Cytochrome bo-type ubiquinol oxidase in the aerobic respiratory chain of Escherichia coli catalyzes the two-electron oxidation of ubiquinol-8 (QH) ()and the four-electron reduction of dioxygen to water(1, 2) . These redox reactions mechanistically couple with the formation of an electrochemical proton gradient across the cytoplasmic membrane not only by scalar protolytic reactions at the inner and outer surfaces of the membrane but also by a proton pumping mechanism(3, 4, 5) . Based on the structural homologies of subunits I, II, and III, cytochrome c oxidases and some bacterial quinol oxidases including the E. coli cytochrome bo are classified in the heme-copper respiratory oxidase superfamily(6, 7) . However, there is a notable difference in electron-donating substrates between the two enzymes, cytochrome c (a hydrophilic one-electron carrier) and quinols (hydrophobic two-electron and two-proton carriers)(8, 9) . As a consequence, the Cu center is absent in subunit II of quinol oxidase(5, 10, 11) .

Although the dioxygen reduction mechanism at the heme-copper binuclear center is thought to be identical in both enzymes(12, 13, 14) , these differences raise the questions whether the electron transfer reactions from the substrates to dioxygen and the proton pumping mechanism coupled to these redox reactions are alike or distinct. It is proposed that the last two steps of the four-electron transfer reactions to dioxygen are linked to proton pumping by cytochrome c oxidase(15, 16, 17) . Thus it becomes increasingly important to analyze the mixed-valence states of oxidase as a model for the intermediate species of the dioxygen reduction chemistry, since the understanding of the redox-linked structural change(s) at the metal center appears to be a key point to reveal the redox-linked proton pumping.

In a previous study, Tsubaki (18) analyzed cyanide binding to the Fe-Cu binuclear center of cytochrome c oxidase. In the resting (air-oxidized) state, a bound cyanide showed an infrared C-N stretching band at 2152 cm, assignable to a bridging structure, Fe-C=N-Cu. This assignment was confirmed recently by structural characterizations and infrared measurements on a series of model complexes containing the [Fe-C=N-Cu] bridge unit(19) . Upon partial reduction of the CN-inhibited cytochrome c oxidase an infrared band appeared at 2131 cm assignable to the Fe-C=N structure. Further reduction resulted in an appearance of two new infrared bands at 2058 and 2045 cm, concomitantly, assignable to the Fe-C=N species. These observations suggest three kinds of conformational change to occur at the Fe-Cu binuclear site as the reduction of the metal centers proceeds(18) .

Subsequently Tsubaki et al. (11) carried out a combined study using EPR and FT-IR spectroscopies to clarify the structural differences of the binuclear center between bo-type ubiquinol oxidase and cytochrome c oxidase. EPR spectra of bo-type ubiquinol oxidase in the air-oxidized state showed EPR signals from an integer spin system confirming the existence of the spin-spin exchange-coupled binuclear site(20, 21, 22, 23) . EPR spectra of the cyanide, azide, and formate complexes in the air-oxidized state indicated that a gross conformation at the binuclear site seems well conserved among the heme-copper oxidase superfamily(11) . FT-IR spectroscopy confirmed these observations: the cyanide that binds to the air-oxidized enzyme exhibits an infrared band at 2146 cm characteristic to the Fe-C=N-Cu structure(11) .

In the present study we extended the FT-IR and EPR spectroscopic studies to clarify the structure at the heme-copper binuclear center using cyanide as a monitoring probe.

EXPERIMENTAL PROCEDURES

Purification of Cytochrome bo-type Ubiquinol Oxidase

()

Purification of Cytochrome c Oxidase

Measurement of Fourier Transform Infrared and Optical Spectra

Measurement of EPR Spectra

Miscellaneous

RESULTS

FT-IR and EPR Spectra of the CN-inhibited bo-type Ubiquinol Oxidase

Figure 1: Cyanide (CN) bindings to the wild-type ubiquinol oxidase in the air-oxidized state. CN was added to a final concentration of 5 mM to the PEG 4000-treated enzyme (0.53 mM) containing 1.1 mol of Q/mol of the enzyme (a and b) and to the untreated enzyme (0.45 mM) containing 2.2 mol of Q/mol of the enzyme (c and d). FT-IR spectra in the C-N stretching region were measured just after (a and c) and 48 h after (b and d) the addition of potassium cyanide. The enzyme at the stage of (d) was filtered through a membrane filter (MWCO = 10,000), and the filtrate was directly introduced into an infrared cell. Then, the FT-IR spectrum of the filtrate was measured with a reference cell containing HO (e). Conditions: infrared cell path length, 51 µm; temperature, 4 °C; spectral accumulation, 200 cycles (40 min); spectral resolution, 4.0 cm.

Figure 2: Cyanide (C) binding to the fully reduced ubiquinol oxidase (a) and the effect of carbon monoxide on the CN binding (b and c). a, cyanide (CN) was anaerobically added to a final concentration of 5 mM to the fully reduced enzyme (0.39 mM) with excess sodium dithionite. b, the enzyme was first fully reduced with excess sodium dithionite in the presence of carbon monoxide and then CN was anaerobically added to the enzyme at a final concentration of 5 mM. c, the ordinate of b, is reduced by one-fourth to clarify the CO binding to the enzyme which shows the 1959.7 cm band. Other conditions are the same as described in the legend to Fig. 1.

EPR spectra of the air-oxidized CN-inhibited ubiquinol oxidase and its dithionite-treated (and quenched at 77 K just after the addition) forms were examined at 15 K. Addition of cyanide to the air-oxidized enzyme reduced the intensity of a g = 6 high spin signal without affecting the g = 3 low spin signal (g = 2.98, 2.26, and 1.45) (Fig. 3, a and b) as described previously(11, 30) . Addition of excess sodium dithionite to the air-oxidized CN-inhibited enzyme caused a rapid disappearance of the g = 3 low-spin signal and an appearance of a new low-spin signal with g = 3.24 (Fig. 3c). Prolonged incubation with sodium dithionite eventually eliminated the g = 3.24 low spin signal. This EPR signal is assignable to the Fe-C=N species (22, 23) on the basis of similarity to the corresponding species (g = 3.58) of the partially reduced CN-inhibited cytochrome c oxidase(32) . Occasionally we observed a weak stretching band at 2123 cm (for CN) which shifted to 2078 cm upon CN substitution (Table 1). This band also appeared in the partially reduced CN-inhibited states (one-fourth-reduced and one-half-reduced states; see later) and, therefore, may be assignable to the Fe-C=N species.

Figure 3: EPR spectra of ubiquinol oxidase in the air-oxidized (a) and the air-oxidized CN-inhibited (b) states, and effect of dithionite-treatment on the air-oxidized CN-inhibited form (c) at 15 K. Cyanide (CN) was added to the air-oxidized enzyme (0.39 mM) (a) at a final concentration of 5 mM, and they were incubated on ice overnight to ensure complete binding of cyanide (b). Then, slight excess sodium dithionite was added anaerobically to the CN-inhibited enzyme in an EPR tube through a rubber septum, mixed quickly, and the sample was frozen in liquid nitrogen (77 K) (c).

Influences of Loosely Bound Q on the FT-IR Spectra of the Air-oxidized CN-inhibited Ubiquinol Oxidase

The FT-IR spectra of these autoreduced CN-inhibited enzymes were characterized with the appearance of a strong cyanide stretching band at 2169 cm (in an HO buffer) (Fig. 1, c and d). Careful measurements on the time-dependent spectral change showed the following. 1) There is a preceding phase forming a 2198 cm band species (Fig. 1c). 2) The formation of the 2169 cm band species follows. This phase also shows weak infrared bands at 2076 and 2038 cm (Fig. 1d). 3) The development of the 2169 cm band intensity reaches a plateau as the 2146 cm band disappears, but the 2034.5 cm band characteristic to the Fe-C=N adduct does not grow so strong. 4) A further incubation causes a gradual decrease in the intensity of the 2169 cm band itself. One of unique features of this 2169 cm species is its peculiar cyanide-isotopic shift pattern that is very different from the usual metal-bound cyanide species (Table 1). The other is its strong DO shift (Table 1). In a DO medium, the 2169 cm band shifted to 2161 cm. Further, this 2169 cm species passed through a membrane filter (MWCO = 10,000) (Fig. 1e) indicating that this is a small molecular complex released from the enzyme.

Influences of Partial and Full Reduction of the CN-inhibited Ubiquinol Oxidase

()

Cyanide Binding to the Binuclear Center Mutant and to the Bound Q-free Wild-type Oxidases

Figure 4: Cyanide (C) bindings to the bound Q-free ubiquinol oxidase (0.21 mM) in the air-oxidized state. a, the FT-IR spectrum in the C-N stretching region after incubation of the enzyme with 5 mMCN for 150 min on ice. b, the FT-IR spectrum in the C-N stretching region after incubation of the enzyme with 5 mMCN and 1 mM Q for 46 h on ice. Other conditions are the same as described in the legend to Fig. 1.

Partial Reduction of the CN-inhibited Cytochrome c Oxidase

Figure 5: FT-IR spectra of the CN-inhibited cytochrome c oxidase at various redox levels in the region from 2000 to 2200 cm. The partially reduced enzyme (1.0 mM) in 50 mM Tris-DCl (pD = 8.0) was incubated with 5 mM KCN. a, CN-inhibited resting state (0/4); b, one-electron equivalent-reduced CN-inhibited state (1/4); c, two-electron equivalents-reduced CN-inhibited state (2/4); d, three-electron equivalents-reduced CN-inhibited state (3/4). Other conditions are the same as described in the legend to Fig. 1.

During these spectral changes we observed an appearance of a 2162 cm band in a DO buffer (Fig. 5b and c). In a similar experiment carried out in an HO buffer, the 2162 cm band in the partially reduced states (one-fourth and one-half) shifted to 2169 cm without affecting the 2152 and 2131 cm bands (spectra not shown). These observations strongly suggest that a cyanide species very similar to that found in the CN-inhibited bo-type ubiquinol oxidase was produced in the partially reduced state(s) of the CN-inhibited cytochrome c oxidase. The intensity of the 2169 cm band (in the DO buffer, or the 2162 cm band in the HO buffer) changed in a dose- and time-dependent manner. A higher cyanide concentration (20 mM) and a longer incubation time (70 h) in the partially reduced state (one-fourth-reduced) caused a stronger intensity of the 2169 cm band (spectra not shown). The 2165 cm band (in a DO buffer) observed by Yoshikawa and Caughey (28, 34) is likely due to the same species observed in the present study.

Metal Content Analysis

DISCUSSION

Implication for the Cyanide Coordination Structure at the Binuclear Center

The large difference of the bound C-N stretching vibration between bo-type ubiquinol oxidase and cytochrome c oxidase in the reduced state is likely due to a specific character of the cyanide-binding to the binuclear center(36) . Cyanide binding to other typical ferrous hemoproteins is extremely weak, except for horseradish peroxidase in which the electrostatic interaction (or hydrogen bond) between a protonated distal His residue and a ferrous heme-bound cyanide plays a substantial role in the stabilization(37) . Thus, it is possible that the ferrous heme-bound cyanide at the binuclear center is stabilized by a protonated His residue in the vicinity of the heme in the fully reduced state. The protonation of the His residue may be directly coupled to the uptake of a proton upon binding of cyanide to the reduced oxidase(38) . Among three invariant His residues (His-284, His-333, and His-334) on the distal side of the high spin heme(6, 7) , His-284 is likely to have such a role since it is probably not an obligatory ligand to Cu unlike His-333 and His-334(12, 24, 30) . Alternatively, His-333 may perform such a part in cytochrome c oxidase, since it seems to be disordered or to have multiple conformations in an x-ray crystal structure for the azide-inhibited air-oxidized cytochrome c oxidase from Paracoccus denitrificans(39) , but not for the air-oxidized cytochrome c oxidase from bovine heart mitochondria(40) . The x-ray crystal structures revealed also that His284 can form hydrogen bond with Tyr-288 and Trp-280 and His-333 with Thr-352 or the carbonyl oxygen of Phe-348(39, 40) . Thus the greater difference in the Fe-C=N stretching vibration is likely due to the difference in the interaction between the protonated distal His residue and the Fe-C=N moiety.

The binuclear center mutant oxidases showed neither CN-bridging infrared band in the air-oxidized state nor Fe-C=N infrared band in the fully reduced state, although several Fe-C=N species seemed to be formed. It is clear that presence of the Cu center is essential for the binding of cyanide to the ferrous heme since these mutant oxidases did somehow bind CO (although with a very broad infrared band around 1970 cm (His333Ala (24) and Y288L) or with very weak affinity (H284A)). However, we could not evaluate the specific role of the imidazole group of His-284 and His-333 and the phenol group of Tyr-288 in the present study.

Structural Implication on the 2169 cmSpecies

This 2169 cm species showed unusual cyanide isotope shifts and a DO shift (Table 1) and was able to pass through a membrane filter (MWCO = 10,000). Metal content analyses of the enzyme before and after the anaerobic cyanide treatment in the presence of excess Q revealed that a substantial amount (30%) of copper ions was released in the filtrate after the treatment (Table 2). These observations suggest that the 2169 cm band arose from a low molecular weight copper-cyano species (i.e. a CuCN complex) released from bo-type ubiquinol oxidase. EPR analysis revealed no indication of a Cu ion in the enzyme preparation that showed the 2169 cm band, suggesting that this CuCN complex was in reduced state (i.e. Cu state).

There are several reports describing the release of copper ions from copper proteins in the presence of cyanide. For cytochrome c oxidase both the Cu and Cu centers of the air-oxidized enzyme could be removed by dialysis against a CN-containing solution(41, 42) . It must be noted, however, that the conditions are very different from the one in the present study. The dialysis was done at alkaline pH (i.e. pH 10), and a much higher concentration (50 mM 1.0 M) of cyanide was required(41, 42) . Among the previous reports, our particular interest is the cyanide binding study for Cu/Zn-superoxide dismutase from bovine erythrocyte(43) . Raman and FT-IR spectroscopic studies revealed that the native Cu-superoxide dismutase binds one cyanide showing a band at 2137 cm. With increased concentration of cyanide the 2137 cm band became weaker, and strong vibrational modes (2123, 2093, and 2075 cm) developed concomitantly. These bands were due to di-, tri-, and tetracyano Cu complexes, respectively, arising from copper removed from the protein. Simultaneously a new band appeared at 2169 cm having an abnormally large CN shift of -60 cm(43) . This 2169 cm species was also observed in the filtrate through a membrane filter(43) . All of these observations strongly suggest that the 2169 cm species found for the superoxide dismutase-CN system is identical with the 2169 cm species in the present study. Han et al. (43) concluded that the 2169 cm species was neither a protein species nor a microcell of CuCN solid because of its abnormal cyanide isotopic shifts.

The 8 cm DO downshift observed for the 2169 cm species is not likely due to a direct hydrogen bonding of an HO (or DO) molecule in medium to the CN moiety of the CuCN complex, as hydrogen bonding becomes weakened by an H-D exchange(44) . For the horseradish peroxidase (Fe)-CN system, an 8 cm DO upshift (from 2029 to 2037 cm) of the C-N stretching frequency has been attributed to the formation of a hydrogen bond between the heme-coordinated cyanide anion and a protonated (or deuterated) distal His residue(37) . It is more likely, therefore, that an HO (or DO) molecule itself also participates in forming the CuCN complex and the resulting intramolecular interactions between cyanide(s) and a water ligand(s) may be essential for the appearance of the 2169 cm band and its unusual vibrational mode pattern.

We have tried to prepare the CuCN complex by mixing copper(I) chloride and/or copper(I) cyanide with varying amounts of cyanide in aqueous solution, but without success. It was reported that a reaction involving copper(I), cyanide, and water under conditions of high temperature and pressure gave a by-product species with (Cu(CN)(HO)) structure, comprising a two-dimensional polymer(45) . We propose that this kind of species may be responsible for the 2169 cm band.

Mechanism of the Formation of the CuCN Complex-The partially reduced conditions seem essential for the formation and release of the CuCN complex. Indeed the 2169 cm species could be quickly produced by anaerobic partial reduction of the CN-inhibited enzyme but not at all from the fully reduced form. The absence of the 2034.5 cm band that is characteristic to the Fe-C=N adduct may be noticed when the 2169 cm species developed fully by the autoreduction of the CN-inhibited enzyme. This observation is consistent with the notion that the presence of the Cu center is essential for the binding of cyanide to the reduced enzyme as discussed in the previous section.

The CN-inhibited bound Q-free oxidase resulted in neither the development of the 2169 cm band nor the release of the Cu center. A simultaneous addition of excess Q with cyanide to the bound Q-free oxidase was not so effective. These observations suggest that the precise structure around the binuclear site or the quinone binding site(s) may be essential for the formation of the CuCN complex. The role of the loosely bound ubiquinones (Q or Q) is not clear, but is likely only for providing electron equivalents to the metal centers of ubiquinol oxidase by an unknown mechanism. This is based on the observation of the 2169 cm species in the one-fourth-reduced or one-half-reduced conditions of the PEG-treated CN-inhibited ubiquinol oxidase, which contains only one molecule of Q at the high affinity binding site.

It is of great importance that the same 2169 cm species could be produced by anaerobic partial reduction of the CN-inhibited cytochrome c oxidase in which no ubiquinone molecule is bound. This observation suggests that there is a common intermediate structure at the binuclear center of the heme-copper respiratory oxidases in the partially reduced CN-inhibited state which is very susceptible to the cyanide binding(s) and release of the Cu center. The greater formation of the 2169 cm species for bo-type ubiquinol oxidase than cytochrome c oxidase may be related to the instability of the Fe-C=N species (although its presence was confirmed with the g = 3.24 EPR signal) in the partially reduced CN-inhibited enzyme. This difference is also likely due to a slight difference(s) of the cyanide coordination structure (including distal His residues) at the binuclear center. The unique property of the heme-copper oxidase revealed in the present study may provide a clue for understanding a mechanism of the dioxygen reduction chemistry and the redox-linked proton pumping.

FOOTNOTES

*

This work was supported in part by Grant-in-Aid for Scientific Research on Priority Areas from the Ministry of Education, Science, Sports and Culture, Japan (to M. T., T. M. (Cellular Energetics), H. H., and T. M. (Bioinorganic Chemistry)). This is a paper XIX in the series ``Structure-Function Studies on the Escherichia coli Cytochrome bo Complex.'' The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore by hereby marked ``advertisement'' in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

§

To whom correspondence should be addressed. Fax: 81-7915-8-0189; :tsubaki{at}sci.himeji-tech.ac.jp.

()

The abbreviations used are: QH, ubiquinol-8, the reduced form of ubiquinone-8; Q, ubiquinone-8; Q, ubiquinone-1; FT, Fourier transform; IR, infrared; MWCO, molecular weight cut-off; PEG, polyethylene glycol; Fe, iron center of heme O; Fe

()

T. Mogi, J. Minagawa, T. Hirano, M. Sato-Watanabe, M. Tsubaki, H. Hori, and Y. Anraku, unpublished results.

()

M. Sato-Watanabe, S. Itoh, T. Mogi, K. Matsuura, H. Miyoshi, and Y. Anraku, unpublished results.

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