A tyrosine residue deprotonates during oxygen reduction by thecaa3 reductase fromRhodothermus marinus

Mitochondrial cytochrome c oxidase: catalysis, coupling and controversies

Mitochondrial cytochrome c oxidase is a member of a diverse superfamily of haem-copper oxidases. Its mechanism of oxygen reduction is reviewed in terms of the cycle of catalytic intermediates and their likely chemical structures. This reaction cycle is coupled to the translocation of protons across the inner mitochondrial membrane in which it is located. The likely mechanism by which this occurs, derived in significant part from studies of bacterial homologues, is presented. These mechanisms of catalysis and coupling, together with current alternative proposals of underlying mechanisms, are critically reviewed.

Exploring membrane respiratory chains

Acquisition of energy is central to life. In addition to the synthesis of ATP, organisms need energy for the establishment and maintenance of a transmembrane difference in electrochemical potential, in order to import and export metabolites or to their motility. The membrane potential is established by a variety of membrane bound respiratory complexes. In this work we explored the diversity of membrane respiratory chains and the presence of the different enzyme complexes in the several phyla of life. We performed taxonomic profiles of the several membrane bound respiratory proteins and complexes evaluating the presence of their respective coding genes in all species deposited in KEGG database. We evaluated 26 quinone reductases, 5 quinol:electron carriers oxidoreductases and 18 terminal electron acceptor reductases. We further included in the analyses enzymes performing redox or decarboxylation driven ion translocation, ATP synthase and transhydrogenase and we also investigated the electron carriers that perform functional connection between the membrane complexes, quinones or soluble proteins. Our results bring a novel, broad and integrated perspective of membrane bound respiratory complexes and thus of the several energetic metabolisms of living systems. This article is part of a Special Issue entitled 'EBEC 2016: 19th European Bioenergetics Conference, Riva del Garda, Italy, July 2-6, 2016', edited by Prof. Paolo Bernardi.

Respiratory conservation of energy with dioxygen: cytochrome C oxidase

Cytochrome c oxidase (CcO) is the terminal oxidase of cell respiration which reduces molecular oxygen (O₂) to H2O coupled with the proton pump. For elucidation of the mechanism of CcO, the three-dimensional location and chemical reactivity of each atom composing the functional sites have been extensively studied by various techniques, such as crystallography, vibrational and time-resolved electronic spectroscopy, since the X-ray structures (2.8 Å resolution) of bovine and bacterial CcO have been published in 1995.X-ray structures of bovine CcO in different oxidation and ligand binding states showed that the O₂reduction site, which is composed of Fe (heme a 3) and Cu (CuB), drives a non-sequential four-electron transfer for reduction of O₂to water without releasing any reactive oxygen species. These data provide the crucial structural basis to solve a long-standing problem, the mechanism of the O₂reduction.Time-resolved resonance Raman and charge translocation analyses revealed the mechanism for coupling between O₂reduction and the proton pump: O₂is received by the O₂reduction site where both metals are in the reduced state (R-intermediate), giving the O₂-bound form (A-intermediate). This is spontaneously converted to the P-intermediate, with the bound O₂fully reduced to 2 O²⁻. Hereafter the P-intermediate receives four electron equivalents from the second Fe site (heme a), one at a time, to form the three intermediates, F, O, and E to regenerate the R-intermediate. Each electron transfer step from heme a to the O₂reduction site is coupled with the proton pump.X-ray structural and mutational analyses of bovine CcO show three possible proton transfer pathways which can transfer pump protons (H) and chemical (water-forming) protons (K and D). The structure of the H-pathway of bovine CcO indicates that the driving force of the proton pump is the electrostatic repulsion between the protons on the H-pathway and positive charges of heme a, created upon oxidation to donate electrons to the O₂reduction site. On the other hand, mutational and time-resolved electrometric findings for the bacterial CcO strongly suggest that the D-pathway transfers both pump and chemical protons. However, the structure for the proton-gating system in the D-pathway has not been experimentally identified. The structural and functional diversities in CcO from various species suggest a basic proton pumping mechanism in which heme a pumps protons while heme a 3 reduces O₂as proposed in 1978.

Infrared and Raman spectroscopic investigation of the reaction mechanism of cytochrome c oxidase

Recent progress in studies on the proton-pumping and O₂reduction mechanisms of cytochrome c oxidase (CcO) elucidated by infrared (IR) and resonance Raman (rR) spectroscopy, is reviewed. CcO is the terminal enzyme of the respiratory chain and its O₂reduction reaction is coupled with H⁺ pumping activity across the inner mitochondrial membrane. The former is catalyzed by heme a3 and its mechanism has been determined using a rR technique, while the latter used the protein moiety and has been investigated with an IR technique. The number of H⁺ relative to e⁻ transferred in the reaction is 1:1, and their coupling is presumably performed by heme a and nearby residues. To perform this function, different parts of the protein need to cooperate with each other spontaneously and sequentially. It is the purpose of this article to describe the structural details on the coupling on the basis of the vibrational spectra of certain specified residues and chromophores involved in the reaction. Recent developments in time-resolved IR and Raman technology concomitant with protein manipulation methods have yielded profound insights into such structural changes. In particular, the new IR techniques that yielded the breakthrough are reviewed and assessed in detail. This article is part of a Special Issue entitled: Vibrational spectroscopies and bioenergetic systems.

Structural insights into electron transfer in caa3-type cytochrome oxidase

Cytochrome c oxidase is a member of the heme copper oxidase superfamily (HCO)¹. HCOs function as the terminal enzymes in the respiratory chain of mitochondria and aerobic prokaryotes, coupling molecular oxygen reduction to transmembrane proton pumping. Integral to the enzyme’s function is the transfer of electrons from cytochrome c to the oxidase via a transient association of the two proteins. Electron entry and exit are proposed to occur from the same site on cytochrome c^2–4. Here we report the crystal structure of the caa₃-type cytochrome oxidase from Thermus thermophilus, which has a covalently tethered cytochrome c domain. Crystals were grown in a bicontinuous mesophase using a synthetic short-chain monoacylglycerol as the hosting lipid. From the electron density map, at 2.36 Å resolution, a novel integral membrane subunit and a native glycoglycerophospholipid embedded in the complex were identified. Contrary to previous electron transfer mechanisms observed for soluble cytochrome c, the structure reveals the architecture of the electron transfer complex for the fused cupredoxin/cytochrome c domain which implicates different sites on cytochrome c for electron entry and exit. Support for an alternative to the classical proton gate characteristic of this HCO class is presented.

Bioenergetics at extreme temperature: Thermus thermophilus ba(3)- and caa(3)-type cytochrome c oxidases

Seven years into the completion of the genome sequencing projects of the thermophilic bacterium Thermus thermophilus strains HB8 and HB27, many questions remain on its bioenergetic mechanisms. A key fact that is occasionally overlooked is that oxygen has a very limited solubility in water at high temperatures. The HB8 strain is a facultative anaerobe whereas its relative HB27 is strictly aerobic. This has been attributed to the absence of nitrate respiration genes from the HB27 genome that are carried on a mobilizable but highly-unstable plasmid. In T. thermophilus, the nitrate respiration complements the primary aerobic respiration. It is widely known that many organisms encode multiple biochemically-redundant components of the respiratory complexes. In this minireview, the presence of the two cytochrome c oxidases (CcO) in T. thermophilus, the ba(3)- and caa(3)-types, is outlined along with functional considerations. We argue for the distinct evolutionary histories of these two CcO including their respective genetic and molecular organizations, with the caa(3)-oxidase subunits having been initially 'fused'. Coupled with sequence analysis, the ba(3)-oxidase crystal structure has provided evolutionary and functional information; for example, its subunit I is more closely related to archaeal sequences than bacterial and the substrate-enzyme interaction is hydrophobic as the elevated growth temperature weakens the electrostatic interactions common in mesophiles. Discussion on the role of cofactors in intra- and intermolecular electron transfer and proton pumping mechanism is also included.

The superfamily of heme-copper oxygen reductases: types and evolutionary considerations

Heme-copper oxygen reductases (HCO) reduce O(2) to water being the last enzymatic complexes of most aerobic respiratory chains. These enzymes promote energy conservation coupling the catalytic reaction to charge separation and charge translocation across the prokaryotic cytoplasmatic or mitochondrial membrane. In this way they contribute to the establishment and maintenance of the transmembrane difference of electrochemical potential, which is vital for solute/nutrient cell import, synthesis of ATP and motility. The HCO enzymes most probably share with the nitric oxide reductases, NORs, a common ancestor. We have proposed the classification of HCOs into three different types, A, B and C; based on the constituents of their proton channels (Pereira, Santana and Teixeira (2001) Biochim Biophys Acta, 1505, 185-208). This classification was recently challenged by the suggestion of other different types of HCOs. Using an enlarged sampling we performed an exhaustive bioinformatic reanalysis of HCOs family. Our results strengthened our previously proposed classification and showed no need for the existence of more divisions. Now, we analyze the taxonomic distribution of HCOs and NORs and the congruence of their sequence trees with the 16S rRNA tree. We observed that HCOs are widely distributed in the two prokaryotic domains and that the different types of enzymes are not confined to a specific taxonomic group or environmental niche.

The alternative complex III: a different architecture using known building modules

Until recently cytochrome bc(1) complexes were the only enzymes known to be able to transfer electrons from reduced quinones to cytochrome c. However, a complex with the same activity and with a unique subunit composition was purified from the membranes of Rhodothermus marinus. This complex, named alternative complex III (ACIII) was then biochemical, spectroscopic and genetically characterized. Later it was observed that the presence of ACIII was not exclusive of R. marinus being the genes coding for ACIII widespread, at least in the Bacteria domain. In this work, a comprehensive description of the current knowledge on ACIII is presented. The relation of ACIII with members of the complex iron-sulfur molybdoenzyme family is investigated by analyzing all the available completely sequenced genomes. It is concluded that ACIII is a new complex composed by a novel combination of modules already identified in other respiratory complexes.

Looking for the minimum common denominator in haem-copper oxygen reductases: towards a unified catalytic mechanism

Haem-copper oxygen reductases are transmembrane protein complexes that reduce dioxygen to water and pump protons across the mitochondrial or periplasmatic membrane, contributing to the transmembrane difference of electrochemical potential. Seven years ago we proposed a classification of these enzymes into three different families (A, B and C), based on the amino acid residues of their proton channels and amino acid sequence comparison, later supported by the so far identified characteristics of the catalytic centre of members from each family. The three families have in common the same general structural fold of the catalytic subunit, which contains the same or analogous prosthetic groups, and proton channels. These observations raise the hypothesis that the mechanisms for dioxygen reduction, proton pumping and the coupling of the two processes may be the same for all these enzymes. Under this hypothesis, they should be performed and controlled by the same or equivalent elements/events, and the identification of retained elements in all families will reveal their importance and may prompt the definition of the enzyme operating mode. Thus, we believe that the search for a minimum common denominator has a crucial importance, and in this article we highlight what is already established for the haem-copper oxygen reductases and emphasize the main questions still unanswered in a comprehensive basis.

Carboxyl group functions in the heme-copper oxidases: information from mid-IR vibrational spectroscopy

Carboxyl groups of possible functional importance in bovine and bacterial cytochrome c oxidases (CcO) are reviewed and assessed. A critical analysis is presented of available mid-infrared vibrational data that pertain to these functional carboxyl groups. These data and their interpretations are discussed in relation to current models of the mechanism of proton and electron coupling in the protonmotive CcO superfamily.

The alternative complex III from Rhodothermus marinus - a prototype of a new family of quinol:electron acceptor oxidoreductases

The biochemical and genetic search for a bc(1) complex in Rhodothermus marinus was always fruitless; however, a functional equivalent, i.e. having quinol:cytochrome c oxidoreductase activity was characterized. Now, with the sequencing of R. marinus genome, it was possible to assign the N-terminal sequences of several proteins of this complex to its coding genes. The alternative complex III from R. marinus has the same genomic organization of the so-called MFIcc complexes, proposed to be oxidoreductases of the respiratory and photosynthetic electron transfer chains. In this report, we establish undoubtedly the existence of an alternative complex III, a functional substitute of the bc(1) complex, by its identification at both the biochemical and genomic level.

Synthetic Models of the Active Site of Cytochromec Oxidase: Influence of Tridentate or Tetradentate Copper Chelates Bearing a HisTyr Linkage Mimic on Dioxygen Adduct Formation by Heme/Cu Complexes

Two synthetic models of the active site of cytochrome c oxidase--[(LN4-OH)CuI-FeII(TMP)]+ (1 a) and [(LN3-OH)CuI-FeII(TMP)]+ (2 a)-have been designed and synthesized. These models each contain a heme and a covalently attached copper moiety supported either by a tetradentate N4-copper chelate or by a tridentate N3-copper chelate including a moiety that acts as a mimic of the crosslinked His-Tyr component of cytochrome c oxidase. Low-temperature oxygenation reactions of these models have been investigated by spectroscopic methods including UV/Vis, resonance Raman, ESI-MS, and EPR spectroscopy. Oxygenation of the tetradentate model 1 a in MeCN and in other solvents produces a low-temperature-stable dioxygen-bridged peroxide [(LN4-OH)CuII-O2-FeIII(TMP)]+ {nuO--O=799 (16O2)/752 cm(-1) (18O2)}, while a heme superoxide species [(TMP)FeIII(O2-)CuIILN3-OH] {nuFe--O2: 576 (16O2)/551 cm(-1) (18O2)} is generated when the tridentate model 2 a is oxygenated in EtCN solution under similar experimental conditions. The coexistence of a heme superoxide species [(TMP)FeIII(O2-)CuIILN3-OH] and a bridged peroxide [(LN3-OH)CuII-O2-FeIII(TMP)]+ species in equal amounts is observed when the oxygenation reaction of 2 a is performed in CH2Cl(2)/7 % EtCN, while the percentage of the peroxide (approximately 70 %) in relation to superoxide (approximately 30 %) increases further when the crosslinked phenol moiety in 2 a is deprotonated to produce the bridged peroxide [(LN3-OH)CuII-O2-FeIII(TMP)]+ {nuO--O: 812 (16O2)/765 cm(-1) (18O2)} as the main dioxygen intermediate. The weak reducibility and decreased O2 reactivity of the tricoordinated CuI site in 2 a are responsible for the solvent-dependent formation of dioxygen adducts. The initial binding of dioxygen to the copper site en route to the formation of a bridged heme-O2-Cu intermediate by model 2 a is suggested and the deprotonated crosslinked His-Tyr moiety might contribute to enhancement of the O2 affinity of the CuI site at an early stage of the dioxygen-binding process.

Structural and Chemical Changes of the PMIntermediate ofParacoccus denitrificansCytochromecOxidase Revealed by IR Spectroscopy with Labeled Tyrosines and Histidine†

Structural and chemical changes in the P(M) intermediate of Paracoccus denitrificans cytochrome c oxidase have been investigated by attenuated total reflection-Fourier transform infrared spectroscopy. Prior studies of P(M) minus oxidized (O) IR difference spectra of unlabeled, universally (15)N-labeled and ring-d(4)-tyrosine-labeled proteins (Iwaki, M., Puustinen, A., Wikström, M., and Rich, P. R. (2004) Biochemistry 43, 14370-14378). provided a basis for band assignments to changes in metal centers and the covalently linked His-Tyr ligand of Cu(B) and highlighted a structural alteration of the protonated Glu278 in the P(M) intermediate. This work has been extended to equivalent measurements on enzymes with (13)C(9)(15)N-labeled and ring-(13)C(6)-labeled tyrosine and with (13)C(6)(15)N(3)-labeled histidine. Histidine labeling allows the assignment of troughs at 1104 and 973 cm(-1) in reduced minus O spectra to histidine changes, whereas tyrosine labeling moves otherwise obscured tyrosine bandshifts to 1454-1437 and 1287-1284 cm(-1). P(M) minus O spectra reveal bands at 1506, 1311, and 1094 cm(-1) in the oxidized state that are replaced by a band at 1519 cm(-1) in P(M). These bands shift with both tyrosine- and histidine-labeling, providing evidence for their assignment to the covalent His-Tyr and for its chemical change in P(M). Comparisons of isotope effects on the amide I regions in P(M) minus O spectra demonstrate that amide carbonyl bonds of tyrosine and histidine are major contributors. This suggests a structural alteration in P(M) that is centered on the His276-Pro277-Glu278-Val279-Tyr280 pentapeptide formed by the His-Tyr covalent linkage. This structural change is proposed to mediate the perturbation of the IR band of the protonated Glu278 headgroup.