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124  structures 1323  species 0  interactions 3270  sequences 57  architectures

Family: COX6B (PF02297)

Summary: Cytochrome oxidase c subunit VIb

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This is the Wikipedia entry entitled "Cytochrome c oxidase". More...

Cytochrome c oxidase Edit Wikipedia article

Cytochrome C Oxidase
Cytochrome C Oxidase 1OCC in Membrane 2.png
The crystal structure of bovine cytochrome c oxidase in a phospholipid bilayer. The intermembrane space lies to top of the image. Adapted from PDB: 1OCC​ (It is a homo dimer in this structure)
EC number1.9.3.1
CAS number9001-16-5
IntEnzIntEnz view
ExPASyNiceZyme view
MetaCycmetabolic pathway
PDB structuresRCSB PDB PDBe PDBsum
Gene OntologyAmiGO / QuickGO
Cytochrome c oxidase
Subunit I and II of Complex IV excluding all other subunits, PDB: 2EIK
SymbolCytochrome c oxidase
OPM superfamily4
OPM protein2dyr

The enzyme cytochrome c oxidase or Complex IV, EC is a large transmembrane protein complex found in bacteria, archaea, and in eukaryotes[1] in their mitochondria.

It is the last enzyme in the respiratory electron transport chain of cells located in the membrane. It receives an electron from each of four cytochrome c molecules, and transfers them to one dioxygen molecule, converting the molecular oxygen to two molecules of water. In this process it binds four protons from the inner aqueous phase to make two water molecules, and translocates another four protons across the membrane, increasing the transmembrane difference of proton electrochemical potential which the ATP synthase then uses to synthesize ATP.


The complex

The complex is a large integral membrane protein composed of several metal prosthetic sites and 14 [2] protein subunits in mammals. In mammals, eleven subunits are nuclear in origin, and three are synthesized in the mitochondria. The complex contains two hemes, a cytochrome a and cytochrome a3, and two copper centers, the CuA and CuB centers.[3] In fact, the cytochrome a3 and CuB form a binuclear center that is the site of oxygen reduction. Cytochrome c, which is reduced by the preceding component of the respiratory chain (cytochrome bc1 complex, complex III), docks near the CuA binuclear center and passes an electron to it, being oxidized back to cytochrome c containing Fe3+. The reduced CuA binuclear center now passes an electron on to cytochrome a, which in turn passes an electron on to the cytochrome a3-CuB binuclear center. The two metal ions in this binuclear center are 4.5 Ã… apart and coordinate a hydroxide ion in the fully oxidized state.

Crystallographic studies of cytochrome c oxidase show an unusual post-translational modification, linking C6 of Tyr(244) and the ε-N of His(240) (bovine enzyme numbering). It plays a vital role in enabling the cytochrome a3- CuB binuclear center to accept four electrons in reducing molecular oxygen to water. The mechanism of reduction was formerly thought to involve a peroxide intermediate, which was believed to lead to superoxide production. However, the currently accepted mechanism involves a rapid four-electron reduction involving immediate oxygen-oxygen bond cleavage, avoiding any intermediate likely to form superoxide.[4]:865–866

The conserved subunits

Table of conserved subunits of cytochrome c oxidase complex[5][6]
No. Subunit name Human protein Protein description from UniProt Pfam family with Human protein
1 Cox1 COX1_HUMAN Cytochrome c oxidase subunit 1 Pfam PF00115
2 Cox2 COX2_HUMAN Cytochrome c oxidase subunit 2 Pfam PF02790, Pfam PF00116
3 Cox3 COX3_HUMAN Cytochrome c oxidase subunit 3 Pfam PF00510
4 Cox4i1 COX41_HUMAN Cytochrome c oxidase subunit 4 isoform 1, mitochondrial Pfam PF02936
5 Cox4a2 COX42_HUMAN Cytochrome c oxidase subunit 4 isoform 2, mitochondrial Pfam PF02936
6 Cox5a COX5A_HUMAN Cytochrome c oxidase subunit 5A, mitochondrial Pfam PF02284
7 Cox5b COX5B_HUMAN Cytochrome c oxidase subunit 5B, mitochondrial Pfam PF01215
8 Cox6a1 CX6A1_HUMAN Cytochrome c oxidase subunit 6A1, mitochondrial Pfam PF02046
9 Cox6a2 CX6A2_HUMAN Cytochrome c oxidase subunit 6A2, mitochondrial Pfam PF02046
10 Cox6b1 CX6B1_HUMAN Cytochrome c oxidase subunit 6B1 Pfam PF02297
11 Cox6b2 CX6B2_HUMAN Cytochrome c oxidase subunit 6B2 Pfam PF02297
12 Cox6c COX6C_HUMAN Cytochrome c oxidase subunit 6C Pfam PF02937
13 Cox7a1 CX7A1_HUMAN Cytochrome c oxidase subunit 7A1, mitochondrial Pfam PF02238
14 Cox7a2 CX7A2_HUMAN Cytochrome c oxidase subunit 7A2, mitochondrial Pfam PF02238
15 Cox7a3 COX7S_HUMAN Putative cytochrome c oxidase subunit 7A3, mitochondrial Pfam PF02238
16 Cox7b COX7B_HUMAN Cytochrome c oxidase subunit 7B, mitochondrial Pfam PF05392
17 Cox7c COX7C_HUMAN Cytochrome c oxidase subunit 7C, mitochondrial Pfam PF02935
18 Cox7r COX7R_HUMAN Cytochrome c oxidase subunit 7A-related protein, mitochondrial Pfam PF02238
19 Cox8a COX8A_HUMAN Cytochrome c oxidase subunit 8A, mitochondrial P Pfam PF02285
20 Cox8c COX8C_HUMAN Cytochrome c oxidase subunit 8C, mitochondrial Pfam PF02285
Assembly subunits[7][8][9]
1 Coa1 COA1_HUMAN Cytochrome c oxidase assembly factor 1 homolog Pfam PF08695
2 Coa3 COA3_HUMAN Cytochrome c oxidase assembly factor 3 homolog, mitochondrial Pfam PF09813
3 Coa4 COA4_HUMAN Cytochrome c oxidase assembly factor 4 homolog, mitochondrial Pfam PF06747
4 Coa5 COA5_HUMAN Cytochrome c oxidase assembly factor 5 Pfam PF10203
5 Coa6 COA6_HUMAN Cytochrome c oxidase assembly factor 6 homolog Pfam PF02297
6 Coa7 COA7_HUMAN Cytochrome c oxidase assembly factor 7, Pfam PF08238
7 Cox11 COX11_HUMAN Cytochrome c oxidase assembly protein COX11 mitochondrial Pfam PF04442
8 Cox14 COX14_HUMAN Cytochrome c oxidase assembly protein Pfam PF14880
9 Cox15 COX15_HUMAN Cytochrome c oxidase assembly protein COX15 homolog Pfam PF02628
10 Cox16 COX16_HUMAN Cytochrome c oxidase assembly protein COX16 homolog mitochondrial Pfam PF14138
11 Cox17 COX17_HUMAN Cytochrome c oxidase copper chaperone Pfam PF05051
12 Cox18[10] COX18_HUMAN Mitochondrial inner membrane protein (Cytochrome c oxidase assembly protein 18) Pfam PF02096
13 Cox19 COX19_HUMAN Cytochrome c oxidase assembly protein Pfam PF06747
14 Cox20 COX20_HUMAN Cytochrome c oxidase protein 20 homolog Pfam PF12597


COX assembly in yeast is a complex process that is not entirely understood due to the rapid and irreversible aggregation of hydrophobic subunits that form the holoenzyme complex, as well as aggregation of mutant subunits with exposed hydrophobic patches.[11] COX subunits are encoded in both the nuclear and mitochondrial genomes. The three subunits that form the COX catalytic core are encoded in the mitochondrial genome.

Hemes and cofactors are inserted into subunits I & II. The two heme molecules reside in subunit I, helping with transport to subunit II where two copper molecules aid with the continued transfer of electrons.[12] Subunits I and IV initiate assembly. Different subunits may associate to form sub-complex intermediates that later bind to other subunits to form the COX complex.[11] In post-assembly modifications, COX will form a homodimer. This is required for activity. Both dimers are connected by a cardiolipin molecule,[11][13][14] which has been found to play a key role in stabilization of the holoenzyme complex. The dissociation of subunits VIIa and III in conjunction with the removal of cardiolipin results in total loss of enzyme activity.[14] Subunits encoded in the nuclear genome are known to play a role in enzyme dimerization and stability. Mutations to these subunits eliminate COX function.[11]

Assembly is known to occur in at least three distinct rate-determining steps. The products of these steps have been found, though specific subunit compositions have not been determined.[11]

Synthesis and assembly of COX subunits I, II, and III are facilitated by translational activators, which interact with the 5’ untranslated regions of mitochondrial mRNA transcripts. Translational activators are encoded in the nucleus. They can operate through either direct or indirect interaction with other components of translation machinery, but exact molecular mechanisms are unclear due to difficulties associated with synthesizing translation machinery in-vitro.[15][16] Though the interactions between subunits I, II, and III encoded within the mitochondrial genome make a lesser contribution to enzyme stability than interactions between bigenomic subunits, these subunits are more conserved, indicating potential unexplored roles for enzyme activity.[17]


Summary reaction:

4 Fe2+-cytochrome c + 8 H+in + O2 → 4 Fe3+-cytochrome c + 2 H2O + 4 H+out

Two electrons are passed from two cytochrome c's, through the CuA and cytochrome a sites to the cytochrome a3- CuB binuclear center, reducing the metals to the Fe2+ form and Cu+. The hydroxide ligand is protonated and lost as water, creating a void between the metals that is filled by O2. The oxygen is rapidly reduced, with two electrons coming from the Fe2+cytochrome a3, which is converted to the ferryl oxo form (Fe4+=O). The oxygen atom close to CuB picks up one electron from Cu+, and a second electron and a proton from the hydroxyl of Tyr(244), which becomes a tyrosyl radical: The second oxygen is converted to a hydroxide ion by picking up two electrons and a proton. A third electron arising from another cytochrome c is passed through the first two electron carriers to the cytochrome a3- CuB binuclear center, and this electron and two protons convert the tyrosyl radical back to Tyr, and the hydroxide bound to CuB2+ to a water molecule. The fourth electron from another cytochrome c flows through CuA and cytochrome a to the cytochrome a3- CuB binuclear center, reducing the Fe4+=O to Fe3+, with the oxygen atom picking up a proton simultaneously, regenerating this oxygen as a hydroxide ion coordinated in the middle of the cytochrome a3- CuB center as it was at the start of this cycle. The net process is that four reduced cytochrome c's are used, along with 4 protons, to reduce O2 to two water molecules.[4]:841–5


COX exists in three conformational states: fully oxidized (pulsed), partially reduced, and fully reduced. Each inhibitor has a high affinity to a different state. In the pulsed state, both the heme a3 and the CuB nuclear centers are oxidized; this is the conformation of the enzyme that has the highest activity. A two-electron reduction initiates a conformational change that allows oxygen to bind at the active site to the partially-reduced enzyme. Four electrons bind to COX to fully reduce the enzyme. Its fully reduced state, which consists of a reduced Fe2+ at the cytochrome a3 heme group and a reduced CuB+ binuclear center, is considered the inactive or resting state of the enzyme.[18]

Cyanide, azide, and carbon monoxide[19] all bind to cytochrome c oxidase, inhibiting the protein from functioning and leading to the chemical asphyxiation of cells. Higher concentrations of molecular oxygen are needed to compensate for increasing inhibitor concentrations, leading to an overall reduction in metabolic activity in the cell in the presence of an inhibitor. Other ligands, such as nitric oxide and hydrogen sulfide, can also inhibit COX by binding to regulatory sites on the enzyme, reducing the rate of cellular respiration.[20]

Cyanide is a non-competitive inhibitor for COX,[21][22] binding with high affinity to the partially-reduced state of the enzyme and hindering further reduction of the enzyme. In the pulsed state, cyanide binds slowly, but with high affinity. The ligand is posited to electrostatically stabilize both metals at once by positioning itself between them. A high nitric oxide concentration, such as one added exogenously to the enzyme, reverses cyanide inhibition of COX.[23]

Nitric oxide can reversibly[24] bind to either metal ion in the binuclear center to be oxidized to nitrite. NO and CN will compete with oxygen to bind at the site, reducing the rate of cellular respiration. Endogenous NO, however, which is produced at lower levels, augments CN inhibition. Higher levels of NO, which correlate with the existence of more enzyme in the reduced state, lead to a greater inhibition of cyanide.[18] At these basal concentrations, NO inhibition of Complex IV is known to have beneficial effects, such as increasing oxygen levels in blood vessel tissues. The inability of the enzyme to reduce oxygen to water results in a buildup of oxygen, which can diffuse deeper into surrounding tissues.[24] NO inhibition of Complex IV has a larger effect at lower oxygen concentrations, increasing its utility as a vasodilator in tissues of need.[24]

Hydrogen sulfide will bind COX in a noncompetitive fashion at a regulatory site on the enzyme, similar to carbon monoxide. Sulfide has the highest affinity to either the pulsed or partially reduced states of the enzyme, and is capable of partially reducing the enzyme at the heme a3 center. It is unclear whether endogenous H2S levels are sufficient to inhibit the enzyme. There is no interaction between hydrogen sulfide and the fully reduced conformation of COX.[20]

Methanol in methylated spirits is converted into formic acid, which also inhibits the same oxidase system. High levels of ATP can allosterically inhibit cytochrome c oxidase, binding from within the mitochondrial matrix.[25]

Extramitochondrial and subcellular localizations

Location of the 3 cytochrome c oxidase subunit genes in the human mitochondrial genome: COXI, COXII, and COXIII (orange boxes).

Cytochrome c oxidase has 3 subunits which are encoded by mitochondrial DNA (cytochrome c oxidase subunit I, subunit II, and subunit III). Of these 3 subunits encoded by mitochondrial DNA, two have been identified in extramitochondrial locations. In pancreatic acinar tissue, these subunits were found in zymogen granules. Additionally, in the anterior pituitary, relatively high amounts of these subunits were found in growth hormone secretory granules.[26] The extramitochondrial function of these cytochrome c oxidase subunits has not yet been characterized. Besides cytochrome c oxidase subunits, extramitochondrial localization has also been observed for large numbers of other mitochondrial proteins.[27][28] This raises the possibility about existence of yet unidentified specific mechanisms for protein translocation from mitochondria to other cellular destinations.[26][28][29]

Genetic defects and disorders

Defects involving genetic mutations altering cytochrome c oxidase (COX) functionality or structure can result in severe, often fatal metabolic disorders. Such disorders usually manifest in early childhood and affect predominantly tissues with high energy demands (brain, heart, muscle). Among the many classified mitochondrial diseases, those involving dysfunctional COX assembly are thought to be the most severe.[30]

The vast majority of COX disorders are linked to mutations in nuclear-encoded proteins referred to as assembly factors, or assembly proteins. These assembly factors contribute to COX structure and functionality, and are involved in several essential processes, including transcription and translation of mitochondrion-encoded subunits, processing of preproteins and membrane insertion, and cofactor biosynthesis and incorporation.[31]

Currently, mutations have been identified in seven COX assembly factors: SURF1, SCO1, SCO2, COX10, COX15, COX20, COA5 and LRPPRC. Mutations in these proteins can result in altered functionality of sub-complex assembly, copper transport, or translational regulation. Each gene mutation is associated with the etiology of a specific disease, with some having implications in multiple disorders. Disorders involving dysfunctional COX assembly via gene mutations include Leigh syndrome, cardiomyopathy, leukodystrophy, anemia, and sensorineural deafness.


The increased reliance of neurons on oxidative phosphorylation for energy[32] facilitates the use of COX histochemistry in mapping regional brain metabolism in animals, since it establishes a direct and positive correlation between enzyme activity and neuronal activity.[33] This can be seen in the correlation between COX enzyme amount and activity, which indicates the regulation of COX at the level of gene expression. COX distribution is inconsistent across different regions of the animal brain, but its pattern of its distribution is consistent across animals. This pattern has been observed in the monkey, mouse, and calf brain. One isozyme of COX has been consistently detected in histochemical analysis of the brain.[34]

Such brain mapping has been accomplished in spontaneous mutant mice with cerebellar disease such as reeler[35] and a transgenic model of Alzheimer's disease.[36] This technique has also been used to map learning activity in animal brain.[37]

Additional images

See also


  1. ^ Castresana J, Lübben M, Saraste M, Higgins DG (June 1994). "Evolution of cytochrome oxidase, an enzyme older than atmospheric oxygen". The EMBO Journal. 13 (11): 2516–25. doi:10.1002/j.1460-2075.1994.tb06541.x. PMC 395125. PMID 8013452.
  2. ^ Balsa E, Marco R, Perales-Clemente E, Szklarczyk R, Calvo E, Landázuri MO, Enríquez JA (September 2012). "NDUFA4 is a subunit of complex IV of the mammalian electron transport chain". Cell Metabolism. 16 (3): 378–86. doi:10.1016/j.cmet.2012.07.015. PMID 22902835.
  3. ^ Tsukihara T, Aoyama H, Yamashita E, Tomizaki T, Yamaguchi H, Shinzawa-Itoh K, Nakashima R, Yaono R, Yoshikawa S (August 1995). "Structures of metal sites of oxidized bovine heart cytochrome c oxidase at 2.8 A". Science. 269 (5227): 1069–74. Bibcode:1995Sci...269.1069T. doi:10.1126/science.7652554. PMID 7652554.
  4. ^ a b Voet D, Voet JG (2011). Biochemistry (4th ed.). Hoboken, NJ: John Wiley & Sons. ISBN 978-0-470-57095-1.
  5. ^ Zhang Z, Huang L, Shulmeister VM, Chi YI, Kim KK, Hung LW, Crofts AR, Berry EA, Kim SH (April 1998). "Electron transfer by domain movement in cytochrome bc1". Nature. 392 (6677): 677–84. Bibcode:1998Natur.392..677Z. doi:10.1038/33612. PMID 9565029.
  6. ^ Kaila VR, Oksanen E, Goldman A, Bloch DA, Verkhovsky MI, Sundholm D, Wikström M (July 2011). "A combined quantum chemical and crystallographic study on the oxidized binuclear center of cytochrome c oxidase". Biochimica et Biophysica Acta. 1807 (7): 769–78. doi:10.1016/j.bbabio.2010.12.016. PMID 21211513.
  7. ^ Szklarczyk R, Wanschers BF, Cuypers TD, Esseling JJ, Riemersma M, van den Brand MA, Gloerich J, Lasonder E, van den Heuvel LP, Nijtmans LG, Huynen MA (February 2012). "Iterative orthology prediction uncovers new mitochondrial proteins and identifies C12orf62 as the human ortholog of COX14, a protein involved in the assembly of cytochrome c oxidase". Genome Biology. 13 (2): R12. doi:10.1186/gb-2012-13-2-r12. PMC 3334569. PMID 22356826.
  8. ^ Mick DU, Dennerlein S, Wiese H, Reinhold R, Pacheu-Grau D, Lorenzi I, Sasarman F, Weraarpachai W, Shoubridge EA, Warscheid B, Rehling P (December 2012). "MITRAC links mitochondrial protein translocation to respiratory-chain assembly and translational regulation". Cell. 151 (7): 1528–41. doi:10.1016/j.cell.2012.11.053. PMID 23260140.
  9. ^ Kozjak-Pavlovic V, Prell F, Thiede B, Götz M, Wosiek D, Ott C, Rudel T (February 2014). "C1orf163/RESA1 is a novel mitochondrial intermembrane space protein connected to respiratory chain assembly". Journal of Molecular Biology. 426 (4): 908–20. doi:10.1016/j.jmb.2013.12.001. PMID 24333015.
  10. ^ Gaisne M, Bonnefoy N (September 2006). "The COX18 gene, involved in mitochondrial biogenesis, is functionally conserved and tightly regulated in humans and fission yeast". FEMS Yeast Research. 6 (6): 869–82. doi:10.1111/j.1567-1364.2006.00083.x. PMID 16911509.
  11. ^ a b c d e Fontanesi F, Soto IC, Horn D, Barrientos A (December 2006). "Assembly of mitochondrial cytochrome c-oxidase, a complicated and highly regulated cellular process". American Journal of Physiology. Cell Physiology. 291 (6): C1129–47. doi:10.1152/ajpcell.00233.2006. PMID 16760263.
  12. ^ Crofts A (1996). "Cytochrome oxidase: Complex IV". University of Illinois at Urbana-Champaign.
  13. ^ Khalimonchuk O, Rödel G (December 2005). "Biogenesis of cytochrome c oxidase". Mitochondrion. 5 (6): 363–88. doi:10.1016/j.mito.2005.08.002. PMID 16199211.
  14. ^ a b Sedlák E, Robinson NC (September 2015). "Destabilization of the Quaternary Structure of Bovine Heart Cytochrome c Oxidase upon Removal of Tightly Bound Cardiolipin". Biochemistry. 54 (36): 5569–77. doi:10.1021/acs.biochem.5b00540. PMID 26284624.
  15. ^ Herrmann JM, Woellhaf MW, Bonnefoy N (February 2013). "Control of protein synthesis in yeast mitochondria: the concept of translational activators". Biochimica et Biophysica Acta. 1833 (2): 286–94. doi:10.1016/j.bbamcr.2012.03.007. PMID 22450032.
  16. ^ Soto IC, Fontanesi F, Liu J, Barrientos A (June 2012). "Biogenesis and assembly of eukaryotic cytochrome c oxidase catalytic core". Biochimica et Biophysica Acta. 1817 (6): 883–97. doi:10.1016/j.bbabio.2011.09.005. PMC 3262112. PMID 21958598.
  17. ^ Aledo JC, Valverde H, Ruíz-Camacho M, Morilla I, López FD (October 2014). "Protein-protein interfaces from cytochrome c oxidase I evolve faster than nonbinding surfaces, yet negative selection is the driving force". Genome Biology and Evolution. 6 (11): 3064–76. doi:10.1093/gbe/evu240. PMC 4255772. PMID 25359921.
  18. ^ a b Leavesley HB, Li L, Prabhakaran K, Borowitz JL, Isom GE (January 2008). "Interaction of cyanide and nitric oxide with cytochrome c oxidase: implications for acute cyanide toxicity". Toxicological Sciences. 101 (1): 101–11. doi:10.1093/toxsci/kfm254. PMID 17906319.
  19. ^ Alonso JR, Cardellach F, López S, Casademont J, Miró O (September 2003). "Carbon monoxide specifically inhibits cytochrome c oxidase of human mitochondrial respiratory chain". Pharmacology & Toxicology. 93 (3): 142–6. doi:10.1034/j.1600-0773.2003.930306.x. PMID 12969439.
  20. ^ a b Nicholls P, Marshall DC, Cooper CE, Wilson MT (October 2013). "Sulfide inhibition of and metabolism by cytochrome c oxidase". Biochemical Society Transactions. 41 (5): 1312–6. doi:10.1042/BST20130070. PMID 24059525.
  21. ^ Roberts M, Reiss MJ, Monger G (2000). Advanced Biology. Nelson Thornes. ISBN 9780174387329.
  22. ^ Roberts MB (1986). Biology: A Functional Approach. Nelson Thornes. ISBN 9780174480198.
  23. ^ Jensen P, Wilson MT, Aasa R, Malmström BG (December 1984). "Cyanide inhibition of cytochrome c oxidase. A rapid-freeze e.p.r. investigation". The Biochemical Journal. 224 (3): 829–37. doi:10.1042/bj2240829. PMC 1144519. PMID 6098268.
  24. ^ a b c Gladwin MT, Shiva S (May 2009). "The ligand binding battle at cytochrome c oxidase: how NO regulates oxygen gradients in tissue". Circulation Research. 104 (10): 1136–8. doi:10.1161/CIRCRESAHA.109.198911. PMID 19461104.
  25. ^ Arnold S, Kadenbach B (October 1997). "Cell respiration s controlled by ATP, an allosteric inhibitor of cytochrome-c oxidase". Eur J Biochem. 249 (1): 350–354. doi:10.1111/j.1432-1033.1997.t01-1-00350.x. PMID 9363790.
  26. ^ a b Sadacharan SK, Singh B, Bowes T, Gupta RS (November 2005). "Localization of mitochondrial DNA encoded cytochrome c oxidase subunits I and II in rat pancreatic zymogen granules and pituitary growth hormone granules". Histochemistry and Cell Biology. 124 (5): 409–21. doi:10.1007/s00418-005-0056-2. PMID 16133117.
  27. ^ Gupta RS, Ramachandra NB, Bowes T, Singh B (2008). "Unusual cellular disposition of the mitochondrial molecular chaperones Hsp60, Hsp70 and Hsp10". Novartis Foundation Symposium. Novartis Foundation Symposia. 291: 59–68, discussion 69–73, 137–40. doi:10.1002/9780470754030.ch5. ISBN 9780470754030. PMID 18575266.
  28. ^ a b Soltys BJ, Gupta RS (1999). "Mitochondrial proteins at unexpected cellular locations: export of proteins from mitochondria from an evolutionary perspective". International Review of Cytology. 194: 133–96. doi:10.1016/S0074-7696(08)62396-7. ISBN 9780123645982. PMID 10494626.
  29. ^ Soltys BJ, Gupta RS (May 1999). "Mitochondrial-matrix proteins at unexpected locations: are they exported?". Trends in Biochemical Sciences. 24 (5): 174–7. doi:10.1016/s0968-0004(99)01390-0. PMID 10322429.
  30. ^ Pecina P, Houstková H, Hansíková H, Zeman J, Houstek J (2004). "Genetic defects of cytochrome c oxidase assembly" (PDF). Physiological Research. 53 Suppl 1: S213–23. PMID 15119951.
  31. ^ Zee JM, Glerum DM (December 2006). "Defects in cytochrome oxidase assembly in humans: lessons from yeast". Biochemistry and Cell Biology. 84 (6): 859–69. doi:10.1139/o06-201. PMID 17215873.
  32. ^ Johar K, Priya A, Dhar S, Liu Q, Wong-Riley MT (November 2013). "Neuron-specific specificity protein 4 bigenomically regulates the transcription of all mitochondria- and nucleus-encoded cytochrome c oxidase subunit genes in neurons". Journal of Neurochemistry. 127 (4): 496–508. doi:10.1111/jnc.12433. PMC 3820366. PMID 24032355.
  33. ^ Wong-Riley MT (March 1989). "Cytochrome oxidase: an endogenous metabolic marker for neuronal activity". Trends in Neurosciences. 12 (3): 94–101. doi:10.1016/0166-2236(89)90165-3. PMID 2469224.
  34. ^ Hevner RF, Wong-Riley MT (November 1989). "Brain cytochrome oxidase: purification, antibody production, and immunohistochemical/histochemical correlations in the CNS". The Journal of Neuroscience. 9 (11): 3884–98. doi:10.1523/jneurosci.09-11-03884.1989. PMC 6569932. PMID 2555458.
  35. ^ Strazielle C, Hayzoun K, Derer M, Mariani J, Lalonde R (April 2006). "Regional brain variations of cytochrome oxidase activity in Relnrl-orl mutant mice". Journal of Neuroscience Research. 83 (5): 821–31. doi:10.1002/jnr.20772. PMID 16511878.
  36. ^ Strazielle C, Sturchler-Pierrat C, Staufenbiel M, Lalonde R (2003). "Regional brain cytochrome oxidase activity in beta-amyloid precursor protein transgenic mice with the Swedish mutation". Neuroscience. 118 (4): 1151–63. doi:10.1016/S0306-4522(03)00037-X. PMID 12732258.
  37. ^ Conejo NM, González-Pardo H, Gonzalez-Lima F, Arias JL (March 2010). "Spatial learning of the water maze: progression of brain circuits mapped with cytochrome oxidase histochemistry". Neurobiology of Learning and Memory. 93 (3): 362–71. doi:10.1016/j.nlm.2009.12.002. PMID 19969098.

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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 oxidase c subunit VIb Provide feedback

Cytochrome c oxidase, a 13 sub-unit complex, EC: is the terminal oxidase in the mitochondrial electron transport chain. This family is composed of the potentially heme-binding subunit IVb of the oxidase.

Literature references

  1. Carrero-Valenzuela RD, Quan F, Lightowlers R, Kennaway NG, Litt M, Forte M; , Gene 1991;102:229-236.: Human cytochrome c oxidase subunit VIb: characterization and mapping of a multigene family. PUBMED:1651883 EPMC:1651883

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR003213

Cytochrome c oxidase ( EC ) is an oligomeric enzymatic complex that is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen [ PUBMED:6307356 ]. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane.

In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptide subunits. One of these subunits is the potentially haem-binding subunit, VIb, which is encoded in the nucleus [ PUBMED:11136449 ]. Subunit VIb is one of three mammalian subunits that lacks a transmembrane region. It is located on the cytosolic side of the membrane and helps form the dimer interface with the corresponding subunit on the other monomer complex [ PUBMED:12874793 , PUBMED:16364442 ].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

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Pfam Clan

This family is a member of clan CHCH (CL0351), which has the following description:

The conserved [coiled coil 1]-[helix 1]-[coiled coil 2]-[helix 2] domain (CHCH domain) superfamily members include NADH-ubiquinone oxidoreductases, some cytochrome oxidases and yeast mitochondrial ribosomal proteins. Within each helix of the CHCH domain there are two cysteines present in a C-X9-C motif.

The clan contains the following 8 members:



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HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...


This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Pfam-B_9188 (release 5.2)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Mian N , Bateman A
Number in seed: 57
Number in full: 3270
Average length of the domain: 66.70 aa
Average identity of full alignment: 31 %
Average coverage of the sequence by the domain: 53.63 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 26.0 26.0
Trusted cut-off 26.0 26.0
Noise cut-off 25.6 25.9
Model length: 76
Family (HMM) version: 19
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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Tree controls


The tree shows the occurrence of this domain across different species. More...


Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.


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 COX6B domain has been found. There are 124 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.

Protein Predicted structure External Information
A0A0G2JUM8 View 3D Structure Click here
A0A0R0FKK9 View 3D Structure Click here
A0A0R0FKP0 View 3D Structure Click here
A0A1D6P7V7 View 3D Structure Click here
A0A1D6Q4N8 View 3D Structure Click here
A0A1D8PQD5 View 3D Structure Click here
A0A1D8PU62 View 3D Structure Click here
B4FCQ4 View 3D Structure Click here
B6T8C0 View 3D Structure Click here
B7Z107 View 3D Structure Click here
B8A5J2 View 3D Structure Click here
D3ZD09 View 3D Structure Click here
G2TRP6 View 3D Structure Click here
I1JGN2 View 3D Structure Click here
I1JGV5 View 3D Structure Click here
I1LGX3 View 3D Structure Click here
I1LVX2 View 3D Structure Click here
I1MAW4 View 3D Structure Click here
O94581 View 3D Structure Click here
P14854 View 3D Structure Click here
P56391 View 3D Structure Click here
Q01519 View 3D Structure Click here
Q3E846 View 3D Structure Click here
Q54P95 View 3D Structure Click here
Q55CY6 View 3D Structure Click here
Q5JTJ3 View 3D Structure Click here
Q6DH63 View 3D Structure Click here
Q6KAE3 View 3D Structure Click here
Q6YFQ1 View 3D Structure Click here
Q6YFQ2 View 3D Structure Click here
Q6Z9E8 View 3D Structure Click here
Q7SXM1 View 3D Structure Click here
Q80ZN9 View 3D Structure Click here
Q8BGD8 View 3D Structure Click here
Q8IKG0 View 3D Structure Click here
Q8RXH9 View 3D Structure Click here
Q945L0 View 3D Structure Click here
Q9BL34 View 3D Structure Click here
Q9FE02 View 3D Structure Click here
Q9LPJ2 View 3D Structure Click here
Q9S7L9 View 3D Structure Click here
Q9SUD3 View 3D Structure Click here
Q9SXV0 View 3D Structure Click here
Q9VWD1 View 3D Structure Click here