CuB promotes both binding and reduction of dioxygen at the heme-copper binuclear center in the Escherichia coli bo-type ubiquinol oxidase

Spectroscopic and Crystallographic Evidence for the Role of a Water-Containing H-Bond Network in Oxidase Activity of an Engineered Myoglobin

Heme-copper oxidases (HCOs) catalyze efficient reduction of oxygen to water in biological respiration. Despite progress in studying native enzymes and their models, the roles of non-covalent interactions in promoting this activity are still not well understood. Here we report EPR spectroscopic studies of cryoreduced oxy-F33Y-CuBMb, a functional model of HCOs engineered in myoglobin (Mb). We find that cryoreduction at 77 K of the O2-bound form, trapped in the conformation of the parent oxyferrous form, displays a ferric-hydroperoxo EPR signal, in contrast to the cryoreduced oxy-wild-type (WT) Mb, which is unable to deliver a proton and shows a signal from the peroxo-ferric state. Crystallography of oxy-F33Y-CuBMb reveals an extensive H-bond network involving H2O molecules, which is absent from oxy-WTMb. This H-bonding proton-delivery network is the key structural feature that transforms the reversible oxygen-binding protein, WTMb, into F33Y-CuBMb, an oxygen-activating enzyme that reduces O2 to H2O. These results provide direct evidence of the importance of H-bond networks involving H2O in conferring enzymatic activity to a designed protein. Incorporating such extended H-bond networks in designing other metalloenzymes may allow us to confer and fine-tune their enzymatic activities.

B3LYP study on reduction mechanisms from O2 to H2O at the catalytic sites of fully reduced and mixed-valence bovine cytochrome c oxidases

Reduction mechanisms of oxygen molecule to water molecules in the fully reduced (FR) and mixed-valence (MV) bovine cytochrome c oxidases (CcO) have been systematically examined based on the B3LYP calculations. The catalytic cycle using four electrons and four protons has been also shown consistently. The MV CcO catalyses reduction to produce one water molecule, while the FR CcO catalyses to produce two water molecules. One water molecule is added into vacant space between His240 and His290 in the catalytic site. This water molecule constructs the network of hydrogen bonds of Tyr244, farnesyl ethyl, and Thr316 that is a terminal residue of the K-pathway. It plays crucial roles for the proton transfer to the dioxygen to produce the water molecules in both MV and FR CcOs. Tyr244 functions as a relay of the proton transfer from the K-pathway to the added water molecule, not as donors of a proton and an electron to the dioxygen. The reduction mechanisms of MV and FR CcOs are strictly distinguished. In the FR CcO, the Cu atom at the Cu(B) site maintains the reduced state Cu(I) during the process of formation of first water molecule and plays an electron storage. At the final stage of formation of first water molecule, the Cu(I) atom releases an electron to Fe-O. During the process of formation of second water molecule, the Cu atom maintains the oxidized state Cu(II). In contrast with experimental proposals, the K-pathway functions for formation of first water molecule, while the D-pathway functions for second water molecule. The intermediates, P(M), P(R), F, and O, obtained in this work are compared with those proposed experimentally.

Electron transfer processes in subunit I mutants of cytochrome bo quinol oxidase in Escherichia coli

Cytochrome bo is a terminal quinol oxidase in the aerobic respiratory chain of Escherichia coli. Subunit I binds all four redox centers, and electrons are transferred from quinols to high-spin heme o and Cu(B) through a bound uniquinone-8 and low-spin heme b. To explore the role of conserved charged amino acid residues, we examined the one-electron transfer processes in subunit I mutants. We found that all the mutants examined increased the electron transfer rate from the bound quinone to heme b more than 40-fold. Tyr288 and Lys362 are key residues in the K-channel for charge compensation of the heme o-Cu(B) binuclear center with protons. The Tyr288Phe and Lys362Gln mutants showed 100-fold decreases in heme b-to-heme o electron transfer, accompanied by large increases in the redox potential of heme o. Our results indicate that electromagnetic coupling of hemes is important for facilitated heme-heme electron transfer in cytochrome bo.

Intramolecular electron transfer processes in Cu(B)-deficient cytochrome bo studied by pulse radiolysis

The Escherichia coli cytochrome bo is a heme-copper terminal ubiquinol oxidase, and functions as a redox-driven proton pump. We applied pulse radiolysis technique for studying the one-electron reduction processes in the Cu(B)-deficient mutant, His333Ala. We found that the Cu(B) deficiency suppressed the heme b-to-heme o electron transfer two order of the magnitude (4.0 x 10(2) s(-1)), as found for the wild-type enzyme in the presence of 1 mM KCN (3.0 x 10(2) s(-1)). Potentiometric analysis of the His333Ala mutant revealed the 40 mV decrease in the E(m) value for low-spin heme b and the 160 mV increase in the E(m) value of high-spin heme o. Our results indicate that Cu(B) not only serves as one-electron donor to the bound dioxygen upon the O-O bond cleavage, but also facilitates dioxygen reduction at the heme-copper binuclear centre by modulating the E(m) value of heme o through magnetic interactions. And the absence of a putative OH(-) bound to Cu(B) seems not to affect the uptake of the first chemical proton via K-channel in the His333Ala mutant.

Interaction of bd-type quinol oxidase from Escherichia coli and carbon monoxide: heme d binds CO with high affinity

Comparative studies on the interaction of the membrane-bound and detergent-solubilized forms of the enzyme in the fully reduced state with carbon monoxide at room temperature have been carried out. CO brings about a bathochromic shift of the heme d band with a maximum at 644 nm and a minimum at 624 nm, and a peak at 540 nm. In the Soret band, CO binding to cytochrome bd results in absorption decrease and minima at 430 and 445 nm. Absorption perturbations in the Soret band and at 540 nm occur in parallel with the changes at 630 nm and reach saturation at 3-5 microM CO. The peak at 540 nm is probably either beta-band of the heme d-CO complex or part of its split alpha-band. In both forms of cytochrome bd, CO reacts predominantly with heme d. Addition of high CO concentrations to the solubilized cytochrome bd results in additional spectral changes in the gamma-band attributable to the reaction of the ligand with 10-15% of low-spin heme b558. High-spin heme b595 does not bind CO even at high concentrations of the ligand. The apparent dissociation constant values for the heme d-CO complex of the membrane-bound and detergent-solubilized forms of the fully reduced enzyme are about 70 and 80 nM, respectively.

A cytochrome C oxidase model catalyzes oxygen to water reduction under rate-limiting electron flux

We studied the selectivity of a functional model of cytochrome c oxidase's active site that mimics the coordination environment and relative locations of Fe(a3), Cu(B), and Tyr(244). To control electron flux, we covalently attached this model and analogs lacking copper and phenol onto self-assembled monolayer-coated gold electrodes. When the electron transfer rate was made rate limiting, both copper and phenol were required to enhance selective reduction of oxygen to water. This finding supports the hypothesis that, during steady-state turnover, the primary role of these redox centers is to rapidly provide all the electrons needed to reduce oxygen by four electrons, thus preventing the release of toxic partially reduced oxygen species.

Improved H+/O ratio and cell yield of Escherichia coli with genetically altered terminal quinol oxidases

Escherichia coli wild-type cells, containing both cytochrome bo- and bd-type terminal oxidases, pumped protons with a H+/O ratio of 4.5-4.9 upon an oxygen pulse, while mutant cells, deprived of either cytochrome bo (deltacyo) or bd (deltacyd), showed values of 3.5-4.1 or 4.8-5.6, respectively. The cell yield of the cyo-less mutant was about 15% lower than that of the wild-type strain, while that of the cyd-less strain which over-produced cytochrome bo was about 10% higher than that of the wild-type. The simple cyd-less strain without over-production of cytochrome bo showed a high H+/O ratio, but its cell yield was low and variable from culture to culture. The growth inhibition and accelerated H+ permeability of the cell membrane of the latter strain seems due to the deletion of cytochrome bd (CydAB), the terminal oxidase having a very low K(m) for O2, which may result in severe stress on the cell. Over-production of cytochrome bo by as much as 0.4 nmol/mg membrane protein could compensate for this defect.

Role of Tyr-288 at the dioxygen reduction site of cytochrome bo studied by stable isotope labeling and resonance raman spectroscopy

To explore the role of a cross-link between side chains of Tyr-288 and His-284 at the heme-copper binuclear center, we prepared cytochrome bo where d(4)-Tyr, 1-[(13)C]Tyr, or 4-[(13)C]Tyr has been biosynthetically incorporated. Unexpectedly, the d(4)-Tyr-labeled enzyme showed a large decrease in the ubiquinol-1 oxidase and CO binding activities. Optical absorption and resonance Raman spectra identified the defect in the distal side of the heme-copper binuclear center. In the CO-bound d(4)-Tyr-labeled enzyme, a large fraction of the nu((Fe-C)) mode was shifted from the normal 520-cm(-1) band to a broad band centered around 491 cm(-1), as found for the Y288F mutant. Our results suggested that the substitution of ring hydrogens of Tyr-288 with deuteriums slows down the formation of the His-Tyr cross-link essential for dioxygen reduction at the binuclear center.

The role of copper and protons in heme-copper oxidases: kinetic study of an engineered heme-copper center in myoglobin

To probe the role of copper and protons in heme-copper oxidase (HCO), we have performed kinetic studies on an engineered heme-copper center in sperm whale myoglobin (Leu-29 --> HisPhe-43 --> His, called Cu(B)Mb) that closely mimics the heme-copper center in HCO. In the absence of metal ions, the engineered Cu(B) center in Cu(B)Mb decreases the O(2) binding affinity of the heme. However, addition of Ag(I), a redox-inactive mimic of Cu(I), increases the O(2)-binding affinity. More importantly, copper ion in the Cu(B) center is essential for O(2) reduction, as no O(2) reduction can be observed in copper-free, Zn(II), or Ag(I) derivatives of Cu(B)Mb. Instead of producing a ferryl-heme as in HCO, the Cu(B)Mb generates verdoheme because the engineered Cu(B)Mb may lack a hydrogen bonding network that delivers protons to promote the heterolytic OO cleavage necessary for the formation of ferryl-heme. Reaction of oxidized Cu(B)Mb with H(2)O(2), a species equivalent in oxidation state to 2e(-), reduced O(2) but, possessing the extra protons, resulted in ferryl-heme formation, as in HCO. The results showed that the Cu(B) center plays a critical role in O(2) binding and reduction, and that proton delivery during the O(2) reduction is important to avoid heme degradation and to promote the HCO reaction.

Functional analogues of the dioxygen reduction site in cytochrome oxidase: mechanistic aspects and possible effects of Cu(B)

Catalytic reduction of O(2) and H(2)O(2) by new synthetic analogues of the heme/Cu site in cytochrome c and ubiquinol oxidases has been studied in aqueous buffers. Among the synthetic porphyrins yet reported, those employed in this study most faithfully mimic the immediate coordination environment of the Fe/Cu core. Under physiologically relevant conditions, these biomimetic catalysts reproduce key aspects of the O(2) and H(2)O(2) chemistry of the enzyme. When deposited on an electrode surface, they catalyze the selective reduction of O(2) to H(2)O at potentials comparable to the midpoint potential of cytochrome c. The pH dependence of the half-wave potentials and other data are consistent with O-O bond activation at these centers proceeding via a slow generation of a formally ferric-hydroperoxo intermediate, followed by its rapid reduction to the level of water. This kinetics is analogous to that proposed for the O-O reduction step at the heme/Cu site. It minimizes the steady-state concentration of the catalytic intermediate whose decomposition would release free H(2)O(2). The maximum catalytic rate constants of O(2) reduction by the ferrous catalyst and of H(2)O(2) reduction by both ferric and ferrous catalysts are comparable to those reported for cytochrome oxidase. The oxidized catalyst also displays catalase activity. Comparison of the catalytic properties of the biomimetic complexes in the FeCu and Cu-free forms indicates that, in the regime of rapid electron flux, Cu does not significantly affect the turnover frequency or the stability of the catalysts, but it suppresses superoxide-releasing autoxidation of an O(2)-catalyst adduct. The distal Cu also accelerates O(2) binding and minimizes O-O bond homolysis in the reduction of H(2)O(2).

Probing molecular structure of dioxygen reduction site of bacterial quinol oxidases through ligand binding to the redox metal centers

Cytochromes bo and bd are structurally unrelated terminal ubiquinol oxidases in the aerobic respiratory chain of Escherichia coli. The high-spin heme o-CuB binuclear center serves as the dioxygen reduction site for cytochrome bo, and the heme b595-heme d binuclear center for cytochrome bd. CuB coordinates three histidine ligands and serves as a transient ligand binding site en route to high-spin heme o one-electron donor to the oxy intermediate, and a binding site for bridging ligands like cyanide. In addition, it can protect the dioxygen reduction site through binding of a peroxide ion in the resting state, and connects directly or indirectly Tyr288 and Glu286 to carry out redox-driven proton pumping in the catalytic cycle. Contrary, heme b595 of cytochrome bd participate a similar role to CuB in ligand binding and dioxygen reduction but cannot perform such versatile roles because of its rigid structure.

Role of a bound ubiquinone on reactions of the Escherichia coli cytochrome bo with ubiquinol and dioxygen

To probe the functional role of a bound ubiquinone-8 in cytochrome bo-type ubiquinol oxidase from Escherichia coli, we examined reactions with ubiquinol-1 and dioxygen. Stopped-flow studies showed that anaerobic reduction of the wild-type and the bound ubiquinone-free (DeltaUbiA) enzymes with ubiquinol-1 immediately takes place with four kinetic phases. Replacement of the bound ubiquinone with 2,6-dibromo-4-cyanophenol (PC32) suppressed the anaerobic reduction of the hemes with ubiquinol-1 by eliminating the fast phase. Flow-flash studies in the reaction of the fully reduced enzyme with dioxygen showed that the heme b-to-heme o electron transfer occurs with a rate constant of approximately 1x10(4) s(-1) in all three preparations. These results support our previous proposal that the bound ubiquinone is involved in facile oxidation of substrates in subunit II and subsequent intramolecular electron transfer to low-spin heme b in subunit I.

Role of a bound ubiquinone on reactions of the Escherichia coli cytochrome bo with ubiquinol and dioxygen

To probe the functional role of a bound ubiquinone-8 in cytochrome bo-type ubiquinol oxidase from Escherichia coli, we examined reactions with ubiquinol-1 and dioxygen. Stopped-flow studies showed that anaerobic reduction of the wild-type and the bound ubiquinone-free (delta UbiA) enzymes with ubiquinol-1 immediately takes place with four kinetic phases. Replacement of the bound ubiquinone with 2,6-dibromo-4-cyanophenol (PC32) suppressed the anaerobic reduction of the hemes with ubiquinol-1 by eliminating the fast phase. Flow-flash studies in the reaction of the fully reduced enzyme with dioxygen showed that the heme b to heme o electron transfer occurs with a rate constant of approximately 10(4) s-1 in all three preparations. These results support our previous proposal that the bound ubiquinone is involved in facile oxidation of substrates in subunit II and subsequent intramolecular electron transfer to low-spin heme b in subunit I.

Exploring subunit-subunit interactions in the Escherichia coli bo-type ubiquinol oxidase by extragenic suppressor mutation analysis

Cytochrome bo-type ubiquinol oxidase is a four-subunit heme-copper terminal oxidase and functions as a redox-coupled proton pump in the aerobic respiratory chain of Escherichia coli. On the basis of deletion and chemical cross-linking analyses on subunit IV, we proposed that subunit IV is essential for CuB binding to subunit I and that it is present in a cleft between subunits I and III (Saiki, K., Nakamura, H., Mogi, T., and Anraku, Y. (1996) J. Biol. Chem. 271, 15336-15340). To extend previous studies, we carried out alanine-scanning mutagenesis for selected 16-amino acid residues in subunit IV to explore subunit-subunit interactions in bo-type ubiquinol oxidase. We found that only the replacement of Phe83 in helix III resulted in the reduction of the catalytic activity but that this did not significantly affect the UV-visible spectroscopic properties and the copper content. This suggests that individual amino acid substitutions, including the six invariant residues, are not enough to alter such properties of the metal centers. Extragenic suppressor mutations were isolated for the Phe83 --> Ala mutation of subunit IV and identified as missense mutations in helices VII and VIII in subunit I. These observations provide further support for specific interactions of subunit IV with helix VII and/or VIII, the CuB binding domain, of subunit I and suggest that subunit IV functions as a domain-specific molecular chaperon in the oxidase complex.

Probing a role of subunit IV of the Escherichia coli bo-type ubiquinol oxidase by deletion and cross-linking analyses

Subunit IV of the Escherichia coli bo-type ubiquinol oxidase is a 12-kDa membrane protein encoded by the cyoD gene and is conserved in the bacterial heme-copper terminal oxidases. To probe the functional role of subunit IV, we carried out deletion analysis and chemical cross-linking experiments with a homobifunctional and cleavable reagent. Spectroscopic properties of the mutant oxidases suggest that the C-terminal two-third (Val45 to His109) containing helices II and III is essential for the functional expression of the oxidase complex and for the CuB binding to the heme-copper binuclear center in subunit I. Cross-linking studies indicate that subunit IV is in close vicinity to subunit III. Based on these observations, we propose that subunit IV is present in a cleft formed by subunits I and III and assists the CuB binding to subunit I during biosynthesis or assembly of the oxidase complex.