Summary: Cytochrome c oxidase subunit III
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Cytochrome c oxidase subunit III Edit Wikipedia article
|, COIII, MTCO3, Cytochrome c oxidase subunit III, cytochrome c oxidase III|
|Cytochrome c oxidase subunit III|
Structure of the 13-subunit oxidized cytochrome c oxidase.
|SCOPe||1occ / SUPFAM|
Cytochrome c oxidase subunit 3 (COX3) is an enzyme that in humans is encoded by the MT-CO3 gene. Cytochrome c oxidase subunit III is one of main transmembrane subunits of cytochrome c oxidase. Variants of MT-CO3 have been associated with isolated myopathy, severe encephalomyopathy, Leber hereditary optic neuropathy, mitochondrial complex IV deficiency, and recurrent myoglobinuria .
The MT-CO3 gene produces a 30 kDa protein composed of 261 amino acids. COX3, the protein encoded by this gene, is a member of the cytochrome c oxidase subunit 3 family. This protein is located on the inner mitochondrial membrane. COX3 is a multi-pass transmembrane protein. It contains 7 transmembrane domains at positions 15-35, 42-59, 81-101, 127-147, 159-179, 197-217, and 239-259.
Cytochrome c oxidase (EC 220.127.116.11) is the terminal enzyme of the respiratory chain of mitochondria and many aerobic bacteria. It catalyzes the transfer of electrons from reduced cytochrome c to molecular oxygen:
- 4 cytochrome c+2 + 4 H+ + O2 4 cytochrome c+3 + 2 H2O
Cytochrome c oxidase is an oligomeric enzymatic complex that is located in the mitochondrial inner membrane of eukaryotes and in the plasma membrane of aerobic prokaryotes. The core structure of prokaryotic and eukaryotic cytochrome c oxidase contains three common subunits, I, II and III. In prokaryotes, subunits I and III can be fused and a fourth subunit is sometimes found, whereas in eukaryotes there are a variable number of additional small subunits.
As the bacterial respiratory systems are branched, they have a number of distinct terminal oxidases, rather than the single cytochrome c oxidase present in the eukaryotic mitochondrial systems. Although the cytochrome o oxidases do not catalyze the cytochrome c but the quinol (ubiquinol) oxidation they belong to the same haem-copper oxidase superfamily as cytochrome c oxidases. Members of this family share sequence similarities in all three core subunits: subunit I is the most conserved subunit, whereas subunit II is the least conserved.
Mutations in mtDNA-encoded cytochrome c oxidase subunit genes have been observed to be associated with isolated myopathy, severe encephalomyopathy, Leber hereditary optic neuropathy, mitochondrial complex IV deficiency, and recurrent myoglobinuria .
Leber hereditary optic neuropathy (LHON)
LHON is a maternally inherited disease resulting in acute or subacute loss of central vision, due to optic nerve dysfunction. Cardiac conduction defects and neurological defects have also been described in some patients. LHON results from primary mitochondrial DNA mutations affecting the respiratory chain complexes. Mutations at positions 9438 and 9804, which result in glycine-78 to serine and alanine-200 to threonine amino acid changes, have been associated with this disease.
Mitochondrial complex IV deficiency (MT-C4D)
Complex IV deficiency (COX deficiency) is a disorder of the mitochondrial respiratory chain with heterogeneous clinical manifestations, ranging from isolated myopathy to severe multisystem disease affecting several tissues and organs. Features include hypertrophic cardiomyopathy, hepatomegaly and liver dysfunction, hypotonia, muscle weakness, exercise intolerance, developmental delay, delayed motor development, mental retardation, lactic acidemia, encephalopathy, ataxia, and cardiac arrhythmia. Some affected individuals manifest a fatal hypertrophic cardiomyopathy resulting in neonatal death and a subset of patients manifest Leigh syndrome. The mutations G7970T and G9952A have been associated with this disease.
Recurrent myoglobinuria mitochondrial (RM-MT)
Recurrent myoglobinuria is characterized by recurrent attacks of rhabdomyolysis (necrosis or disintegration of skeletal muscle) associated with muscle pain and weakness, and followed by excretion of myoglobin in the urine. It has been associated with mitochondrial complex IV deficiency.
- Cytochrome o ubiquinol oxidase, subunit III InterPro: IPR014206
- Cytochrome aa3 quinol oxidase, subunit III InterPro: IPR014246
- GRCh38: Ensembl release 89: ENSG00000198938 - Ensembl, May 2017
- GRCm38: Ensembl release 89: ENSMUSG00000064358 - Ensembl, May 2017
- "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
- "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
- Miki K, Sogabe S, Uno A, Ezoe T, Kasai N, Saeda M, Matsuura Y, Miki M (May 1994). "Application of an automatic molecular-replacement procedure to crystal structure analysis of cytochrome c2 from Rhodopseudomonas viridis". Acta Crystallographica Section D. 50 (Pt 3): 271â€“5. doi:10.1107/S0907444993013952. PMID 15299438.
- "Entrez Gene: COX3 cytochrome c oxidase subunit III". This article incorporates text from this source, which is in the public domain.
- HorvÃ¡th R, Schoser BG, MÃ¼ller-HÃ¶cker J, VÃ¶lpel M, Jaksch M, LochmÃ¼ller H (December 2005). "Mutations in mtDNA-encoded cytochrome c oxidase subunit genes causing isolated myopathy or severe encephalomyopathy". Neuromuscular Disorders. 15 (12): 851â€“7. doi:10.1016/j.nmd.2005.09.005. PMID 16288875.
- "MT-CO3 - Cytochrome c oxidase subunit 3 - Homo sapiens (Human) - MT-CO3 gene & protein". www.uniprot.org. Retrieved 2018-08-21. This article incorporates text available under the CC BY 4.0 license.
- "UniProt: the universal protein knowledgebase". Nucleic Acids Research. 45 (D1): D158â€“D169. January 2017. doi:10.1093/nar/gkw1099. PMC 5210571. PMID 27899622.
- Yao, Daniel. "Cardiac Organellar Protein Atlas Knowledgebase (COPaKB) â€”â€” Protein Information". amino.heartproteome.org. Retrieved 2018-08-21.
- Zong NC, Li H, Li H, Lam MP, Jimenez RC, Kim CS, Deng N, Kim AK, Choi JH, Zelaya I, Liem D, Meyer D, Odeberg J, Fang C, Lu HJ, Xu T, Weiss J, Duan H, Uhlen M, Yates JR, Apweiler R, Ge J, Hermjakob H, Ping P (October 2013). "Integration of cardiac proteome biology and medicine by a specialized knowledgebase". Circulation Research. 113 (9): 1043â€“53. doi:10.1161/CIRCRESAHA.113.301151. PMC 4076475. PMID 23965338.
- Michel H (November 1999). "Cytochrome c oxidase: catalytic cycle and mechanisms of proton pumping--a discussion". Biochemistry. 38 (46): 15129â€“40. doi:10.1021/bi9910934. PMID 10563795.
- Belevich I, Verkhovsky MI, WikstrÃ¶m M (April 2006). "Proton-coupled electron transfer drives the proton pump of cytochrome c oxidase". Nature. 440 (7085): 829â€“32. doi:10.1038/nature04619. PMID 16598262.
- Mather MW, Springer P, Hensel S, Buse G, Fee JA (March 1993). "Cytochrome oxidase genes from Thermus thermophilus. Nucleotide sequence of the fused gene and analysis of the deduced primary structures for subunits I and III of cytochrome caa3". The Journal of Biological Chemistry. 268 (8): 5395â€“408. PMID 8383670.
- Santana M, Kunst F, Hullo MF, Rapoport G, Danchin A, Glaser P (May 1992). "Molecular cloning, sequencing, and physiological characterization of the qox operon from Bacillus subtilis encoding the aa3-600 quinol oxidase". The Journal of Biological Chemistry. 267 (15): 10225â€“31. PMID 1316894.
- Chepuri V, Lemieux L, Au DC, Gennis RB (July 1990). "The sequence of the cyo operon indicates substantial structural similarities between the cytochrome o ubiquinol oxidase of Escherichia coli and the aa3-type family of cytochrome c oxidases". The Journal of Biological Chemistry. 265 (19): 11185â€“92. PMID 2162835.
- GarcÃa-Horsman JA, Barquera B, Rumbley J, Ma J, Gennis RB (September 1994). "The superfamily of heme-copper respiratory oxidases". Journal of Bacteriology. 176 (18): 5587â€“600. doi:10.1128/jb.176.18.5587-5600.1994. PMC 196760. PMID 8083153.
- Johns DR, Neufeld MJ (October 1993). "Cytochrome c oxidase mutations in Leber hereditary optic neuropathy". Biochemical and Biophysical Research Communications. 196 (2): 810â€“5. doi:10.1006/bbrc.1993.2321. PMID 8240356.
- Hanna MG, Nelson IP, Rahman S, Lane RJ, Land J, Heales S, Cooper MJ, Schapira AH, Morgan-Hughes JA, Wood NW (July 1998). "Cytochrome c oxidase deficiency associated with the first stop-codon point mutation in human mtDNA". American Journal of Human Genetics. 63 (1): 29â€“36. doi:10.1086/301910. PMC 1377234. PMID 9634511.
- Keightley JA, Hoffbuhr KC, Burton MD, Salas VM, Johnston WS, Penn AM, Buist NR, Kennaway NG (April 1996). "A microdeletion in cytochrome c oxidase (COX) subunit III associated with COX deficiency and recurrent myoglobinuria". Nature Genetics. 12 (4): 410â€“6. doi:10.1038/ng0496-410. PMID 8630495.
- "2 binary interactions found for search term COX3". IntAct Molecular Interaction Database. EMBL-EBI. Retrieved 2018-08-21.
- Moraes CT, Andreetta F, Bonilla E, Shanske S, DiMauro S, Schon EA (March 1991). "Replication-competent human mitochondrial DNA lacking the heavy-strand promoter region". Molecular and Cellular Biology. 11 (3): 1631â€“7. doi:10.1128/MCB.11.3.1631. PMC 369459. PMID 1996112.
- Chomyn A, Cleeter MW, Ragan CI, Riley M, Doolittle RF, Attardi G (October 1986). "URF6, last unidentified reading frame of human mtDNA, codes for an NADH dehydrogenase subunit". Science. 234 (4776): 614â€“8. doi:10.1126/science.3764430. PMID 3764430.
- Chomyn A, Mariottini P, Cleeter MW, Ragan CI, Matsuno-Yagi A, Hatefi Y, Doolittle RF, Attardi G (1985). "Six unidentified reading frames of human mitochondrial DNA encode components of the respiratory-chain NADH dehydrogenase". Nature. 314 (6012): 592â€“7. doi:10.1038/314592a0. PMID 3921850.
- Anderson S, Bankier AT, Barrell BG, de Bruijn MH, Coulson AR, Drouin J, Eperon IC, Nierlich DP, Roe BA, Sanger F, Schreier PH, Smith AJ, Staden R, Young IG (April 1981). "Sequence and organization of the human mitochondrial genome". Nature. 290 (5806): 457â€“65. doi:10.1038/290457a0. PMID 7219534.
- Montoya J, Ojala D, Attardi G (April 1981). "Distinctive features of the 5'-terminal sequences of the human mitochondrial mRNAs". Nature. 290 (5806): 465â€“70. doi:10.1038/290465a0. PMID 7219535.
- Andrews RM, Kubacka I, Chinnery PF, Lightowlers RN, Turnbull DM, Howell N (October 1999). "Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA". Nature Genetics. 23 (2): 147. doi:10.1038/13779. PMID 10508508.
- Ingman M, Kaessmann H, PÃ¤Ã¤bo S, Gyllensten U (December 2000). "Mitochondrial genome variation and the origin of modern humans". Nature. 408 (6813): 708â€“13. doi:10.1038/35047064. PMID 11130070.
- Maca-Meyer N, GonzÃ¡lez AM, Larruga JM, Flores C, Cabrera VM (2003). "Major genomic mitochondrial lineages delineate early human expansions". BMC Genetics. 2: 13. doi:10.1186/1471-2156-2-13. PMC 55343. PMID 11553319.
- Herrnstadt C, Elson JL, Fahy E, Preston G, Turnbull DM, Anderson C, Ghosh SS, Olefsky JM, Beal MF, Davis RE, Howell N (May 2002). "Reduced-median-network analysis of complete mitochondrial DNA coding-region sequences for the major African, Asian, and European haplogroups". American Journal of Human Genetics. 70 (5): 1152â€“71. doi:10.1086/339933. PMC 447592. PMID 11938495.
- Silva WA, Bonatto SL, Holanda AJ, Ribeiro-Dos-Santos AK, PaixÃ£o BM, Goldman GH, Abe-Sandes K, Rodriguez-Delfin L, Barbosa M, PaÃ§Ã³-Larson ML, Petzl-Erler ML, Valente V, Santos SE, Zago MA (July 2002). "Mitochondrial genome diversity of Native Americans supports a single early entry of founder populations into America". American Journal of Human Genetics. 71 (1): 187â€“92. doi:10.1086/341358. PMC 384978. PMID 12022039.
- Elkon H, Don J, Melamed E, Ziv I, Shirvan A, Offen D (June 2002). "Mutant and wild-type alpha-synuclein interact with mitochondrial cytochrome C oxidase". Journal of Molecular Neuroscience. 18 (3): 229â€“38. doi:10.1385/JMN:18:3:229. PMID 12059041.
- Mishmar D, Ruiz-Pesini E, Golik P, Macaulay V, Clark AG, Hosseini S, Brandon M, Easley K, Chen E, Brown MD, Sukernik RI, Olckers A, Wallace DC (January 2003). "Natural selection shaped regional mtDNA variation in humans". Proceedings of the National Academy of Sciences of the United States of America. 100 (1): 171â€“6. doi:10.1073/pnas.0136972100. PMC 140917. PMID 12509511.
- Ingman M, Gyllensten U (July 2003). "Mitochondrial genome variation and evolutionary history of Australian and New Guinean aborigines". Genome Research. 13 (7): 1600â€“6. doi:10.1101/gr.686603. PMC 403733. PMID 12840039.
- Kong QP, Yao YG, Sun C, Bandelt HJ, Zhu CL, Zhang YP (September 2003). "Phylogeny of east Asian mitochondrial DNA lineages inferred from complete sequences". American Journal of Human Genetics. 73 (3): 671â€“6. doi:10.1086/377718. PMC 1180693. PMID 12870132.
- Temperley RJ, Seneca SH, Tonska K, Bartnik E, Bindoff LA, Lightowlers RN, Chrzanowska-Lightowlers ZM (September 2003). "Investigation of a pathogenic mtDNA microdeletion reveals a translation-dependent deadenylation decay pathway in human mitochondria". Human Molecular Genetics. 12 (18): 2341â€“8. doi:10.1093/hmg/ddg238. PMID 12915481.
- Maca-Meyer N, GonzÃ¡lez AM, Pestano J, Flores C, Larruga JM, Cabrera VM (October 2003). "Mitochondrial DNA transit between West Asia and North Africa inferred from U6 phylogeography". BMC Genetics. 4: 15. doi:10.1186/1471-2156-4-15. PMC 270091. PMID 14563219.
- Coble MD, Just RS, O'Callaghan JE, Letmanyi IH, Peterson CT, Irwin JA, Parsons TJ (June 2004). "Single nucleotide polymorphisms over the entire mtDNA genome that increase the power of forensic testing in Caucasians". International Journal of Legal Medicine. 118 (3): 137â€“46. doi:10.1007/s00414-004-0427-6. PMID 14760490.
- Palanichamy MG, Sun C, Agrawal S, Bandelt HJ, Kong QP, Khan F, Wang CY, Chaudhuri TK, Palla V, Zhang YP (December 2004). "Phylogeny of mitochondrial DNA macrohaplogroup N in India, based on complete sequencing: implications for the peopling of South Asia". American Journal of Human Genetics. 75 (6): 966â€“78. doi:10.1086/425871. PMC 1182158. PMID 15467980.
- Starikovskaya EB, Sukernik RI, Derbeneva OA, Volodko NV, Ruiz-Pesini E, Torroni A, Brown MD, Lott MT, Hosseini SH, Huoponen K, Wallace DC (January 2005). "Mitochondrial DNA diversity in indigenous populations of the southern extent of Siberia, and the origins of Native American haplogroups". Annals of Human Genetics. 69 (Pt 1): 67â€“89. doi:10.1046/j.1529-8817.2003.00127.x. PMC 3905771. PMID 15638829.
- Rajkumar R, Banerjee J, Gunturi HB, Trivedi R, Kashyap VK (April 2005). "Phylogeny and antiquity of M macrohaplogroup inferred from complete mt DNA sequence of Indian specific lineages". BMC Evolutionary Biology. 5: 26. doi:10.1186/1471-2148-5-26. PMC 1079809. PMID 15804362.
This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.
Cytochrome c oxidase subunit III Provide feedback
No Pfam abstract.
Tsukihara T, Aoyama H, Yamashita E, Tomizaki T, Yamaguchi H, Shinzawa-Itoh K, Nakashima R, Yaono R, Yoshikawa S; , Science 1996;272:1136-1144.: The whole structure of the 13-subunit oxidized cytochrome c oxidase at 2.8 A. PUBMED:8638158 EPMC:8638158
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This tab holds annotation information from the InterPro database.
InterPro entry IPR000298
Cytochrome c oxidase ( EC ) is the terminal enzyme of the respiratory chain of mitochondria and many aerobic bacteria. It catalyses the transfer of electrons from reduced cytochrome c to molecular oxygen:
Cytochrome c oxidase is an oligomeric enzymatic complex that is located in the mitochondrial inner membrane of eukaryotes and in the plasma membrane of aerobic prokaryotes. The core structure of prokaryotic and eukaryotic cytochrome c oxidase contains three common subunits, I, II and III. In prokaryotes, subunits I and III can be fused and a fourth subunit is sometimes found, whereas in eukaryotes there are a variable number of additional small polypeptidic subunits [ PUBMED:8383670 ]. The functional role of subunit III is not yet understood.
As the bacterial respiratory systems are branched, they have a number of distinct terminal oxidases, rather than the single cytochrome c oxidase present in the eukaryotic mitochondrial systems. Even though the cytochrome o complex oxidises quinol (ubiquinol) and does not catalyse the oxidation of reduced cytochrome c, they belong to the same haem-copper oxidase superfamily as cytochrome c oxidases. Members of this family share sequence similarities in all three core subunits: subunit I is the most conserved subunit, whereas subunit II is the least conserved [ PUBMED:1316894 , PUBMED:2162835 , PUBMED:8083153 ].
This entry represents a structural domain found in cytochrome c and ubiquinol oxidase subunit III. The overall structure of these enzymes is similar [ PUBMED:11017202 ].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Cellular component||membrane (GO:0016020)|
|Molecular function||heme-copper terminal oxidase activity (GO:0015002)|
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Key: available, not generated, — not available.
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|Seed source:||Pfam-B_78 (release 1.0)|
|Number in seed:||8|
|Number in full:||10603|
|Average length of the domain:||189.80 aa|
|Average identity of full alignment:||27 %|
|Average coverage of the sequence by the domain:||84.76 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||20|
|Download:||download the raw HMM for this family|
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Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
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The tree shows the occurrence of this domain across different species. More...
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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the COX3 domain has been found. There are 137 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.
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AlphaFold Structure Predictions
The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.