COX5B_BOVIN
ID COX5B_BOVIN Reviewed; 129 AA.
AC P00428; A6QL66; P11949; Q3T041;
DT 21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
DT 27-JUN-2006, sequence version 2.
DT 03-AUG-2022, entry version 179.
DE RecName: Full=Cytochrome c oxidase subunit 5B, mitochondrial;
DE AltName: Full=Cytochrome c oxidase polypeptide VIa;
DE AltName: Full=Cytochrome c oxidase polypeptide Vb;
DE Flags: Precursor;
GN Name=COX5B;
OS Bos taurus (Bovine).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Laurasiatheria; Artiodactyla; Ruminantia; Pecora; Bovidae;
OC Bovinae; Bos.
OX NCBI_TaxID=9913;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=Crossbred X Angus, and Hereford; TISSUE=Heart ventricle, and Ileum;
RG NIH - Mammalian Gene Collection (MGC) project;
RL Submitted (JUN-2007) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP PROTEIN SEQUENCE OF 32-129.
RX PubMed=6292069; DOI=10.1515/bchm2.1982.363.2.1141;
RA Biewald R., Buse G.;
RT "Studies on cytochrome c oxidase, IX. The primary structure of polypeptide
RT VIa.";
RL Hoppe-Seyler's Z. Physiol. Chem. 363:1141-1153(1982).
RN [3]
RP PROTEIN SEQUENCE OF 32-57.
RC TISSUE=Liver;
RX PubMed=2844245; DOI=10.1021/bi00413a048;
RA Yanamura W., Zhang Y.-Z., Takamiya S., Capaldi R.A.;
RT "Tissue-specific differences between heart and liver cytochrome c
RT oxidase.";
RL Biochemistry 27:4909-4914(1988).
RN [4]
RP NUCLEOTIDE SEQUENCE [MRNA] OF 51-129.
RX PubMed=2840351; DOI=10.1016/0378-1119(88)90411-8;
RA Zeviani M., Sakoda S., Sherbany A., Nakase H., Rizzuto R., Samitt C.E.,
RA Dimauro S., Schon E.A.;
RT "Sequence of cDNAs encoding subunit Vb of human and bovine cytochrome c
RT oxidase.";
RL Gene 65:1-11(1988).
RN [5]
RP SUBUNIT.
RX PubMed=26698328; DOI=10.1074/jbc.m115.680553;
RA Shinzawa-Itoh K., Shimomura H., Yanagisawa S., Shimada S., Takahashi R.,
RA Oosaki M., Ogura T., Tsukihara T.;
RT "Purification of active respiratory supercomplex from bovine heart
RT mitochondria enables functional studies.";
RL J. Biol. Chem. 291:4178-4184(2016).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) IN COMPLEX WITH ZINC.
RX PubMed=8638158; DOI=10.1126/science.272.5265.1136;
RA Tsukihara T., Aoyama H., Yamashita E., Tomizaki T., Yamaguchi H.,
RA Shinzawa-Itoh K., Nakashima R., Yaono R., Yoshikawa S.;
RT "The whole structure of the 13-subunit oxidized cytochrome c oxidase at 2.8
RT A.";
RL Science 272:1136-1144(1996).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS).
RC TISSUE=Heart;
RX PubMed=10089392; DOI=10.1107/s0907444998006362;
RA Tomizaki T., Yamashita E., Yamaguchi H., Aoyama H., Tsukihara T.,
RA Shinzawa-Itoh K., Nakashima R., Yaono R., Yoshikawa S.;
RT "Structure analysis of bovine heart cytochrome c oxidase at 2.8 A
RT resolution.";
RL Acta Crystallogr. D 55:31-45(1999).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (2.9 ANGSTROMS).
RC TISSUE=Heart;
RX PubMed=10771420; DOI=10.1107/s0907444900002213;
RA Fei M.J., Yamashita E., Inoue N., Yao M., Yamaguchi H., Tsukihara T.,
RA Shinzawa-Itoh K., Nakashima R., Yoshikawa S.;
RT "X-ray structure of azide-bound fully oxidized cytochrome c oxidase from
RT bovine heart at 2.9 A resolution.";
RL Acta Crystallogr. D 56:529-535(2000).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) IN COMPLEX WITH ZINC.
RX PubMed=20385840; DOI=10.1073/pnas.0910410107;
RA Muramoto K., Ohta K., Shinzawa-Itoh K., Kanda K., Taniguchi M.,
RA Nabekura H., Yamashita E., Tsukihara T., Yoshikawa S.;
RT "Bovine cytochrome c oxidase structures enable O2 reduction with
RT minimization of reactive oxygens and provide a proton-pumping gate.";
RL Proc. Natl. Acad. Sci. U.S.A. 107:7740-7745(2010).
RN [10]
RP STRUCTURE BY ELECTRON MICROSCOPY (9.10 ANGSTROMS).
RX PubMed=27830641; DOI=10.7554/elife.21290;
RA Sousa J.S., Mills D.J., Vonck J., Kuehlbrandt W.;
RT "Functional asymmetry and electron flow in the bovine respirasome.";
RL Elife 5:0-0(2016).
RN [11]
RP X-RAY CRYSTALLOGRAPHY (1.50 ANGSTROMS) IN COMPLEX WITH ZINC.
RX PubMed=27605664; DOI=10.1074/jbc.m115.711770;
RA Yano N., Muramoto K., Shimada A., Takemura S., Baba J., Fujisawa H.,
RA Mochizuki M., Shinzawa-Itoh K., Yamashita E., Tsukihara T., Yoshikawa S.;
RT "The Mg2+-containing water cluster of mammalian cytochrome c oxidase
RT collects four pumping proton equivalents in each catalytic cycle.";
RL J. Biol. Chem. 291:23882-23894(2016).
RN [12]
RP X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS).
RX PubMed=31533957; DOI=10.1073/pnas.1907183116;
RA Shinzawa-Itoh K., Sugimura T., Misaki T., Tadehara Y., Yamamoto S.,
RA Hanada M., Yano N., Nakagawa T., Uene S., Yamada T., Aoyama H.,
RA Yamashita E., Tsukihara T., Yoshikawa S., Muramoto K.;
RT "Monomeric structure of an active form of bovine cytochrome c oxidase.";
RL Proc. Natl. Acad. Sci. U.S.A. 116:19945-19951(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 subunit 2 and heme A of subunit 1
CC to the active site in subunit 1, a binuclear center (BNC) formed by
CC heme A3 and copper B (CU(B)). The BNC reduces molecular oxygen to 2
CC water molecules using 4 electrons from cytochrome c in the IMS and 4
CC protons from the mitochondrial matrix. {ECO:0000250|UniProtKB:P04037}.
CC -!- PATHWAY: Energy metabolism; oxidative phosphorylation.
CC {ECO:0000250|UniProtKB:P04037}.
CC -!- SUBUNIT: Component of the cytochrome c oxidase (complex IV, CIV), a
CC multisubunit enzyme composed of 14 subunits. The complex is composed of
CC a catalytic core of 3 subunits MT-CO1, MT-CO2 and MT-CO3, encoded in
CC the mitochondrial DNA, and 11 supernumerary subunits COX4I1 (or
CC COX4I2), COX5A, COX5B, COX6A2 (or COX6A1), COX6B1 (or COX6B2), COX6C,
CC COX7A1 (or COX7A2), COX7B, COX7C, COX8B and NDUFA4, which are encoded
CC in the nuclear genome (PubMed:8638158). The complex exists as a monomer
CC or a dimer and forms supercomplexes (SCs) in the inner mitochondrial
CC membrane with NADH-ubiquinone oxidoreductase (complex I, CI) and
CC ubiquinol-cytochrome c oxidoreductase (cytochrome b-c1 complex, complex
CC III, CIII), resulting in different assemblies (supercomplex
CC SCI(1)III(2)IV(1) and megacomplex MCI(2)III(2)IV(2)) (PubMed:26698328,
CC PubMed:27830641). {ECO:0000269|PubMed:26698328,
CC ECO:0000269|PubMed:27830641, ECO:0000269|PubMed:8638158}.
CC -!- SUBCELLULAR LOCATION: Mitochondrion inner membrane
CC {ECO:0000269|PubMed:27605664, ECO:0000269|PubMed:31533957}; Peripheral
CC membrane protein {ECO:0000269|PubMed:27605664,
CC ECO:0000269|PubMed:31533957}; Matrix side {ECO:0000269|PubMed:27605664,
CC ECO:0000269|PubMed:31533957}.
CC -!- SIMILARITY: Belongs to the cytochrome c oxidase subunit 5B family.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAA30465.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR EMBL; BC102579; AAI02580.1; -; mRNA.
DR EMBL; BC147855; AAI47856.1; -; mRNA.
DR EMBL; M19962; AAA30465.1; ALT_INIT; mRNA.
DR PIR; A00495; OGBO6A.
DR RefSeq; NP_001029218.1; NM_001034046.2.
DR PDB; 1OCC; X-ray; 2.80 A; F/S=32-129.
DR PDB; 1OCO; X-ray; 2.80 A; F/S=32-129.
DR PDB; 1OCR; X-ray; 2.35 A; F/S=32-129.
DR PDB; 1OCZ; X-ray; 2.90 A; F/S=32-129.
DR PDB; 1V54; X-ray; 1.80 A; F/S=32-129.
DR PDB; 1V55; X-ray; 1.90 A; F/S=32-129.
DR PDB; 2DYR; X-ray; 1.80 A; F/S=32-129.
DR PDB; 2DYS; X-ray; 2.20 A; F/S=32-129.
DR PDB; 2EIJ; X-ray; 1.90 A; F/S=32-129.
DR PDB; 2EIK; X-ray; 2.10 A; F/S=32-129.
DR PDB; 2EIL; X-ray; 2.10 A; F/S=32-129.
DR PDB; 2EIM; X-ray; 2.60 A; F/S=32-129.
DR PDB; 2EIN; X-ray; 2.70 A; F/S=32-129.
DR PDB; 2OCC; X-ray; 2.30 A; F/S=32-129.
DR PDB; 2Y69; X-ray; 1.95 A; F/S=1-129.
DR PDB; 2YBB; EM; 19.00 A; Q=32-129.
DR PDB; 2ZXW; X-ray; 2.50 A; F/S=32-129.
DR PDB; 3ABK; X-ray; 2.00 A; F/S=32-129.
DR PDB; 3ABL; X-ray; 2.10 A; F/S=32-129.
DR PDB; 3ABM; X-ray; 1.95 A; F/S=32-129.
DR PDB; 3AG1; X-ray; 2.20 A; F/S=32-129.
DR PDB; 3AG2; X-ray; 1.80 A; F/S=32-129.
DR PDB; 3AG3; X-ray; 1.80 A; F/S=32-129.
DR PDB; 3AG4; X-ray; 2.05 A; F/S=32-129.
DR PDB; 3ASN; X-ray; 3.00 A; F/S=32-129.
DR PDB; 3ASO; X-ray; 2.30 A; F/S=32-129.
DR PDB; 3WG7; X-ray; 1.90 A; F/S=32-129.
DR PDB; 3X2Q; X-ray; 2.00 A; F/S=32-129.
DR PDB; 5B1A; X-ray; 1.50 A; F/S=32-129.
DR PDB; 5B1B; X-ray; 1.60 A; F/S=32-129.
DR PDB; 5B3S; X-ray; 1.68 A; F/S=32-129.
DR PDB; 5GPN; EM; 5.40 A; 3=32-129.
DR PDB; 5IY5; X-ray; 2.00 A; F/S=32-129.
DR PDB; 5LUF; EM; 9.10 A; 3=32-129.
DR PDB; 5W97; X-ray; 2.30 A; F/f=32-129.
DR PDB; 5WAU; X-ray; 1.95 A; F/f=32-129.
DR PDB; 5X19; X-ray; 2.20 A; F/S=32-129.
DR PDB; 5X1B; X-ray; 2.40 A; F/S=32-129.
DR PDB; 5X1F; X-ray; 2.20 A; F/S=32-129.
DR PDB; 5XDQ; X-ray; 1.77 A; F/S=32-125.
DR PDB; 5XDX; X-ray; 1.99 A; F/S=32-125.
DR PDB; 5XTH; EM; 3.90 A; 2=32-129.
DR PDB; 5XTI; EM; 17.40 A; 2/B2=32-129.
DR PDB; 5Z84; X-ray; 1.85 A; F/S=32-129.
DR PDB; 5Z85; X-ray; 1.85 A; F/S=32-129.
DR PDB; 5Z86; X-ray; 1.85 A; F/S=32-129.
DR PDB; 5ZCO; X-ray; 1.90 A; F/S=32-129.
DR PDB; 5ZCP; X-ray; 1.65 A; F/S=32-129.
DR PDB; 5ZCQ; X-ray; 1.65 A; F/S=32-129.
DR PDB; 6J8M; X-ray; 1.90 A; F/S=32-129.
DR PDB; 6JUW; X-ray; 1.80 A; F/S=32-129.
DR PDB; 6JY3; X-ray; 1.85 A; F=32-129.
DR PDB; 6JY4; X-ray; 1.95 A; F=32-129.
DR PDB; 6NKN; X-ray; 2.50 A; F/S=32-129.
DR PDB; 6NMF; X-ray; 2.80 A; F/S=32-129.
DR PDB; 6NMP; X-ray; 2.90 A; F/S=32-129.
DR PDB; 7COH; X-ray; 1.30 A; F/S=32-129.
DR PDB; 7CP5; X-ray; 1.76 A; F/S=32-125.
DR PDB; 7D5W; X-ray; 1.84 A; F/S=32-125.
DR PDB; 7D5X; X-ray; 1.74 A; F/S=32-125.
DR PDB; 7EV7; X-ray; 1.70 A; F/S=32-129.
DR PDB; 7THU; X-ray; 1.93 A; FFF/SSS=32-129.
DR PDB; 7TIE; X-ray; 1.90 A; FFF/SSS=32-129.
DR PDB; 7TIH; X-ray; 2.35 A; FFF/SSS=32-129.
DR PDB; 7TII; X-ray; 2.45 A; FFF/SSS=32-129.
DR PDBsum; 1OCC; -.
DR PDBsum; 1OCO; -.
DR PDBsum; 1OCR; -.
DR PDBsum; 1OCZ; -.
DR PDBsum; 1V54; -.
DR PDBsum; 1V55; -.
DR PDBsum; 2DYR; -.
DR PDBsum; 2DYS; -.
DR PDBsum; 2EIJ; -.
DR PDBsum; 2EIK; -.
DR PDBsum; 2EIL; -.
DR PDBsum; 2EIM; -.
DR PDBsum; 2EIN; -.
DR PDBsum; 2OCC; -.
DR PDBsum; 2Y69; -.
DR PDBsum; 2YBB; -.
DR PDBsum; 2ZXW; -.
DR PDBsum; 3ABK; -.
DR PDBsum; 3ABL; -.
DR PDBsum; 3ABM; -.
DR PDBsum; 3AG1; -.
DR PDBsum; 3AG2; -.
DR PDBsum; 3AG3; -.
DR PDBsum; 3AG4; -.
DR PDBsum; 3ASN; -.
DR PDBsum; 3ASO; -.
DR PDBsum; 3WG7; -.
DR PDBsum; 3X2Q; -.
DR PDBsum; 5B1A; -.
DR PDBsum; 5B1B; -.
DR PDBsum; 5B3S; -.
DR PDBsum; 5GPN; -.
DR PDBsum; 5IY5; -.
DR PDBsum; 5LUF; -.
DR PDBsum; 5W97; -.
DR PDBsum; 5WAU; -.
DR PDBsum; 5X19; -.
DR PDBsum; 5X1B; -.
DR PDBsum; 5X1F; -.
DR PDBsum; 5XDQ; -.
DR PDBsum; 5XDX; -.
DR PDBsum; 5XTH; -.
DR PDBsum; 5XTI; -.
DR PDBsum; 5Z84; -.
DR PDBsum; 5Z85; -.
DR PDBsum; 5Z86; -.
DR PDBsum; 5ZCO; -.
DR PDBsum; 5ZCP; -.
DR PDBsum; 5ZCQ; -.
DR PDBsum; 6J8M; -.
DR PDBsum; 6JUW; -.
DR PDBsum; 6JY3; -.
DR PDBsum; 6JY4; -.
DR PDBsum; 6NKN; -.
DR PDBsum; 6NMF; -.
DR PDBsum; 6NMP; -.
DR PDBsum; 7COH; -.
DR PDBsum; 7CP5; -.
DR PDBsum; 7D5W; -.
DR PDBsum; 7D5X; -.
DR PDBsum; 7EV7; -.
DR PDBsum; 7THU; -.
DR PDBsum; 7TIE; -.
DR PDBsum; 7TIH; -.
DR PDBsum; 7TII; -.
DR AlphaFoldDB; P00428; -.
DR SMR; P00428; -.
DR CORUM; P00428; -.
DR DIP; DIP-38985N; -.
DR IntAct; P00428; 3.
DR STRING; 9913.ENSBTAP00000024678; -.
DR iPTMnet; P00428; -.
DR PaxDb; P00428; -.
DR PRIDE; P00428; -.
DR GeneID; 287012; -.
DR KEGG; bta:287012; -.
DR CTD; 1329; -.
DR eggNOG; KOG3352; Eukaryota.
DR HOGENOM; CLU_127178_0_0_1; -.
DR InParanoid; P00428; -.
DR OrthoDB; 1528134at2759; -.
DR TreeFam; TF105063; -.
DR BRENDA; 7.1.1.9; 908.
DR UniPathway; UPA00705; -.
DR EvolutionaryTrace; P00428; -.
DR Proteomes; UP000009136; Unplaced.
DR GO; GO:0005751; C:mitochondrial respiratory chain complex IV; IEA:InterPro.
DR GO; GO:0045277; C:respiratory chain complex IV; IDA:UniProtKB.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006123; P:mitochondrial electron transport, cytochrome c to oxygen; IBA:GO_Central.
DR CDD; cd00924; Cyt_c_Oxidase_Vb; 1.
DR Gene3D; 2.60.11.10; -; 1.
DR InterPro; IPR002124; Cyt_c_oxidase_su5b.
DR InterPro; IPR036972; Cyt_c_oxidase_su5b_sf.
DR PANTHER; PTHR10122; PTHR10122; 1.
DR Pfam; PF01215; COX5B; 1.
DR PROSITE; PS00848; COX5B_1; 1.
DR PROSITE; PS51359; COX5B_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Acetylation; Direct protein sequencing; Membrane;
KW Metal-binding; Mitochondrion; Mitochondrion inner membrane;
KW Reference proteome; Transit peptide; Zinc.
FT TRANSIT 1..31
FT /note="Mitochondrion"
FT /evidence="ECO:0000269|PubMed:2844245,
FT ECO:0000269|PubMed:6292069"
FT CHAIN 32..129
FT /note="Cytochrome c oxidase subunit 5B, mitochondrial"
FT /id="PRO_0000197028"
FT BINDING 91
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:20385840,
FT ECO:0000269|PubMed:27605664, ECO:0000269|PubMed:8638158"
FT BINDING 93
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:20385840,
FT ECO:0000269|PubMed:27605664, ECO:0000269|PubMed:8638158"
FT BINDING 113
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:20385840,
FT ECO:0000269|PubMed:27605664, ECO:0000269|PubMed:8638158"
FT BINDING 116
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:20385840,
FT ECO:0000269|PubMed:27605664, ECO:0000269|PubMed:8638158"
FT MOD_RES 68
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000250|UniProtKB:P19536"
FT MOD_RES 86
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000250|UniProtKB:P19536"
FT MOD_RES 121
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000250|UniProtKB:P19536"
FT HELIX 40..43
FT /evidence="ECO:0007829|PDB:7COH"
FT HELIX 46..56
FT /evidence="ECO:0007829|PDB:7COH"
FT STRAND 74..76
FT /evidence="ECO:0007829|PDB:7COH"
FT STRAND 78..81
FT /evidence="ECO:0007829|PDB:7COH"
FT STRAND 83..91
FT /evidence="ECO:0007829|PDB:7COH"
FT STRAND 94..96
FT /evidence="ECO:0007829|PDB:1OCZ"
FT STRAND 101..109
FT /evidence="ECO:0007829|PDB:7COH"
FT STRAND 111..113
FT /evidence="ECO:0007829|PDB:1OCC"
FT TURN 114..116
FT /evidence="ECO:0007829|PDB:7COH"
FT STRAND 119..123
FT /evidence="ECO:0007829|PDB:7COH"
FT STRAND 125..127
FT /evidence="ECO:0007829|PDB:5W97"
SQ SEQUENCE 129 AA; 13834 MW; C78CE7552CE6C313 CRC64;
MASRLLRGVG ALASQALRAR GPNGVSVVRS MASGGGVPTD EEQATGLERE VMLAARKGQD
PYNILAPKAT SGTKEDPNLV PSITNKRIVG CICEEDNSTV IWFWLHKGEA QRCPSCGTHY
KLVPHQLAH
