3.D.4 The Proton-translocating Cytochrome Oxidase (COX) Superfamily

Multi-subunit enzyme complexes of the COX superfamily are found in bacteria, archaea and eukarya. These enzyme complexes reduce O2 to water and concomitantly pump four protons across the membrane. Specific proposals, based on the three-dimensional structure of the enzyme complex, have been put forth to explain proton pumping (Branden et al., 2006; Brzezinski, 2004; Namslauer et al., 2007). They possess a unique bimetallic active site consisting of a heme and a closely associated copper atom where O2 is reduced. The COX superfamily is therefore also called the heme-copper superfamily. Mitochondrial COX is also referred to as Mitochondrial Respiratory Complex IV. There are two main enzyme types in the COX superfamily which have distinct substrate specificities: cytochrome c oxidases and quinol oxidases. The reduced substrates of the latter enzymes are ubiquinol or menaquinol rather than reduced cytochrome c. Both types of oxidases pump protons. COX pumps one H+ per electron transferred to O2 (Brzezinski and Johansson, 2010).

Eukaryotic COX complexes contain 3 mitochondrially encoded subunits (I, II and III) and up to ten nuclearly-encoded subunits. All prokaryotic members of the COX superfamily contain homologues of subunit I and most also contain homologues of subunits II and III. The nuclearly-encoded subunits of the eukaryotic complexes are not found in bacteria. The cytochrome oxidases of Paracoccus denitrificans and Rhodobacter sphaeroides contain only 3 subunits, but they function as efficiently as the 13-subunit bovine enzyme complex. Some evidence suggests that the monomeric complex of the Rhodobacter enzyme is fully functional for electron flow and proton pumping in artificial membrane (Cvetkov and Prochaska, 2007). For Rhodobacter sphaeroides CytcO (cytochrome aa3), the E286 side chain of subunit I appears to be a branching point from which protons are shuttled either to the catalytic site for O2 reduction or to the acceptor site for pumped protons (Busenlehner et al., 2008). The 3-dimensional structures of the bovine and Paracoccus enzymes have been elucidated by x-ray crystallography. Liu et al. (2011) published crystallographic and online spectral evidence for the roles of conformational changes and conserved water in the Rhodobacter spheroides cytochrome oxidase proton pump.

The E. coli homologue, a ubiquinol oxidase, cytochrome bo, has homologues of subunits I, II and III. Subunits I of various COXs have at least twelve (but not more than 20) transmembrane spanners. Subunits I bind crucial prosthetic groups and probably provide the proton channel. The probable pathways of H+ translocation and the mechanism involved has been reviewed by Schultz and Chan (2001). Most phylogenetic analyses have been conducted with the sequences of subunits I and II. The cytochrome bd complex includes one of two homologous small subunit, either AppX or CydX.  Members of the CydX/AppX family of small proteins (30 - 50 aas with 1 TMS) interact with and activate the Cytochrome bd oxidase complex (TC# 3.D.4.3.2) (VanOrsdel et al. 2013).

In the chemolithotrophic, thermophilic, acidophilic crenarchaeota, Acidianus ambivalens, the essential residues comprising the H+ channel of the quinol oxidase (TC #3.D.4.9.1) are lacking, and the enzyme is believed to pump protons purely by chemical charge separation. In this six subunit enzyme complex, only the heme-bearing subunit I (DoxB) is demonstrably homologous to subunits in other quinol oxidases.

The bacterial respiratory nitric oxide reductase (NOR (3.D.4.10.1 and 2)) is a member of the super-family of O2-reducing, proton-pumping, heme-copper oxidases. Even though NO reduction is a highly exergonic reaction, NOR is not a proton pump and rather than taking up protons from the cytoplasmic (membrane potential negative) side of the membrane, like the heme-copper oxidases, NOR derives its substrate protons from the periplasmic (membrane potential positive) side of the membrane. In these complexes, Glu-122 in NorB contributes to defining the aperture of a non-electrogenic 'E-pathway' that serves to deliver protons from the periplasm to the buried active site in NOR (Flock et al., 2007).

Cytochrome c oxidase catalyses the one-electron oxidation of four molecules of cytochrome c and the four-electron reduction of O2 to water. Electron transfer through the enzyme is coupled to proton pumping across the membrane. Protons that are pumped as well as those that are used for O2 reduction are transferred though a specific intraprotein (D) pathway. Replacement of residue Asn139 by an Asp, at the beginning of the D pathway, results in blocking proton pumping without slowing uptake of substrate protons used for O2 reduction. Introduction of the acidic residue results in an increase of the apparent pK(a) of E286, an internal proton donor to the catalytic site, from 9.4 to ~11. Lepp et al (2008) investigated intramolecular electron and proton transfer in a mutant cytochrome c oxidase in which a neutral residue, Thr, was introduced at the 139 site. The mutation resulted in uncoupling of proton pumping from O2 reduction with a decrease in the apparent pK(a) of E286 from 9.4 to 7.6.

Human diseases associated with COX deficiency including encephalomyopathies, Leigh syndrome, hypertrophic cardiomyopathies, and fatal lactic acidosis are caused by mutations in COX subunits or assembly factors (Diaz, 2010).  A mutation in COA3 causes a phenotype characterised by neuropathy, exercise intolerance, obesity, and short stature (Ostergaard et al. 2015).

Heme-copper oxidases (HCuOs) terminate the respiratory chain in mitochondria and most bacteria. They are transmembrane proteins that catalyse the reduction of oxygen and use the liberated free energy to maintain a proton-motive force across the membrane. The HCuO superfamily has been divided into the oxygen-reducing A-, B- and C-type oxidases as well as the bacterial NO reductases (NOR), catalysing the reduction of NO in the denitrification process. Proton transfer to the catalytic site in the mitochondrial-like A family occurs through two well-defined pathways termed the D- and K-pathways. The B, C, and NOR families differ in the pathways as well as the mechanisms for proton transfer to the active site and across the membrane. Structural and functional investigations, focussing on proton transfer in the B, C and NOR families are discussed by Lee et al. (2012).

The generalized transport reaction catalyzed by cytochrome c (Cyt c) oxidases is:

2Cyt c (red) + 1/2 O2 + 6H+ (in) → 2Cyt c (ox) + H2O + 4H+ (out).

The generalized transport reaction catalyzed by quinol oxidases is:

quinol + 1/2 O2 + 4H+ (in) → quinone + H2O + 4H+ (out)

This family belongs to the .



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TC#NameOrganismal TypeExample
3.D.4.1.1Quinol oxidase, SoxABC (Lubben et al., 1992)Archaea SoxABC of Sulfolobus acidocaldarius
SoxA (168 aas; P39479)
SoxB (517 aas; P98004)
SoxC (563 aas; P39480)

The cytochrome ba complex consisting of the Sox/CbsA/cytb protein of 553 aas and 12 TMSs, and the CbsB or cytochrome b573 protein of 311 aas and 9 TMSs (Bandeiras et al. 2009).  May function with SoxL (Q3LCJ1; 329 aas and 2 TMSs) and CbsB (Q3LCJ3; 311 aas and 2 TMSs).

Cytba of Acidianus ambivalens (Desulfurolobus ambivalens)


TC#NameOrganismal TypeExample

Nitric oxide reductase (EC # (NorBC) (component of the anerobic, respiratory chain that converts NO3- to N2; denitrification) [reaction catalyzed by Nor: 2 nitric oxide (NO) + 2e- + 2H+ → nitrous oxide (N20) + H2O].  This enzyme does not pump protons across the bacterial membrane (Reimann et al. 2007), but the protons needed for the reaction are taken from the periplasmic side of the membrane (from which side the electrons are donated). P. denitrificans NOR uses a single defined proton pathway with residues Glu-58 and Lys-54 from the NorC subunit at the entrance (ter Beek et al. 2016).  norC and norB encode the cytochrome-c-containing subunit II and cytochrome b-containing subunit I of nitric-oxide reductase (NO reductase), respectively. norQ encodes a protein with an ATP-binding motif and is similar to NirQ from Pseudomonas stutzeri and Pseudomonas aeruginosa and CbbQ from Pseudomonas hydrogenothermophila. norE encodes a protein with five putative transmembrane alpha-helices and has similarity to CoxIII, the third subunit of the aa3-type cytochrome-c oxidases. norF encodes a small protein with two putative transmembrane alpha-helices. Mutagenesis of norC, norB, norQ or norD resulted in cells unable to grow anaerobically. Nitrite reductase and NO reductase (with succinate or ascorbate as substrates) and nitrous oxide reductase (with succinate as substrate) activities were not detected in these mutant strains. Nitrite extrusion was detected in the medium, indicating that nitrate reductase was active. The norQ and norD mutant strains retained about 16% and 23% of the wild-type level of NorC, respectively. The norE and norF mutant strains had specific growth rates and NorC contents similar to those of the wild-type strain, but had reduced NOR and NIR activities, indicating that their gene products are involved in regulation of enzyme activity (de Boer et al. 1996).


NorBC of Paracoccus denitrificans
NorB (Q51603; 462 aas; 12 TMSs)
NorC (Q51662; 150 aas; 1 N-terminal TMS)
NorD (Q51665;638 aas; 0 TMSs)
NorE (Q51666; 167 aas; 5 TMSs)
NorF (Q51667; 77 aas and 2 TMSs)


Bacterial respiratory, anaerobic, nitric oxide reductase (NorBC) (not a proton pump; Flock et al., 2008 )

Gram-negative bacteria

NorBC of Pseudomonas stutzeri
NorB (cytochrome b subunit; 474 aas) (P98008)
NorC (cytochrom c subunit, 146 aas) (Q52527)


Nitric oxide reductase, NorBC. 3-d structure known (PDB# 3o0R) (Lee et al., 2012)


NorBC of Pseudomonas aeruginosa 
NorB (Chain B) (Q59647)
NorC (Chain C) (Q59646) 


Nitric oxide reductase of 787 aas and 14 TMSs, NorZ.  This copper-A-dependent NOR uses cytochrome c₅₅₁ as electron donor but lacks menaquinol activity (Al-Attar and de Vries 2015).  Employing reduced phenazine ethosulfate (PESH) as electron donor, the main NO reduction pathway catalyzed by Cu(A)Nor reconstituted in liposomes involves transmembrane cycling of the PES radical. Cu(A)Nor reconstituted in liposomes generates a proton electrochemical gradient across the membrane similar in magnitude to cytochrome aa₃, suggesting that bacilli using Cu(A)Nor to exploit NO reduction to increase cellular ATP production (Al-Attar and de Vries 2015).

NOR of Bacillus azotoformans


Nitric oxide reductase large subunit, NorB, of 753 aas and 14 TMSs (Al-Attar and de Vries 2015). 

NorB of Bacillus azotoformans


TC#NameOrganismal TypeExample

Cytochrome oxidase (Cox or CcO).  Reversible hydration-level changes of the cavity can be a key factor that regulates the branching of proton transfer events and therefore contributes to the vectorial efficiency of proton transport (Son et al. 2017). Cox16 is required for the assembly of the mitochondrial cytochrome c oxidase (respiratory chain complex IV (CIV)), possibly by promoting the insertion of copper into the active site of cytochrome c oxidase subunit II (MT-CO2/COX2) (Cerqua et al. 2018; Aich et al. 2018).


Cox of Homo sapiens (CoxI-VIII3)
CoxI (Cox1) (P00395)
CoxII (Cox2) (P00403)
CoxIII (Cox3) (P00414)
CoxIV-1 (isoform 1) (Cox41) (P13073)
CoxIV-2 (isoform 2) (Cox42) (Q96KJ9)
CoxVa (Cox5a) (P20674)
CoxVb (Cox5b) (P10601)
CoxVIa (Cox6A2) (Q02221)
CoxVIb (Cox6B2) (Q6YFQ2)
CoxVIIa-H (Cox7A1) (P24310)
CoxVIIa-L (Cox7A2) (P14406)
CoxVIIb2 (Cox7B2) (Q8TF08)
CoxVIIc (Cox7c) (P15954)
CoxVIII-1 (Cox 81) (P48772) (Mouse; human not available)
CoxVIII-2 (Cox82) (P10176)
CoxVIII-3 (Cox83) (Q7Z4L0)
Cox 16, auxillary subunit (Q9P0S2)


TC#NameOrganismal TypeExample

Cytochrome ba3 oxidase, CbaABC. The 3-d structure is known (PDB# 1EHK) (Lee et al., 2012). Proton transfer has been reviewed (von Ballmoos et al., 2012). A mutation in subunit A, D372I, a probable pump H+ binding site, uncouples H+ transport from electron flow (von Ballmoos et al. 2015). In this cytochrome ba3, O2 molecules that arrive at the reduction site diffuse through the X-ray-observed tunnel, supporting its role as the main O2 delivery pathway in cytochrome this ba3 as well as the cytokchrome aa3 of Rhodobacter spheroides (Mahinthichaichan et al. 2018).


CbaABC of Thermus thermophilus
CbaA (Q56408)
CbaB (P98052)
CbaC (P82543) 


TC#NameOrganismal TypeExample
3.D.4.3.1Cytochrome oxidase Archaea Coxl,2 of Halobacterium halobium
Cox1 (P33518)
Cox2 (AAC82824)

Cytochrome bd quinol oxidoreductase, CydA/CydB. Borisov et al. (2011) have presented evidence concerning a proton channel connecting the site of oxygen reduction to the bacteria cytoplasm and the molecular mechanism by which a membrane potential is generated. The CydX protein of 37 aas and 1 TMS, is encoded in the cydAB operon and functions as a subunit of the Cytochrome bd oxidase complex, activating its activity (VanOrsdel et al. 2013). The AppX protein of 30 aas and 1 TMS, is a paralogue of CydX and can substitute for it in activating the Cytochrome bd oxidase complex (VanOrsdel et al. 2013).


CydA/CydB/CydX/AppX of E. coli
CydA (P0ABJ9) 
CydB (P0ABK2)
CydX (P56100)
AppX (P24244)


Cbb3 cytochrome c oxidase (COX; Cbb3; CcoNOP).  The 3-d structure is known to 3.2 Å resolution (PDB# 3MK7; 5DJQ) (Buschmann et al. 2010Lee et al., 2012).  The structure explains a proton-pumping mechanism and the high activity of family-C heme-copper oxidases compared to that of families A and B (Buschmann et al., 2010Lee et al., 2012). A small subunit of 36 aas and 1 TMS, CcoM, was identified in the structure and plays a role in assembly and stability (Kohlstaedt et al. 2016; Carvalheda and Pisliakov 2017). CcoQ, another small protein of 62 aas (acc # F8H837) is an assembly factor for Cbb3-1 and Cbb3-2 (Kohlstaedt et al. 2017). The A-, B- and C-type oxygen reductases each have an active-site tyrosine that forms a unique cross-linked histidine-tyrosine cofactor. In the C-type oxygen reductases (also called cbb3 oxidases), this post-translationally generated co-factor occurs in a different TMS than for the A- and B-type reductases (Hemp et al. 2006).


CcoNOP of Pseudomonas stutzeri
CcoN (Chain A) (H7F0T0)
CcoO (Chain B) (F8H841)
CcoP (Chain C) (D9IA45)
CcoM (Chain D) (H7ESS5)
CcoQ (assembly factor) (Q8KS20)


Cytochrome oxidase subunit I (CydA) of 481 aas and 9 or 10 TMSs, and subunit II (CydB) of 337 aas and 9 TMSs (Soo et al. 2017).

CydAB of Thermosynechococcus elongatus


TC#NameOrganismal TypeExample

Cytochrome oxidase including heme A synthase (HAS) and 4 subunits of the cytochrome oxidase.  The 3-d structure of heme A synthase (of 306 aas and 8 TMSs) at 2.2 Å resolution has been solved revealing that the N- and C-terminal halves of HAS consist of four-helix bundles and they align in a pseudo twofold symmetry manner. Each bundle contains a pair of histidine residues and forms a heme-binding domain. The C-half domain binds a cofactor-heme molecule, while the N-half domain is vacant (Niwa et al. 2018).


CtaACDEF of Bacillus subtilis

3.D.4.4.2Cytochrome c oxidase (Cytaa3, subunits 1-4) (Niebisch and Bott, 2003)BacteriaCytaa3 of Corynebacterium glutamicum
subunit I (584 aas) (Q79VD7)
subunit II (359 aas) (Q8NNK2)
subunit III (205 aas) (Q9AEL8)
subunit IV (143 aas) (Q8NNK3)

The proton pumping Caa3-type cytochrome oxidase chains A-F. The crystal structure (PDB: 2YEV) is known (2.36Å resolution; Lyons et al., 2012). It has a covalently teathered cytochrome c domain. In the cytochrome aa3, O2 molecules that arrive at the reduction site diffuse through the X-ray-observed tunnel, supporting its role as the main O2 delivery pathway in this cytochrome ba3 as well as the cytochrome aa3 of Rhodobacter spheroides (Mahinthichaichan et al. 2018).


Caa(3)-type cytochrome oxidase of Thermus thermophilus 
Subunit I + III, Chain A 791aas; 19 TMSs. (P98005)
Subunit II; Chain B 337aas; 2 TMSs. (Q5SLI2)
Subunit IV; Chain C 66aas; 2 TMSs. (Q5SH67) 


Cytochrome c oxidase, subunits CtaC (337 aas) CtaD (552 aas) and CtaE (201 aas) (also called CoxABC; Soo et al. 2017).

CtaCDE of Thermosynechococcus elongatus


TC#NameOrganismal TypeExample

Quinol oxidase (CyoABCD)


CyoABCD of E. coli


TC#NameOrganismal TypeExample
3.D.4.6.1Cytochrome oxidase (CtaBD/CycA)Bacteria CtaBD/CycA of Paracoccus denitrificans
CtaB (subunit 2) (P08306)
CtaD (subunit 1) (P98002)
CycA (P00096)

Cytochrome c aa3 oxidase (COX). The 3-d structure is known (PDB# 1M56) (Lee et al., 2012).  There are three hydrophobic channels connecting the hydrophobic membrane through the protein to the heme A3/CuB binuclear center (BNC), two of which are probably preferred for O2 diffusion (Oliveira et al. 2014). The D channel is the proton transporting channel, and mutations in residues along this channel, especially N139 in subunit 1, uncouple H+ transport from electron flow (Han et al. 2005). Liang et al. 2017 provided insight into the decoupling mechanisms of CcO mutants, and explained how kinetic gating in the D-channel is imperative to achieving high proton-pumping efficiency in the WT CcO. The O2 molecules that arrived in the reduction site diffuse through the X-ray-observed tunnel, despite its apparent constriction, supporting its role as the main O2 delivery pathway in cytochrome aa3 (Mahinthichaichan et al. 2018).


COX chains A-D of Rhodobacter spheroides 
Chain A (P33517)
Chain B (Q03736)
Chain C (Q3J5F6)
Chain D (Q3IZW6) 


TC#NameOrganismal TypeExample
3.D.4.7.1Cytochrome oxidase (Cox1-3) Eukaryotes Coxl-3 of Bos taurus

TC#NameOrganismal TypeExample

Cytochrome oxidase (Cox)


Cytochrome oxidase (Cox) of Saccharomyces cerevisiae
Cox1p; Cox subunit I [Q0045] (NP_009305)
Cox2p; Cox subunit II [Q0250] (NP_009326)
Cox3p; Cox subunit III [Q0275] (NP_009328)
Cox4p; Cox subunit IV [YGL187c] (NP_011328)
Cox5Ap; Cox subunit Va [YNL052w] (aerobically induced) (NP_014346)
Cox5Bp; Cox subunit Vb [YIL111w] (anaerobically induced) (NP_012155)
Cox6p; Cox subunit VI [YHR051w] (NP_011918)
Cox7p; Cox subunit VII [YMR256c] (NP_013983)
Cox8p; Cox subunit VIII [YLR395c] (NP_013499)
Cox9p; Cox subunit VIIa [YDL067c] (NP_010216)
Cox11p; Cox assembly protein [YPL132w] (NP_015193)
Cox12p; Cox subunit VIb [YLR038c] (NP_013139)
Cox13p; Cox subunit VIa [YGL191w] (NP_011324)
Shylp; Cox chaperone [YGR112w] (NP_011627)


TC#NameOrganismal TypeExample

Quinol oxidase (proton gradient generated only by chemical charge separation) (Purschke et al., 1997) [DoxA + DoxD comprise a novel membrane-bound thiosulfate: quinone oxidoreductase, Dox (Müller et al., 2004)]


DoxABCDEF of Acidianus ambivalens
DoxA (173 aas) (CAA69987)
DoxB (587 aas) (CAA69980)
DoxC (344 aas) (CAA69981)
DoxD (174 aas) (CAA69986)
DoxE (64 aas) (CAA69982)
DoxF (67 aas) (CAA69983)