COX2_YEAST
ID COX2_YEAST Reviewed; 251 AA.
AC P00410; A0A0A7NYF9;
DT 21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
DT 21-JUL-1986, sequence version 1.
DT 03-AUG-2022, entry version 201.
DE RecName: Full=Cytochrome c oxidase subunit 2;
DE EC=7.1.1.9 {ECO:0000269|PubMed:30598554};
DE AltName: Full=Cytochrome c oxidase polypeptide II;
DE Flags: Precursor;
GN Name=COX2; Synonyms=OXI1; OrderedLocusNames=Q0250;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OG Mitochondrion.
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=DS200/A1;
RX PubMed=225327; DOI=10.1016/s0021-9258(19)86848-5;
RA Coruzzi G., Tzagoloff A.;
RT "Assembly of the mitochondrial membrane system. DNA sequence of subunit 2
RT of yeast cytochrome oxidase.";
RL J. Biol. Chem. 254:9324-9330(1979).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 24657 / D273-10B;
RX PubMed=230513; DOI=10.1073/pnas.76.12.6534;
RA Fox T.D.;
RT "Five TGA 'stop' codons occur within the translated sequence of the yeast
RT mitochondrial gene for cytochrome c oxidase subunit II.";
RL Proc. Natl. Acad. Sci. U.S.A. 76:6534-6538(1979).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 96604 / S288c / FY1679;
RX PubMed=9872396; DOI=10.1016/s0014-5793(98)01467-7;
RA Foury F., Roganti T., Lecrenier N., Purnelle B.;
RT "The complete sequence of the mitochondrial genome of Saccharomyces
RT cerevisiae.";
RL FEBS Lett. 440:325-331(1998).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 96604 / S288c / FY1679;
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 [5]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-117.
RX PubMed=2547760; DOI=10.1016/s0021-9258(18)80007-2;
RA Cameron V.L., Fox T.D., Poyton R.O.;
RT "Isolation and characterization of a yeast strain carrying a mutation in
RT the mitochondrial promoter for COX2.";
RL J. Biol. Chem. 264:13391-13394(1989).
RN [6]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 121-132.
RX PubMed=226981; DOI=10.1073/pnas.76.8.3784;
RA Macino G., Coruzzi G., Nobrega F.G., Li M., Tzagoloff A.;
RT "Use of the UGA terminator as a tryptophan codon in yeast mitochondria.";
RL Proc. Natl. Acad. Sci. U.S.A. 76:3784-3785(1979).
RN [7]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 46-200.
RC STRAIN=ATCC 18824 / CBS 1171 / DSM 70449 / IFO 10217 / NRRL Y-12632;
RA Nakagawa Y.;
RL Submitted (JUN-1995) to the EMBL/GenBank/DDBJ databases.
RN [8]
RP PROTEIN SEQUENCE OF 16-34, 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 [9]
RP PROTEIN SEQUENCE OF 16-18, 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 [10]
RP POST-TRANSLATIONAL CLEAVAGE.
RX PubMed=6313350; DOI=10.1002/j.1460-2075.1983.tb01544.x;
RA Pratje E., Mannhaupt G., Michaelis G., Beyreuther K.;
RT "A nuclear mutation prevents processing of a mitochondrially encoded
RT membrane protein in Saccharomyces cerevisiae.";
RL EMBO J. 2:1049-1054(1983).
RN [11]
RP POST-TRANSLATIONAL CLEAVAGE BY IMP1.
RX PubMed=8879245; DOI=10.1007/bf02173009;
RA Esser K., Pratje E., Michaelis G.;
RT "SOM1, a small new gene required for mitochondrial inner membrane peptidase
RT function in Saccharomyces cerevisiae.";
RL Mol. Gen. Genet. 252:437-445(1996).
RN [12]
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 [13]
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 [14]
RP STRUCTURE BY ELECTRON MICROSCOPY (3.23 ANGSTROMS) IN COMPLEX WITH COPPER.
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 [15]
RP STRUCTURE BY ELECTRON MICROSCOPY (3.35 ANGSTROMS) IN COMPLEX WITH COPPER
RP AND MAGNESIUM, FUNCTION, AND CATALYTIC ACTIVITY.
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 unsing 4 electrons from cytochrome c in the IMS and 4 protons from the
CC mitochondrial matrix (Probable). COX2 is a catalytic core subunit which
CC transfers the electrons from cytochrome c via its dinuclear copper A
CC center (CU(A)) to the BNC of the COX1 (PubMed:30598554).
CC {ECO:0000269|PubMed:30598554, ECO:0000305|PubMed:30598554}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=4 Fe(II)-[cytochrome c] + 8 H(+)(in) + O2 = 4 Fe(III)-
CC [cytochrome c] + 4 H(+)(out) + 2 H2O; Xref=Rhea:RHEA:11436,
CC Rhea:RHEA-COMP:10350, Rhea:RHEA-COMP:14399, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:15379, ChEBI:CHEBI:29033,
CC ChEBI:CHEBI:29034; EC=7.1.1.9;
CC Evidence={ECO:0000269|PubMed:30598554};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:11437;
CC Evidence={ECO:0000269|PubMed:30598554};
CC -!- COFACTOR:
CC Name=Cu cation; Xref=ChEBI:CHEBI:23378;
CC Evidence={ECO:0000269|PubMed:30598554, ECO:0000269|PubMed:30598556};
CC Note=Binds a dinuclear copper A center per subunit.
CC {ECO:0000269|PubMed:30598554, ECO:0000269|PubMed:30598556};
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 The complex exists as a monomer or a dimer and forms supercomplexes
CC (SCs) in the inner mitochondrial membrane with a dimer of ubiquinol-
CC cytochrome c oxidoreductase (cytochrome b-c1 complex, complex III,
CC CIII), resulting in 2 different assemblies (supercomplexes III(2)IV and
CC III(2)IV(2)) (PubMed:10775262, PubMed:10764779, PubMed:30598556,
CC PubMed:30598554). {ECO:0000269|PubMed:10764779,
CC ECO:0000269|PubMed:10775262, ECO:0000269|PubMed:30598554,
CC ECO:0000269|PubMed:30598556, ECO:0000269|PubMed:7851399}.
CC -!- INTERACTION:
CC P00410; Q04935: COX20; NbExp=3; IntAct=EBI-5024, EBI-36910;
CC -!- SUBCELLULAR LOCATION: Mitochondrion inner membrane
CC {ECO:0000269|PubMed:30598554}; Multi-pass membrane protein
CC {ECO:0000269|PubMed:30598554}.
CC -!- PTM: The N-terminal sequence of COX2 is processed by IMP1.
CC -!- SIMILARITY: Belongs to the cytochrome c oxidase subunit 2 family.
CC {ECO:0000305}.
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DR EMBL; K02200; AAA32158.2; -; Genomic_DNA.
DR EMBL; V00706; CAA24078.1; -; Genomic_DNA.
DR EMBL; V00685; CAA24056.1; -; Genomic_DNA.
DR EMBL; KP263414; AIZ98897.1; -; Genomic_DNA.
DR EMBL; J05007; AAA32155.2; -; Genomic_DNA.
DR EMBL; L36888; AAA67528.1; -; Genomic_DNA.
DR EMBL; D55725; BAA09539.1; -; Genomic_DNA.
DR PIR; A00478; OBBY2.
DR RefSeq; NP_009326.1; NC_001224.1.
DR PDB; 6GIQ; EM; 3.23 A; b=1-251.
DR PDB; 6HU9; EM; 3.35 A; b/n=16-251.
DR PDB; 6T0B; EM; 2.80 A; b/o=16-251.
DR PDB; 6T15; EM; 3.29 A; b=16-251.
DR PDB; 6YMX; EM; 3.17 A; b=16-251.
DR PDB; 6YMY; EM; 3.41 A; b=16-251.
DR PDBsum; 6GIQ; -.
DR PDBsum; 6HU9; -.
DR PDBsum; 6T0B; -.
DR PDBsum; 6T15; -.
DR PDBsum; 6YMX; -.
DR PDBsum; 6YMY; -.
DR AlphaFoldDB; P00410; -.
DR SMR; P00410; -.
DR BioGRID; 34812; 61.
DR ComplexPortal; CPX-1721; Mitochondrial respiratory chain complex IV, COX5A variant.
DR ComplexPortal; CPX-1722; Mitochondrial respiratory chain complex IV, COX5B variant.
DR DIP; DIP-7592N; -.
DR IntAct; P00410; 9.
DR MINT; P00410; -.
DR STRING; 4932.Q0250; -.
DR TCDB; 3.D.4.8.1; the proton-translocating cytochrome oxidase (cox) superfamily.
DR MaxQB; P00410; -.
DR PaxDb; P00410; -.
DR PRIDE; P00410; -.
DR EnsemblFungi; Q0250_mRNA; Q0250; Q0250.
DR GeneID; 854622; -.
DR KEGG; sce:Q0250; -.
DR SGD; S000007281; COX2.
DR VEuPathDB; FungiDB:Q0250; -.
DR eggNOG; KOG4767; Eukaryota.
DR GeneTree; ENSGT00390000017410; -.
DR HOGENOM; CLU_036876_2_3_1; -.
DR InParanoid; P00410; -.
DR OMA; WSYEYTD; -.
DR BioCyc; MetaCyc:Q0250-MON; -.
DR BioCyc; YEAST:Q0250-MON; -.
DR PRO; PR:P00410; -.
DR Proteomes; UP000002311; Mitochondrion.
DR RNAct; P00410; 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:0005507; F:copper ion binding; IEA:InterPro.
DR GO; GO:0004129; F:cytochrome-c oxidase activity; IEA:UniProtKB-EC.
DR GO; GO:0009060; P:aerobic respiration; IMP:SGD.
DR GO; GO:0042773; P:ATP synthesis coupled electron transport; IBA:GO_Central.
DR GO; GO:0045333; P:cellular respiration; IDA:ComplexPortal.
DR GO; GO:0006123; P:mitochondrial electron transport, cytochrome c to oxygen; IDA:SGD.
DR CDD; cd13912; CcO_II_C; 1.
DR Gene3D; 1.10.287.90; -; 1.
DR Gene3D; 2.60.40.420; -; 1.
DR InterPro; IPR045187; CcO_II.
DR InterPro; IPR002429; CcO_II-like_C.
DR InterPro; IPR034210; CcO_II_C.
DR InterPro; IPR001505; Copper_CuA.
DR InterPro; IPR008972; Cupredoxin.
DR InterPro; IPR014222; Cyt_c_oxidase_su2.
DR InterPro; IPR011759; Cyt_c_oxidase_su2_TM_dom.
DR InterPro; IPR036257; Cyt_c_oxidase_su2_TM_sf.
DR PANTHER; PTHR22888; PTHR22888; 1.
DR Pfam; PF00116; COX2; 1.
DR Pfam; PF02790; COX2_TM; 1.
DR SUPFAM; SSF49503; SSF49503; 1.
DR SUPFAM; SSF81464; SSF81464; 1.
DR TIGRFAMs; TIGR02866; CoxB; 1.
DR PROSITE; PS00078; COX2; 1.
DR PROSITE; PS50857; COX2_CUA; 1.
DR PROSITE; PS50999; COX2_TM; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Copper; Direct protein sequencing; Electron transport;
KW Membrane; Metal-binding; Mitochondrion; Mitochondrion inner membrane;
KW Reference proteome; Respiratory chain; Translocase; Transmembrane;
KW Transmembrane helix; Transport.
FT PROPEP 1..15
FT /note="Removed in mature form"
FT /evidence="ECO:0000269|PubMed:1331058,
FT ECO:0000269|PubMed:6313350, ECO:0000269|PubMed:7851399,
FT ECO:0000269|PubMed:8879245"
FT /id="PRO_0000419180"
FT CHAIN 16..251
FT /note="Cytochrome c oxidase subunit 2"
FT /id="PRO_0000006048"
FT TOPO_DOM 16..30
FT /note="Mitochondrial intermembrane"
FT /evidence="ECO:0000269|PubMed:30598554"
FT TRANSMEM 31..64
FT /note="Helical; Name=1"
FT /evidence="ECO:0000269|PubMed:30598554"
FT TOPO_DOM 65..78
FT /note="Mitochondrial matrix"
FT /evidence="ECO:0000269|PubMed:30598554"
FT TRANSMEM 79..108
FT /note="Helical; Name=2"
FT /evidence="ECO:0000269|PubMed:30598554"
FT TOPO_DOM 109..251
FT /note="Mitochondrial intermembrane"
FT /evidence="ECO:0000269|PubMed:30598554"
FT BINDING 186
FT /ligand="Cu cation"
FT /ligand_id="ChEBI:CHEBI:23378"
FT /ligand_label="A1"
FT /evidence="ECO:0000269|PubMed:30598554"
FT BINDING 221
FT /ligand="Cu cation"
FT /ligand_id="ChEBI:CHEBI:23378"
FT /ligand_label="A1"
FT /evidence="ECO:0000269|PubMed:30598554"
FT BINDING 221
FT /ligand="Cu cation"
FT /ligand_id="ChEBI:CHEBI:23378"
FT /ligand_label="A2"
FT /evidence="ECO:0000269|PubMed:30598554"
FT BINDING 223
FT /ligand="Cu cation"
FT /ligand_id="ChEBI:CHEBI:23378"
FT /ligand_label="A2"
FT /evidence="ECO:0000269|PubMed:30598554"
FT BINDING 223
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_note="ligand shared with COX1"
FT /evidence="ECO:0000269|PubMed:30598554,
FT ECO:0000269|PubMed:30598556"
FT BINDING 225
FT /ligand="Cu cation"
FT /ligand_id="ChEBI:CHEBI:23378"
FT /ligand_label="A1"
FT /evidence="ECO:0000269|PubMed:30598554"
FT BINDING 225
FT /ligand="Cu cation"
FT /ligand_id="ChEBI:CHEBI:23378"
FT /ligand_label="A2"
FT /evidence="ECO:0000269|PubMed:30598554"
FT BINDING 229
FT /ligand="Cu cation"
FT /ligand_id="ChEBI:CHEBI:23378"
FT /ligand_label="A2"
FT /evidence="ECO:0000269|PubMed:30598554,
FT ECO:0000269|PubMed:30598556"
FT BINDING 232
FT /ligand="Cu cation"
FT /ligand_id="ChEBI:CHEBI:23378"
FT /ligand_label="A1"
FT /evidence="ECO:0000269|PubMed:30598554"
FT SITE 15..16
FT /note="Cleavage; by IMP1"
FT /evidence="ECO:0000269|PubMed:8879245"
FT CONFLICT 59
FT /note="Y -> N (in Ref. 5; AAA32155)"
FT /evidence="ECO:0000305"
FT HELIX 31..65
FT /evidence="ECO:0007829|PDB:6T0B"
FT HELIX 79..85
FT /evidence="ECO:0007829|PDB:6T0B"
FT HELIX 88..107
FT /evidence="ECO:0007829|PDB:6T0B"
FT STRAND 116..122
FT /evidence="ECO:0007829|PDB:6T0B"
FT STRAND 125..129
FT /evidence="ECO:0007829|PDB:6T0B"
FT STRAND 136..140
FT /evidence="ECO:0007829|PDB:6T0B"
FT STRAND 142..145
FT /evidence="ECO:0007829|PDB:6T0B"
FT HELIX 150..152
FT /evidence="ECO:0007829|PDB:6HU9"
FT STRAND 155..157
FT /evidence="ECO:0007829|PDB:6GIQ"
FT TURN 159..161
FT /evidence="ECO:0007829|PDB:6YMX"
FT STRAND 163..165
FT /evidence="ECO:0007829|PDB:6T0B"
FT STRAND 167..173
FT /evidence="ECO:0007829|PDB:6T0B"
FT STRAND 175..184
FT /evidence="ECO:0007829|PDB:6T0B"
FT STRAND 186..190
FT /evidence="ECO:0007829|PDB:6T0B"
FT TURN 191..194
FT /evidence="ECO:0007829|PDB:6T0B"
FT STRAND 195..199
FT /evidence="ECO:0007829|PDB:6T0B"
FT STRAND 201..203
FT /evidence="ECO:0007829|PDB:6YMX"
FT STRAND 205..209
FT /evidence="ECO:0007829|PDB:6T0B"
FT STRAND 215..220
FT /evidence="ECO:0007829|PDB:6T0B"
FT HELIX 227..229
FT /evidence="ECO:0007829|PDB:6T0B"
FT STRAND 233..239
FT /evidence="ECO:0007829|PDB:6T0B"
FT TURN 242..246
FT /evidence="ECO:0007829|PDB:6T0B"
FT HELIX 247..250
FT /evidence="ECO:0007829|PDB:6T0B"
SQ SEQUENCE 251 AA; 28567 MW; BA5717C37330DF41 CRC64;
MLDLLRLQLT TFIMNDVPTP YACYFQDSAT PNQEGILELH DNIMFYLLVI LGLVSWMLYT
IVMTYSKNPI AYKYIKHGQT IEVIWTIFPA VILLIIAFPS FILLYLCDEV ISPAMTIKAI
GYQWYWKYEY SDFINDSGET VEFESYVIPD ELLEEGQLRL LDTDTSMVVP VDTHIRFVVT
AADVIHDFAI PSLGIKVDAT PGRLNQVSAL IQREGVFYGA CSELCGTGHA NMPIKIEAVS
LPKFLEWLNE Q
