COX5A_YEAST
ID COX5A_YEAST Reviewed; 153 AA.
AC P00424; D6W1C7;
DT 21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
DT 13-AUG-1987, sequence version 1.
DT 03-AUG-2022, entry version 196.
DE RecName: Full=Cytochrome c oxidase subunit 5A, mitochondrial;
DE AltName: Full=Cytochrome c oxidase polypeptide Va;
DE Flags: Precursor;
GN Name=COX5A; OrderedLocusNames=YNL052W; ORFNames=N2474, YNL2474W;
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=2836092; DOI=10.1007/bf00434047;
RA Seraphin B., Simon M., Faye G.;
RT "Primary structure of a gene for subunit V of the cytochrome c oxidase from
RT Saccharomyces cerevisiae.";
RL Curr. Genet. 9:435-439(1985).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=2991248; DOI=10.1016/s0021-9258(17)39261-x;
RA Koerner T.J., Hill J., Tzagoloff A.;
RT "Cloning and characterization of the yeast nuclear gene for subunit 5 of
RT cytochrome oxidase.";
RL J. Biol. Chem. 260:9513-9515(1985).
RN [3]
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 [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=S288c / FY1676;
RX PubMed=8533472; DOI=10.1002/yea.320111008;
RA Bergez P., Doignon F., Crouzet M.;
RT "The sequence of a 44 420 bp fragment located on the left arm of chromosome
RT XIV from Saccharomyces cerevisiae.";
RL Yeast 11:967-974(1995).
RN [5]
RP ERRATUM OF PUBMED:8533472.
RX PubMed=8904343;
RX DOI=10.1002/(sici)1097-0061(19960315)12:3<297::aid-yea940>3.0.co;2-d;
RA Bergez P., Doignon F., Crouzet M.;
RL Yeast 12:297-297(1996).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169873;
RA Philippsen P., Kleine K., Poehlmann R., Duesterhoeft A., Hamberg K.,
RA Hegemann J.H., Obermaier B., Urrestarazu L.A., Aert R., Albermann K.,
RA Altmann R., Andre B., Baladron V., Ballesta J.P.G., Becam A.-M.,
RA Beinhauer J.D., Boskovic J., Buitrago M.J., Bussereau F., Coster F.,
RA Crouzet M., D'Angelo M., Dal Pero F., De Antoni A., del Rey F., Doignon F.,
RA Domdey H., Dubois E., Fiedler T.A., Fleig U., Floeth M., Fritz C.,
RA Gaillardin C., Garcia-Cantalejo J.M., Glansdorff N., Goffeau A.,
RA Gueldener U., Herbert C.J., Heumann K., Heuss-Neitzel D., Hilbert H.,
RA Hinni K., Iraqui Houssaini I., Jacquet M., Jimenez A., Jonniaux J.-L.,
RA Karpfinger-Hartl L., Lanfranchi G., Lepingle A., Levesque H., Lyck R.,
RA Maftahi M., Mallet L., Maurer C.T.C., Messenguy F., Mewes H.-W., Moestl D.,
RA Nasr F., Nicaud J.-M., Niedenthal R.K., Pandolfo D., Pierard A.,
RA Piravandi E., Planta R.J., Pohl T.M., Purnelle B., Rebischung C.,
RA Remacha M.A., Revuelta J.L., Rinke M., Saiz J.E., Sartorello F.,
RA Scherens B., Sen-Gupta M., Soler-Mira A., Urbanus J.H.M., Valle G.,
RA Van Dyck L., Verhasselt P., Vierendeels F., Vissers S., Voet M.,
RA Volckaert G., Wach A., Wambutt R., Wedler H., Zollner A., Hani J.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XIV and its
RT evolutionary implications.";
RL Nature 387:93-98(1997).
RN [7]
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 [8]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=17322287; DOI=10.1101/gr.6037607;
RA Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F.,
RA Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J.,
RA Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J.,
RA Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D.,
RA LaBaer J.;
RT "Approaching a complete repository of sequence-verified protein-encoding
RT clones for Saccharomyces cerevisiae.";
RL Genome Res. 17:536-543(2007).
RN [9]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 21-98.
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 [10]
RP PROTEIN SEQUENCE OF 21-69.
RX PubMed=6327686; DOI=10.1016/s0021-9258(20)82180-2;
RA Power S.D., Lochrie M.A., Poyton R.O.;
RT "The nuclear-coded subunits of yeast cytochrome c oxidase. III.
RT Identification of homologous subunits in yeast, bovine heart, and
RT Neurospora crassa cytochrome c oxidases.";
RL J. Biol. Chem. 259:6575-6578(1984).
RN [11]
RP PROTEIN SEQUENCE OF 21-35.
RX PubMed=6300105; DOI=10.1016/s0021-9258(18)32519-5;
RA Cerletti N., Bohni P.C., Suda K.;
RT "Import of proteins into mitochondria. Isolated yeast mitochondria and a
RT solubilized matrix protease correctly process cytochrome c oxidase subunit
RT V precursor at the NH2 terminus.";
RL J. Biol. Chem. 258:4944-4949(1983).
RN [12]
RP PROTEIN SEQUENCE OF 21-34, AND COMPOSITION OF THE CYTOCHROME C OXIDASE
RP COMPLEX.
RX PubMed=1331058; DOI=10.1016/s0021-9258(18)41697-3;
RA Taanman J.-W., Capaldi R.A.;
RT "Purification of yeast cytochrome c oxidase with a subunit composition
RT resembling the mammalian enzyme.";
RL J. Biol. Chem. 267:22481-22485(1992).
RN [13]
RP PROTEIN SEQUENCE OF 21-23, AND COMPOSITION OF THE CYTOCHROME C OXIDASE
RP COMPLEX.
RX PubMed=7851399; DOI=10.1111/j.1432-1033.1995.tb20388.x;
RA Geier B.M., Schagger H., Ortwein C., Link T.A., Hagen W.R., Brandt U.,
RA Von Jagow G.;
RT "Kinetic properties and ligand binding of the eleven-subunit cytochrome-c
RT oxidase from Saccharomyces cerevisiae isolated with a novel large-scale
RT purification method.";
RL Eur. J. Biochem. 227:296-302(1995).
RN [14]
RP SUBUNIT, AND INDUCTION.
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 [15]
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 [16]
RP FORMATION OF CYTOCHROME BC1-CYTOCHROME C OXIDASE SUPERCOMPLEX.
RX PubMed=10775262; DOI=10.1093/emboj/19.8.1777;
RA Schaegger H., Pfeiffer K.;
RT "Supercomplexes in the respiratory chains of yeast and mammalian
RT mitochondria.";
RL EMBO J. 19:1777-1783(2000).
RN [17]
RP FORMATION OF CYTOCHROME BC1-CYTOCHROME C OXIDASE SUPERCOMPLEX.
RX PubMed=10764779; DOI=10.1074/jbc.m001901200;
RA Cruciat C.M., Brunner S., Baumann F., Neupert W., Stuart R.A.;
RT "The cytochrome bc1 and cytochrome c oxidase complexes associate to form a
RT single supracomplex in yeast mitochondria.";
RL J. Biol. Chem. 275:18093-18098(2000).
RN [18]
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 [19]
RP STRUCTURE BY ELECTRON MICROSCOPY (3.23 ANGSTROMS) OF 1-153.
RX PubMed=30598556; DOI=10.1038/s41594-018-0169-7;
RA Rathore S., Berndtsson J., Marin-Buera L., Conrad J., Carroni M.,
RA Brzezinski P., Ott M.;
RT "Cryo-EM structure of the yeast respiratory supercomplex.";
RL Nat. Struct. Mol. Biol. 26:50-57(2019).
RN [20]
RP STRUCTURE BY ELECTRON MICROSCOPY (3.35 ANGSTROMS), AND FUNCTION.
RX PubMed=30598554; DOI=10.1038/s41594-018-0172-z;
RA Hartley A.M., Lukoyanova N., Zhang Y., Cabrera-Orefice A., Arnold S.,
RA Meunier B., Pinotsis N., Marechal A.;
RT "Structure of yeast cytochrome c oxidase in a supercomplex with cytochrome
RT bc1.";
RL Nat. Struct. Mol. Biol. 26:78-83(2019).
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:0000305|PubMed:30598554}.
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:7851399, PubMed:30598556, PubMed:30598554).
CC COX5A is the predominant subunit V during aerobic/normoxic growth, it
CC gets replaced by COX5B under anaerobic/hypoxic conditions
CC (PubMed:2546055). The complex exists as a monomer or a dimer and forms
CC supercomplexes (SCs) in the inner mitochondrial membrane with a dimer
CC of ubiquinol-cytochrome c oxidoreductase (cytochrome b-c1 complex,
CC complex III, CIII), resulting in 2 different assemblies (supercomplexes
CC III(2)IV and III(2)IV(2)) (PubMed:10775262, PubMed:10764779,
CC PubMed:30598556, PubMed:30598554). COX5A interacts with COR1, CYT1 and
CC QCR6 at the CIII-CIV interface (PubMed:30598556, PubMed:30598554).
CC {ECO:0000269|PubMed:10764779, ECO:0000269|PubMed:10775262,
CC ECO:0000269|PubMed:2546055, ECO:0000269|PubMed:30598554,
CC ECO:0000269|PubMed:30598556, ECO:0000269|PubMed:7851399}.
CC -!- SUBCELLULAR LOCATION: Mitochondrion inner membrane
CC {ECO:0000269|PubMed:30598554}; Single-pass membrane protein
CC {ECO:0000269|PubMed:30598554}.
CC -!- INDUCTION: By oxygen at the level of transcription through heme
CC (PubMed:2546055). Expression drops rapidly when the oxygen
CC concentration falls below 0.5 uM O(2) (PubMed:9169434).
CC {ECO:0000269|PubMed:2546055, ECO:0000269|PubMed:9169434}.
CC -!- MISCELLANEOUS: Present with 3670 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; X02561; CAA26403.1; -; Genomic_DNA.
DR EMBL; M11770; AAA34518.1; -; Genomic_DNA.
DR EMBL; M17800; AAA34520.1; -; Genomic_DNA.
DR EMBL; U12141; AAA99660.1; -; Genomic_DNA.
DR EMBL; Z71328; CAA95921.1; -; Genomic_DNA.
DR EMBL; AY558131; AAS56457.1; -; Genomic_DNA.
DR EMBL; M11141; AAA34519.1; -; Genomic_DNA.
DR EMBL; BK006947; DAA10493.1; -; Genomic_DNA.
DR PIR; S05833; OTBY5A.
DR RefSeq; NP_014346.1; NM_001182891.1.
DR PDB; 6GIQ; EM; 3.23 A; e=1-153.
DR PDB; 6HU9; EM; 3.35 A; e/q=21-153.
DR PDB; 6YMX; EM; 3.17 A; e=25-152.
DR PDB; 6YMY; EM; 3.41 A; e=25-152.
DR PDBsum; 6GIQ; -.
DR PDBsum; 6HU9; -.
DR PDBsum; 6YMX; -.
DR PDBsum; 6YMY; -.
DR AlphaFoldDB; P00424; -.
DR SMR; P00424; -.
DR BioGRID; 35772; 221.
DR ComplexPortal; CPX-1721; Mitochondrial respiratory chain complex IV, COX5A variant.
DR DIP; DIP-6820N; -.
DR IntAct; P00424; 5.
DR MINT; P00424; -.
DR STRING; 4932.YNL052W; -.
DR TCDB; 3.D.4.8.1; the proton-translocating cytochrome oxidase (cox) superfamily.
DR MaxQB; P00424; -.
DR PaxDb; P00424; -.
DR PRIDE; P00424; -.
DR EnsemblFungi; YNL052W_mRNA; YNL052W; YNL052W.
DR GeneID; 855675; -.
DR KEGG; sce:YNL052W; -.
DR SGD; S000004997; COX5A.
DR VEuPathDB; FungiDB:YNL052W; -.
DR eggNOG; KOG4075; Eukaryota.
DR GeneTree; ENSGT00390000002407; -.
DR HOGENOM; CLU_070101_2_0_1; -.
DR InParanoid; P00424; -.
DR OMA; PNIEASW; -.
DR BioCyc; MetaCyc:YNL052W-MON; -.
DR BioCyc; YEAST:YNL052W-MON; -.
DR UniPathway; UPA00705; -.
DR PRO; PR:P00424; -.
DR Proteomes; UP000002311; Chromosome XIV.
DR RNAct; P00424; protein.
DR GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
DR GO; GO:0005743; C:mitochondrial inner membrane; TAS:Reactome.
DR GO; GO:0005758; C:mitochondrial intermembrane space; TAS:Reactome.
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; Direct protein sequencing; Membrane; Mitochondrion;
KW Mitochondrion inner membrane; Oxidoreductase; Reference proteome;
KW Transit peptide; Transmembrane; Transmembrane helix.
FT TRANSIT 1..20
FT /note="Mitochondrion"
FT /evidence="ECO:0000269|PubMed:1331058,
FT ECO:0000269|PubMed:6300105, ECO:0000269|PubMed:6327686,
FT ECO:0000269|PubMed:7851399"
FT CHAIN 21..153
FT /note="Cytochrome c oxidase subunit 5A, mitochondrial"
FT /id="PRO_0000006097"
FT TOPO_DOM 21..88
FT /note="Mitochondrial matrix"
FT /evidence="ECO:0000269|PubMed:30598554"
FT TRANSMEM 89..111
FT /note="Helical"
FT /evidence="ECO:0000269|PubMed:30598554"
FT TOPO_DOM 112..153
FT /note="Mitochondrial intermembrane"
FT /evidence="ECO:0000269|PubMed:30598554"
FT CONFLICT 51
FT /note="Missing (in Ref. 10; AA sequence)"
FT /evidence="ECO:0000305"
FT HELIX 28..31
FT /evidence="ECO:0007829|PDB:6YMX"
FT STRAND 35..38
FT /evidence="ECO:0007829|PDB:6YMX"
FT HELIX 43..46
FT /evidence="ECO:0007829|PDB:6YMX"
FT HELIX 49..56
FT /evidence="ECO:0007829|PDB:6YMX"
FT STRAND 57..59
FT /evidence="ECO:0007829|PDB:6YMX"
FT HELIX 61..63
FT /evidence="ECO:0007829|PDB:6HU9"
FT HELIX 66..77
FT /evidence="ECO:0007829|PDB:6YMX"
FT STRAND 78..81
FT /evidence="ECO:0007829|PDB:6YMX"
FT HELIX 92..99
FT /evidence="ECO:0007829|PDB:6YMX"
FT TURN 100..102
FT /evidence="ECO:0007829|PDB:6YMX"
FT HELIX 103..115
FT /evidence="ECO:0007829|PDB:6YMX"
FT STRAND 125..127
FT /evidence="ECO:0007829|PDB:6YMX"
FT HELIX 128..137
FT /evidence="ECO:0007829|PDB:6YMX"
FT TURN 138..140
FT /evidence="ECO:0007829|PDB:6YMX"
FT STRAND 141..145
FT /evidence="ECO:0007829|PDB:6YMX"
SQ SEQUENCE 153 AA; 17140 MW; 1B1F8A3FE12CF783 CRC64;
MLRNTFTRAG GLSRITSVRF AQTHALSNAA VMDLQSRWEN MPSTEQQDIV SKLSERQKLP
WAQLTEPEKQ AVWYISYGEW GPRRPVLNKG DSSFIAKGVA AGLLFSVGLF AVVRMAGGQD
AKTMNKEWQL KSDEYLKSKN ANPWGGYSQV QSK
