007829|PDB:6T0B"
FT STRAND 141..143
FT /evidence="ECO:0007829|PDB:6T0B"
SQ SEQUENCE 151 AA; 17197 MW; 566B4E69631CBDE0 CRC64;
MLRTSLTKGA RLTGTRFVQT KALSKATLTD LPERWENMPN LEQKEIADNL TERQKLPWKT
LNNEEIKAAW YISYGEWGPR RPVHGKGDVA FITKGVFLGL GISFGLFGLV RLLANPETPK
TMNREWQLKS DEYLKSKNAN PWGGYSQVQS K
