COX13_YEAST
ID COX13_YEAST Reviewed; 129 AA.
AC P32799; D6VTW3;
DT 01-OCT-1993, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1993, sequence version 1.
DT 03-AUG-2022, entry version 180.
DE RecName: Full=Cytochrome c oxidase subunit 13, mitochondrial;
DE AltName: Full=Cytochrome c oxidase polypeptide VIa;
DE Flags: Precursor;
GN Name=COX13; OrderedLocusNames=YGL191W; ORFNames=G1341;
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=S288c / GRF88;
RX PubMed=8395517; DOI=10.1016/s0021-9258(17)46694-4;
RA Taanman J.-W., Capaldi R.A.;
RT "Subunit VIa of yeast cytochrome c oxidase is not necessary for assembly of
RT the enzyme complex but modulates the enzyme activity. Isolation and
RT characterization of the nuclear-coded gene.";
RL J. Biol. Chem. 268:18754-18761(1993).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 96604 / S288c / FY1679;
RX PubMed=9046087;
RX DOI=10.1002/(sici)1097-0061(199701)13:1<55::aid-yea48>3.0.co;2-9;
RA Coglievina M., Klima R., Bertani I., Delneri D., Zaccaria P., Bruschi C.V.;
RT "Sequencing of a 40.5 kb fragment located on the left arm of chromosome VII
RT from Saccharomyces cerevisiae.";
RL Yeast 13:55-64(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169869;
RA Tettelin H., Agostoni-Carbone M.L., Albermann K., Albers M., Arroyo J.,
RA Backes U., Barreiros T., Bertani I., Bjourson A.J., Brueckner M.,
RA Bruschi C.V., Carignani G., Castagnoli L., Cerdan E., Clemente M.L.,
RA Coblenz A., Coglievina M., Coissac E., Defoor E., Del Bino S., Delius H.,
RA Delneri D., de Wergifosse P., Dujon B., Durand P., Entian K.-D., Eraso P.,
RA Escribano V., Fabiani L., Fartmann B., Feroli F., Feuermann M.,
RA Frontali L., Garcia-Gonzalez M., Garcia-Saez M.I., Goffeau A.,
RA Guerreiro P., Hani J., Hansen M., Hebling U., Hernandez K., Heumann K.,
RA Hilger F., Hofmann B., Indge K.J., James C.M., Klima R., Koetter P.,
RA Kramer B., Kramer W., Lauquin G., Leuther H., Louis E.J., Maillier E.,
RA Marconi A., Martegani E., Mazon M.J., Mazzoni C., McReynolds A.D.K.,
RA Melchioretto P., Mewes H.-W., Minenkova O., Mueller-Auer S., Nawrocki A.,
RA Netter P., Neu R., Nombela C., Oliver S.G., Panzeri L., Paoluzi S.,
RA Plevani P., Portetelle D., Portillo F., Potier S., Purnelle B., Rieger M.,
RA Riles L., Rinaldi T., Robben J., Rodrigues-Pousada C.,
RA Rodriguez-Belmonte E., Rodriguez-Torres A.M., Rose M., Ruzzi M.,
RA Saliola M., Sanchez-Perez M., Schaefer B., Schaefer M., Scharfe M.,
RA Schmidheini T., Schreer A., Skala J., Souciet J.-L., Steensma H.Y.,
RA Talla E., Thierry A., Vandenbol M., van der Aart Q.J.M., Van Dyck L.,
RA Vanoni M., Verhasselt P., Voet M., Volckaert G., Wambutt R., Watson M.D.,
RA Weber N., Wedler E., Wedler H., Wipfli P., Wolf K., Wright L.F.,
RA Zaccaria P., Zimmermann M., Zollner A., Kleine K.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome VII.";
RL Nature 387:81-84(1997).
RN [4]
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 [5]
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 [6]
RP PARTIAL PROTEIN SEQUENCE, 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 [7]
RP PROTEIN SEQUENCE OF 10-12, 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 [8]
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 [9]
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 [10]
RP STRUCTURE BY ELECTRON MICROSCOPY (3.23 ANGSTROMS) OF 57-74.
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 [11]
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 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). COX13 interacts with COX1 and COX3 on the
CC intermembrane space (IMS) and COX4 on the matrix side
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 -!- SUBCELLULAR LOCATION: Mitochondrion inner membrane
CC {ECO:0000269|PubMed:30598554}; Single-pass membrane protein
CC {ECO:0000269|PubMed:30598554}.
CC -!- SIMILARITY: Belongs to the cytochrome c oxidase subunit 6A family.
CC {ECO:0000305}.
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DR EMBL; X72970; CAA51479.1; -; Genomic_DNA.
DR EMBL; X91837; CAA62953.1; -; Genomic_DNA.
DR EMBL; Z72713; CAA96903.1; -; Genomic_DNA.
DR EMBL; AY558489; AAS56815.1; -; Genomic_DNA.
DR EMBL; BK006941; DAA07924.1; -; Genomic_DNA.
DR PIR; A48520; A48520.
DR RefSeq; NP_011324.1; NM_001181056.1.
DR PDB; 6GIQ; EM; 3.23 A; k=1-129.
DR PDB; 6HU9; EM; 3.35 A; k/w=10-129.
DR PDB; 6T0B; EM; 2.80 A; k/x=10-129.
DR PDB; 6T15; EM; 3.29 A; k=10-129.
DR PDB; 6YMX; EM; 3.17 A; k=16-129.
DR PDB; 6YMY; EM; 3.41 A; k=16-129.
DR PDB; 6ZDB; NMR; -; A/B=1-129.
DR PDBsum; 6GIQ; -.
DR PDBsum; 6HU9; -.
DR PDBsum; 6T0B; -.
DR PDBsum; 6T15; -.
DR PDBsum; 6YMX; -.
DR PDBsum; 6YMY; -.
DR PDBsum; 6ZDB; -.
DR AlphaFoldDB; P32799; -.
DR SMR; P32799; -.
DR BioGRID; 33065; 51.
DR ComplexPortal; CPX-1721; Mitochondrial respiratory chain complex IV, COX5A variant.
DR ComplexPortal; CPX-1722; Mitochondrial respiratory chain complex IV, COX5B variant.
DR IntAct; P32799; 17.
DR STRING; 4932.YGL191W; -.
DR TCDB; 3.D.4.8.1; the proton-translocating cytochrome oxidase (cox) superfamily.
DR MaxQB; P32799; -.
DR PaxDb; P32799; -.
DR PRIDE; P32799; -.
DR EnsemblFungi; YGL191W_mRNA; YGL191W; YGL191W.
DR GeneID; 852684; -.
DR KEGG; sce:YGL191W; -.
DR SGD; S000003159; COX13.
DR VEuPathDB; FungiDB:YGL191W; -.
DR eggNOG; KOG3469; Eukaryota.
DR GeneTree; ENSGT00940000168355; -.
DR HOGENOM; CLU_122515_0_1_1; -.
DR InParanoid; P32799; -.
DR OMA; WRKLSLY; -.
DR BioCyc; MetaCyc:YGL191W-MON; -.
DR BioCyc; YEAST:YGL191W-MON; -.
DR UniPathway; UPA00705; -.
DR PRO; PR:P32799; -.
DR Proteomes; UP000002311; Chromosome VII.
DR RNAct; P32799; 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; IDA:SGD.
DR GO; GO:0004129; F:cytochrome-c oxidase activity; IEA:InterPro.
DR GO; GO:0030234; F:enzyme regulator activity; IDA:SGD.
DR GO; GO:0009060; P:aerobic respiration; IMP:SGD.
DR GO; GO:0045333; P:cellular respiration; IDA:ComplexPortal.
DR GO; GO:0006123; P:mitochondrial electron transport, cytochrome c to oxygen; IDA:ComplexPortal.
DR GO; GO:0097250; P:mitochondrial respirasome assembly; IMP:SGD.
DR CDD; cd00925; Cyt_c_Oxidase_VIa; 1.
DR Gene3D; 4.10.95.10; -; 1.
DR InterPro; IPR001349; Cyt_c_oxidase_su6a.
DR InterPro; IPR018507; Cyt_c_oxidase_su6a_CS.
DR InterPro; IPR036418; Cyt_c_oxidase_su6a_sf.
DR PANTHER; PTHR11504; PTHR11504; 1.
DR Pfam; PF02046; COX6A; 1.
DR PIRSF; PIRSF000277; COX6A1; 1.
DR SUPFAM; SSF81411; SSF81411; 1.
DR PROSITE; PS01329; COX6A; 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..9
FT /note="Mitochondrion"
FT /evidence="ECO:0000269|PubMed:1331058,
FT ECO:0000269|PubMed:7851399"
FT CHAIN 10..129
FT /note="Cytochrome c oxidase subunit 13, mitochondrial"
FT /id="PRO_0000006127"
FT TOPO_DOM 10..43
FT /note="Mitochondrial matrix"
FT /evidence="ECO:0000269|PubMed:30598554"
FT TRANSMEM 44..71
FT /note="Helical"
FT /evidence="ECO:0000269|PubMed:30598554"
FT TOPO_DOM 72..129
FT /note="Mitochondrial intermembrane"
FT /evidence="ECO:0000269|PubMed:30598554"
FT HELIX 15..17
FT /evidence="ECO:0007829|PDB:6T0B"
FT STRAND 18..22
FT /evidence="ECO:0007829|PDB:6T0B"
FT HELIX 28..57
FT /evidence="ECO:0007829|PDB:6T0B"
FT HELIX 60..84
FT /evidence="ECO:0007829|PDB:6T0B"
FT HELIX 89..91
FT /evidence="ECO:0007829|PDB:6T15"
FT TURN 97..99
FT /evidence="ECO:0007829|PDB:6YMX"
FT HELIX 103..106
FT /evidence="ECO:0007829|PDB:6ZDB"
FT STRAND 107..111
FT /evidence="ECO:0007829|PDB:6YMX"
FT STRAND 114..116
FT /evidence="ECO:0007829|PDB:6YMX"
FT TURN 119..121
FT /evidence="ECO:0007829|PDB:6T0B"
SQ SEQUENCE 129 AA; 15021 MW; 91C3AD6EAC23CFD3 CRC64;
MFRQCAKRYA SSLPPNALKP AFGPPDKVAA QKFKESLMAT EKHAKDTSNM WVKISVWVAL
PAIALTAVNT YFVEKEHAEH REHLKHVPDS EWPRDYEFMN IRSKPFFWGD GDKTLFWNPV
VNRHIEHDD
