On the anomalous temperature behaviour of the EPR signal of monovalent nickel in hydrogenase

Characterization of a cyanobacterial-like uptake [NiFe] hydrogenase: EPR and FTIR spectroscopic studies of the enzyme from Acidithiobacillus ferrooxidans

Electron paramagnetic resonance (EPR) and Fourier transform IR studies on the soluble hydrogenase from Acidithiobacillus ferrooxidans are presented. In addition, detailed sequence analyses of the two subunits of the enzyme have been performed. They show that the enzyme belongs to a group of uptake [NiFe] hydrogenases typical for Cyanobacteria. The sequences have also a close relationship to those of the H(2)-sensor proteins, but clearly differ from those of standard [NiFe] hydrogenases. It is concluded that the structure of the catalytic centre is similar, but not identical, to that of known [NiFe] hydrogenases. The active site in the majority of oxidized enzyme molecules, 97% in cells and more than 50% in the purified enzyme, is EPR-silent. Upon contact with H(2) these sites remain EPR-silent and show only a limited IR response. Oxidized enzyme molecules with an EPR-detectable active site show a Ni(r)*-like EPR signal which is light-sensitive at cryogenic temperatures. This is a novelty in the field of [NiFe] hydrogenases. Reaction with H(2) converts these active sites to the well-known Ni(a)-C* state. Illumination below 160 K transforms this state into the Ni(a)-L* state. The reversal, in the dark at 200 K, proceeds via an intermediate Ni EPR signal only observed with the H(2)-sensor protein from Ralstonia eutropha. The EPR-silent active sites in as-isolated and H(2)-treated enzyme are also light-sensitive as observed by IR spectra at cryogenic temperatures. The possible origin of the light sensitivity is discussed. This study represents the first spectral characterization of an enzyme of the group of cyanobacterial uptake hydrogenases.

Direct monitoring of the electron pool effect of cytochrome c3 by highly sensitive EQCM measurements

Cytochrome c(3) from Desulfovibrio vulgaris has four hemes per molecule, and a redox change at the hemes alters the conformation of the protein, leading to a redox-dependent change in the interaction of cytochrome c(3) with redox partners (an electron acceptor or an electron donor). The redox-dependent change in this interaction was directly monitored by the high-performance electrochemical quartz crystal microbalance (EQCM) technique that has been improved to give high sensitivity in solution. In this method, cytochrome c(3) molecules in solution associate electrostatically with a viologen-immobilized quartz crystal electrode as a monolayer, and redox of the associating cytochrome c(3) is controlled by the immobilized viologen. This technique makes it possible to measure the access of cytochrome c(3) to the electrode or repulsion from the electrode, and hence interconversion between an electrostatic complex and an electron transfer complex on the cytochrome c(3) and the viologen as a mass change accompanying a potential sweep is monitored. In addition, simultaneous measurement of a mass change and a potential step reveals that the cytochrome c(3) stores electrons when the four hemes are reduced (an electron pool effect), that is, the oxidized cytochrome c(3) facilitates acceptance of electrons from the immobilized viologen molecule, but the reduced cytochrome c(3) donates the accepted electrons to the viologen with difficulty.

The membrane-bound [NiFe]-hydrogenase (Ech) from Methanosarcina barkeri: unusual properties of the iron-sulphur clusters

The purified membrane-bound [NiFe]-hydrogenase from Methanosarcina barkeri was studied with electron paramagnetic resonance (EPR) focusing on the properties of the iron-sulphur clusters. The EPR spectra showed signals from three different [4Fe-4S] clusters. Two of the clusters could be reduced under 101 kPa of H2, whereas the third cluster was only partially reduced. Magnetic interaction of one of the clusters with an unpaired electron localized on the Ni-Fe site indicated that this was the proximal cluster as found in all [NiFe]-hydrogenases. Hence, this cluster was assigned to be located in the EchC subunit. The other two clusters could therefore be assigned to be bound to the EchF subunit, which has two conserved four-Cys motifs for the binding of a [4Fe-4S] cluster. Redox titrations at different pH values demonstrated that the proximal cluster and one of the clusters in the EchF subunit had a pH-dependent midpoint potential. The possible relevance of these properties for the function of this proton-pumping [NiFe]-hydrogenase is discussed.

The H2 sensor of Ralstonia eutropha. Biochemical characteristics, spectroscopic properties, and its interaction with a histidine protein kinase

Previous genetic studies have revealed a multicomponent signal transduction chain, consisting of an H(2) sensor, a histidine protein kinase, and a response regulator, which controls hydrogenase gene transcription in the proteobacterium Ralstonia eutropha. In this study, we isolated the H(2) sensor and demonstrated that the purified protein forms a complex with the histidine protein kinase. Biochemical and spectroscopic analysis revealed that the H(2) sensor is a cytoplasmic [NiFe]-hydrogenase with unique features. The H(2)-oxidizing activity was 2 orders of magnitude lower than that of standard hydrogenases and insensitive to oxygen, carbon monoxide, and acetylene. Interestingly, only H(2) production but no HD formation was detected in the D(2)/H(+) exchange assay. Fourier transform infrared data showed an active site similar to that of standard [NiFe]-hydrogenases. It is suggested that the protein environment accounts for a restricted gas diffusion and for the typical kinetic parameters of the H(2) sensor. EPR analysis demonstrated that the [4Fe-4S] clusters within the small subunit were not reduced under hydrogen even in the presence of dithionite. Optical spectra revealed the presence of a novel, redox-active, n = 2 chromophore that is reduced by H(2). The possible involvement of this chromophore in signal transduction is discussed.

Pre-steady-state kinetics of the reactions of [NiFe]-hydrogenase from Chromatium vinosum with H2 and CO

Results are presented of the first rapid-mixing/rapid-freezing studies with a [NiFe]-hydrogenase. The enzyme from Chromatium vinosum was used. In particular the reactions of active enzyme with H2 and CO were monitored. The conversion from fully reduced, active hydrogenase (Nia-SR state) to the Nia-C* state was completed in less than 8 ms, a rate consistent with the H2-evolution activity of the enzyme. The reaction of CO with fully reduced enzyme was followed from 8 to 200 ms. The Nia-SR state did not react with CO. It was discovered, contrary to expectations, that the Nia-C* state did not react with CO when reactions were performed in the dark. When H2 was replaced by CO, a Nia-C* EPR signal appeared within 11 ms; this was also the case when H2 was replaced by Ar. With CO, however, the Nia-C* state decayed within 40 ms, due to the generation of the Nia-S.CO state (the EPR-silent state of the enzyme with bound CO). The Nia-C* state, induced after 11 ms by replacing H2 by CO in the dark, could be converted, in the frozen enzyme, into the EPR-detectable state with CO bound to nickel (Nia*.CO) by illumination at 30 K (evoking the Nia-L* state), followed by dark adaptation at 200 K. This can be explained by assuming that the Nia-C* state represents a formally trivalent state of nickel, which is unable to bind CO, whereas nickel in the Nia-L* and the Nia*.CO states is formally monovalent.

Characterization of the active site of a hydrogen sensor from Alcaligenes eutrophus

A third hydrogenase was recently identified in the proteobacterium Alcaligenes eutrophus as a constituent of a novel H2-sensing multicomponent regulatory system. This regulatory hydrogenase (RH) has been overexpressed in cells deficient in both the NAD+-reducing [NiFe]-hydrogenase and the membrane-bound [NiFe]-hydrogenase. EPR, FTIR and activity studies of membrane-free extracts revealed that the RH has an active site much like that of standard [NiFe]-hydrogenases, i.e. a Ni-Fe site with two CN- groups and one CO molecule. Its catalytic power is low, but the RH is always active, insensitive to oxygen, and occurs in only two redox states.

On the redox equilibrium between H2 and hydrogenase

Redox titrations of the nickel ion in active hydrogenase from Methanobacterium thermoautotrophicum and Chromatium vinosum were performed in the absence of artificial redox mediators, by variation of the H2-partial pressure. These experiments revealed a redox behaviour of the nickel ion which differed remarkably from previous redox titrations in the presence of redox mediators. Notably the EPR signal of the species earlier characterized as monovalent nickel with bound hydrogen, behaved as an n = 2 redox component upon reduction under varying H2-partial pressures. The EPR signal was not a transient one and persisted upon removal of hydrogen. Possible redox processes to explain these observations are discussed. A similar behaviour of nickel was also observed in enzyme as present in intact cells of M. thermoautotrophicum. These results suggest that nickel hydrogenases possess a second site for reaction with H2.

Structure-function relationships among the nickel-containing hydrogenases

The enzymology of the heterodimeric (NiFe) and (NiFeSe) hydrogenases, the monomeric nickel-containing hydrogenases plus the multimeric F420-(NiFe) and NAD(+)-(NiFe) hydrogenases are summarized and discussed in terms of subunit localization of the redox-active nickel and non-heme iron clusters. It is proposed that nickel is ligated solely by amino acid residues of the large subunit and that the non-heme iron clusters are ligated by other cysteine-rich polypeptides encoded in the hydrogenase operons which are not necessarily homologous in either structure or function. Comparison of the hydrogenase operons or putative operons and their hydrogenase genes indicate that the arrangement, number and types of genes in these operons are not conserved among the various types of hydrogenases except for the gene encoding the large subunit. Thus, the presence of the gene for the large subunit is the sole feature common to all known nickel-containing hydrogenases and unites these hydrogenases into a large but diverse gene family. Although the different genes for the large subunits may possess only nominal general derived amino acid homology, all large subunit genes sequenced to date have the sequence R-X-C-X-X-C fully conserved in the amino terminal region of the polypeptide chain and the sequence of D-P-C-X-X-C fully conserved in the carboxyl terminal region. It is proposed that these conserved motifs of amino acids provide the ligands required for the binding of the redox-active nickel. The existing EXAFS (Extended X-ray Absorption Fine Structure) information is summarized and discussed in terms of the numbers and types of ligands to the nickel and the various redox species of nickel defined by EPR spectroscopy. New information concerning the ligands to nickel is presented based on site-directed mutagenesis of the gene encoding the large subunit of the (NiFe) hydrogenase-1 of Escherichia coli. Based on considerations of the biochemical, molecular and biophysical information, ligand environments of the nickel in different redox states of the (NiFe) hydrogenase are proposed.

Effect of 17O2 and 13CO on EPR spectra of nickel in hydrogenase from Chromatium vinosum

Oxygen, either molecular oxygen or a reduction adduct, can tightly bind in the vicinity of the two forms of trivalent nickel occurring in hydrogenase from Chromatium vinosum, as evident from studies with 17O-enriched O2. This oxygen is not in the first coordination sphere of nickel. As has been reported earlier for hydrogenase from Desulfovibrio gigas (Fernandez, V.M., Hatchikian, A.C., Patil, D.S. and Cammack, R. (1986) Biochim. Biophys. Acta 883, 145-154), also the relative activity of the C.vinosum enzyme correlates well with the presence of only one of the two Ni(III) forms in the oxidized preparation. These results make it less likely that a specific oxygenation of only one of the Ni(III) forms would be the reason for the reversible inactivation of nickel hydrogenases by oxygen. Reaction of H2-reduced enzyme with 13CO now demonstrated beyond doubt that: (i) One 13CO molecule is a direct ligand to nickel in axial position; and (ii) hydrogen binds at the same coordination site as CO. It can also be concluded that hydrogen is not bound as a hydride ion, but presumably as molecular hydrogen. A simple way to explain the EPR spectra from the 13CO-adduct of the enzyme is to assume a monovalent state for the nickel.

The structure and mechanism of iron-hydrogenases

Hydrogenases devoid of nickel and containing only Fe-S clusters have been found so far only in some strictly anaerobic bacteria. Four Fe-hydrogenases have been characterized: from Megasphaera elsdenii, Desulfovibrio vulgaris (strain Hildenborough), and two from Clostridium pasteurianum. All contain two or more [4Fe-4S]1+,2+ or F clusters and a unique type of Fe-S center termed the H cluster. The H cluster appears to be remarkably similar in all the hydrogenases, and is proposed as the site of H2 oxidation and H2 production. The F clusters serve to transfer electrons between the H cluster and the external electron carrier. In all of the hydrogenases the H cluster is comprised of at least three Fe atoms, and possibly six. In the oxidized state it contains two types of magnetically distinct Fe atoms, has an S = 1/2 spin state, and exhibits a novel rhombic EPR signal. The reduced cluster is diamagnetic (S = 0). The oxidized H cluster appears to undergo a conformation change upon reduction with H2 with an increase in Fe-Fe distances of about 0.5 A. Studies using resonance Raman, magnetic circular dichroism and electron spin echo spectroscopies suggest that the H cluster has significant non-sulfur coordination. The H cluster has two binding sites for CO, at least one of which can also bind O2. Binding to one site changes the EPR properties of the cluster and gives a photosensitive adduct, but does not affect catalytic activity. Binding to the other site, which only becomes exposed during the catalytic cycle, leads to loss of catalytic activity. Mechanisms of H2 activation and electron transfer are proposed to explain the effects of CO binding and the ability of one of the hydrogenases to preferentially catalyze H2 oxidation.

Spectroscopic characterization of the nickel and iron-sulphur clusters of hydrogenase from the purple photosynthetic bacterium Thiocapsa roseopersicina. 1. Electron spin resonance spectroscopy

The thermostable hydrogenase from Thiocapsa roseopersicina was examined by low-temperature ESR spectroscopy. Two types of signals were detected, from an oxidized iron-sulphur cluster and a nickel centre (Ni-A). In the oxidized protein additional signals were observed due to spin-spin interaction between the two paramagnetic centres. This interaction could be reversibly abolished by reduction to a redox potential below 105 mV. This implies that an additional redox centre is involved in the interaction, for which an Fe3+ ion is suggested. Reduction with hydrogen induced a second type of nickel ESR signal (Ni-C), corresponding to an intermediate redox state seen in other nickel hydrogenases. The Ni-C species was light-sensitive at cryogenic temperatures. At temperatures near to 4.2 K the Ni-C signal showed evidence of interaction with another paramagnetic centre, presumably a second iron-sulphur cluster. On reoxidation a signal due to a third Ni(III) species, Ni-B, increased in amplitude. These results establish that metal centres in the hydrogenase from T. roseopersicina are closely similar to those of the well-studied hydrogenase from Chromatium vinosum.

Immunological comparison of subunits isolated from various hydrogenases of aerobic hydrogen bacteria

Polyclonal, monospecific antibodies were produced against the two subunits (Mr 62,000, and Mr 31,000), isolated from the membrane-bound hydrogenase of Alcaligenes eutrophus H16. The antibodies (IgG fractions) were purified from crude sera by Protein A-Sepharose CL-4B chromatography. By double immunodiffusion assays and tandem-crossed immunoelectrophoresis the large and the small subunit were demonstrated not to be immunologically related. Immunological comparison of these subunits with the four non-identical subunits (Mr 63,000, 56,000, 30,000 and 26,000) of the NAD-linked, soluble hydrogenase from A. eutrophus H16 showed that the subunits of the membrane-bound hydrogenase did not cross-react with any of the antibodies raised against the four subunits of the NAD-linked enzyme and that, vice versa, none of these four subunits cross-reacted with antibodies raised against the two subunits of the membrane-bound hydrogenase. This means that A. eutrophus H16 contains altogether six non-identical immunologically unrelated hydrogenase polypeptides. The membrane-bound hydrogenases were isolated and purified from various aerobic H2-oxidizing bacteria: A. eutrophus H16, A. eutrophus type strain, A. eutrophus CH34, A. eutrophus Z1, A. hydrogenophilus, Paracoccus denitrificans and strain Cd2/01. All these proteins resembled each other and each consisted of two non-identical polypeptides. A complete separation of these subunits was achieved at high-yield by preparative FPLC gel filtration on three Superose 12 columns connected in series, using SDS and DTT-containing sodium phosphate buffer (pH 7.0). The small subunits of these enzymes turned out to be immunologically closely related to each other; they were either identical or almost identical. The large subunits were also related, but less pronounced. Only the large subunits from Z1 and type strain reacted fully identical with the H16 subunit. Of the two isolated, homogeneous subunits of the membrane-bound hydrogenase from A. eutrophus H16, the amino acid compositions and the NH2-terminal sequences have been determined. The results confirmed the diversity of the large and the small subunit. Furthermore, for comparison also the NH2-terminal sequences of the two subunits from the hydrogenase of A. eutrophus CH34 have been analysed.