ESR-detectable nickel and iron-sulphur centres in relation to the reversible activation of Desulfovibrio gigas hydrogenase

New insights into the oxidation process from neutron and X-ray crystal structures of an O2-sensitive [NiFe]-hydrogenase

[NiFe]-hydrogenase from Desulfovibrio vulgaris Miyazaki F is an O2-sensitive enzyme that is inactivated in the presence of O2 but the oxidized enzyme can recover its catalytic activity by reacting with H2 under anaerobic conditions. Here, we report the first neutron structure of [NiFe]-hydrogenase in its oxidized state, determined at a resolution of 2.20 Å. This resolution allowed us to reinvestigate the structure of the oxidized active site and to observe the positions of protons in several short hydrogen bonds. X-ray anomalous scattering data revealed that a part of the Ni ion is dissociated from the active site Ni-Fe complex and forms a new square-planar Ni complex, accompanied by rearrangement of the coordinated thiolate ligands. One of the thiolate Sγ atoms is oxidized to a sulfenate anion but remains attached to the Ni ion, which was evaluated by quantum chemical calculations. These results suggest that the square-planar complex can be generated by the attack of reactive oxygen species derived from O2, as distinct from one-electron oxidation leading to a conventional oxidized form of the Ni-Fe complex. Another major finding of this neutron structure analysis is that the Cys17S thiolate Sγ atom coordinating to the proximal Fe-S cluster forms an unusual hydrogen bond with the main-chain amide N atom of Gly19S with a distance of 3.25 Å, where the amide proton appears to be delocalized between the donor and acceptor atoms. This observation provides insight into the contribution of the coordinated thiolate ligands to the redox reaction of the Fe-S cluster.

Second and Outer Coordination Sphere Effects in Nitrogenase, Hydrogenase, Formate Dehydrogenase, and CO Dehydrogenase

Gases like H2, N2, CO2, and CO are increasingly recognized as critical feedstock in "green" energy conversion and as sources of nitrogen and carbon for the agricultural and chemical sectors. However, the industrial transformation of N2, CO2, and CO and the production of H2 require significant energy input, which renders processes like steam reforming and the Haber-Bosch reaction economically and environmentally unviable. Nature, on the other hand, performs similar tasks efficiently at ambient temperature and pressure, exploiting gas-processing metalloenzymes (GPMs) that bind low-valent metal cofactors based on iron, nickel, molybdenum, tungsten, and sulfur. Such systems are studied to understand the biocatalytic principles of gas conversion including N2 fixation by nitrogenase and H2 production by hydrogenase as well as CO2 and CO conversion by formate dehydrogenase, carbon monoxide dehydrogenase, and nitrogenase. In this review, we emphasize the importance of the cofactor/protein interface, discussing how second and outer coordination sphere effects determine, modulate, and optimize the catalytic activity of GPMs. These may comprise ionic interactions in the second coordination sphere that shape the electron density distribution across the cofactor, hydrogen bonding changes, and allosteric effects. In the outer coordination sphere, proton transfer and electron transfer are discussed, alongside the role of hydrophobic substrate channels and protein structural changes. Combining the information gained from structural biology, enzyme kinetics, and various spectroscopic techniques, we aim toward a comprehensive understanding of catalysis beyond the first coordination sphere.

Protonation mechanisms of Nickel Complexes Relevant to Industrial and Biological Catalysis

The sites of protonation and the subsequent rearrangement reactions of simple nickel complexes containing hydride, thiolate and alkyl ligands are reviewed, and the relevance of these reactions to the action of certain nickelbased catalysts are discussed.

Summary

Protonation at the metal and ligand is central to the understanding of how both enzymes and industrial catalysts operate at the molecular level. The recurring theme in studies on the protonation of all metal complexes is that the ultimate residence of the proton is not necessarily the initial binding site, and the movement of proton between sites can occur by a variety of mechanisms. These features are also evident in the reactions of simple nickel complexes and mechanistic studies are revealing the subtle interplay between ligand and metal which are the basis of the kinetic and thermodynamic control of protonation reactions at these sites.

Structure and electrochemistry of proteins harboring iron-sulfur clusters of different nuclearities. Part IV. Canonical, non-canonical and hybrid iron-sulfur proteins

A plethora of proteins are able to express iron-sulfur clusters, but have a clear picture of the different types of proteins and the different iron-sulfur clusters they harbor it is not easy. In the last five years we have reviewed structure/electrochemistry of metalloproteins expressing: (i) single types of iron-sulfur clusters (namely: {Fe(Cys)₄}, {[Fe₂S₂](Cys)₄}, {[Fe₂S₂](Cys)₃(X)} (X = Asp, Arg, His), {[Fe₂S₂](Cys)₂(His)₂}, {[Fe₃S₄](Cys)₃}, {[Fe₄S₄](Cys)₄} and {[Fe₄S₄](Cys)₃(nonthiolate ligand)} cores); (ii) metalloproteins harboring iron-sulfur centres of different nuclearities (namely: [4Fe-4S] and [2Fe-2S], [4Fe-4S] and [3Fe-4S], and [4Fe-4S], [3Fe-4S] and [2Fe-2S] clusters. Our target is now to review structure and electrochemistry of proteins harboring canonical, non-canonical and hybrid iron-sulfur proteins.

Hydrogenases

Hydrogenases catalyze the simple yet important interconversion between H₂ and protons and electrons. Found throughout prokaryotes, lower eukaryotes, and archaea, hydrogenases are used for a variety of redox and signaling purposes and are found in many different forms. This diverse group of metalloenzymes is divided into [NiFe], [FeFe], and [Fe] variants, based on the transition metal contents of their active sites. A wide array of biochemical and spectroscopic methods has been used to elucidate hydrogenases, and this along with a general description of the main enzyme types and catalytic mechanisms is discussed in this chapter.

Reactivation of the Ready and Unready Oxidized States of [NiFe]-Hydrogenases: Mechanistic Insights from DFT Calculations

The apparently simple dihydrogen formation from protons and electrons (2H⁺ + 2e^- ⇄ H₂) is one of the most challenging reactions in nature. It is catalyzed by metalloenzymes of amazing complexity, called hydrogenases. A better understanding of the chemistry of these enzymes, especially that of the [NiFe]-hydrogenases subgroup, has important implications for production of H₂ as alternative sustainable fuel. In this work, reactivation mechanism of the oxidized and inactive Ni-B and Ni-A states of the [NiFe]-hydrogenases active site has been investigated using density functional theory. Results obtained from this study show that one-electron reduction and protonation of the active site promote the removal of the bridging hydroxide ligand contained in Ni-B and Ni-A. However, this process is sufficient to activate only the Ni-B state. H₂ binding to the active site is required to convert Ni-A to the active Ni-SI_a state. Here, we also propose a reasonable structure for the spectroscopically well-characterized Ni-SI_r and Ni-SU species, formed respectively from the one-electron reduction of Ni-B and Ni-A. Ni-SI_r, depending on the pH at which the reaction occurs, features a bridging hydroxide ligand or a water molecule terminally coordinated to the Ni atom, whereas in Ni-SU a water molecule is terminally coordinated to the Fe atom, and the Cys64 residue is oxidized to sulfenate. The sulfenate oxygen atom in the Ni-A state affects the stereoelectronic properties of the binuclear cluster by modifying the coordination geometry of Ni, and consequently, by switching the regiochemistry of H₂O and H₂ binding from the Ni to the Fe atom. This effect is predicted to be at the origin of the different reactivation kinetics of the oxidized and inactive Ni-B and Ni-A states.

Redox-dependent conformational changes of a proximal [4Fe-4S] cluster in Hyb-type [NiFe]-hydrogenase to protect the active site from O2

Citrobacter sp. S-77 [NiFe]-hydrogenase harbors a standard [4Fe-4S] cluster proximal to the Ni-Fe active site. The presence of relocatable water molecules and a flexible aspartate enables the [4Fe-4S] to display redox-dependent conformational changes. These structural features are proposed to be the key aspects that protect the active site from O2 attack.

Reactivation of standard [NiFe]-hydrogenase and bioelectrochemical catalysis of proton reduction and hydrogen oxidation in a mediated-electron-transfer system

Standard [NiFe]-hydrogenase from Desulfovibrio vulgaris Miyazaki F (DvMF-H₂ase) catalyzes the uptake and production of hydrogen (H₂) and is a promising biocatalyst for future energy devices. However, DvMF-H₂ase experiences oxidative inactivation under oxidative stress to generate Ni-A and Ni-B states. It takes a long time to reactivate the Ni-A state by chemical reduction, whereas the Ni-B state is quickly reactivated under reducing conditions. Oxidative inhibition limits the application of DvMF-H₂ase in practical devices. In this research, we constructed a mediated-electron-transfer system by co-immobilizing DvMF-H₂ase and a viologen redox polymer (VP) on electrodes. The system can avoid oxidative inactivation into the Ni-B state at high electrode potentials and rapidly reactivate the Ni-A state by electrochemical reduction of VP. H₂ oxidation and H⁺ reduction were realized by adjusting the pH from a thermodynamic viewpoint. Using carbon felt as a working-electrode material, high current densities-up to (200 ± 70) and -(100 ± 9) mA cm^-3 for the H₂-oxidation and H⁺-reduction reactions, respectively-were attained.

Theoretical investigation of aerobic and anaerobic oxidative inactivation of the [NiFe]-hydrogenase active site

The extraordinary capability of [NiFe]-hydrogenases to catalyse the reversible interconversion of protons and electrons into dihydrogen (H₂) has stimulated numerous experimental and theoretical studies addressing the direct utilization of these enzymes in H₂ production processes.

The [NiFe]-Hydrogenase of Pyrococcus furiosus Exhibits a New Type of Oxygen Tolerance

We report the first direct electrochemical characterization of the impact of oxygen on the hydrogen oxidation activity of an oxygen-tolerant, group 3, soluble [NiFe]-hydrogenase: hydrogenase I from Pyrococcus furiosus (PfSHI), which grows optimally near 100 °C. Chronoamperometric experiments were used to probe the sensitivity of PfSHI hydrogen oxidation activity to both brief and prolonged exposure to oxygen. For experiments between 15 and 80 °C, following short (<200 s) exposure to 14 μM O2 under oxidizing conditions, PfSHI always maintains some fraction of its initial hydrogen oxidation activity; i.e., it is oxygen-tolerant. Reactivation experiments show that two inactive states are formed by interaction with oxygen and both can be quickly (<150 s) reactivated. Analogous experiments, in which the interval of oxygen exposure is extended to 900 s, reveal that the response is highly temperature-dependent. At 25 °C, under sustained 1% O2/ 99% H2 exposure, the H2oxidation activity drops nearly to zero. However, at 80 °C, up to 32% of the enzyme's oxidation activity is retained. Reactivation of PfSHI following sustained exposure to oxygen occurs on a much longer time scale (tens of minutes), suggesting that a third inactive species predominates under these conditions. These results stand in contrast to the properties of oxygen-tolerant, group 1 [NiFe]-hydrogenases, which form a single state upon reaction with oxygen, and we propose that this new type of hydrogenase should be referred to as oxygen-resilient. Furthermore, PfSHI, like other group 3 [NiFe]-hydrogenases, does not possess the proximal [4Fe3S] cluster associated with the oxygen tolerance of some group 1 enzymes. Thus, a new mechanism is necessary to explain the observed oxygen tolerance in soluble, group 3 [NiFe]-hydrogenases, and we present a model integrating both electrochemical and spectroscopic results to define the relationships of these inactive states.

Control of the transition between Ni-C and Ni-SI(a) states by the redox state of the proximal Fe-S cluster in the catalytic cycle of [NiFe] hydrogenase

[NiFe] hydrogenase catalyzes the reversible cleavage of H2. The electrons produced by the H2 cleavage pass through three Fe-S clusters in [NiFe] hydrogenase to its redox partner. It has been reported that the Ni-SI(a), Ni-C, and Ni-R states of [NiFe] hydrogenase are involved in the catalytic cycle, although the mechanism and regulation of the transition between the Ni-C and Ni-SI(a) states remain unrevealed. In this study, the FT-IR spectra under light irradiation at 138-198 K show that the Ni-L state of [NiFe] hydrogenase is an intermediate between the transition of the Ni-C and Ni-SI(a) states. The transition of the Ni-C state to the Ni-SI(a) state occurred when the proximal [Fe4S4]p(2+/+) cluster was oxidized, but not when it was reduced. These results show that the catalytic cycle of [NiFe] hydrogenase is controlled by the redox state of its [Fe4S4]p(2+/+) cluster, which may function as a gate for the electron flow from the NiFe active site to the redox partner.

The oxidative inactivation of FeFe hydrogenase reveals the flexibility of the H-cluster

Nature is a valuable source of inspiration in the design of catalysts, and various approaches are used to elucidate the mechanism of hydrogenases, the enzymes that oxidize or produce H2. In FeFe hydrogenases, H2 oxidation occurs at the H-cluster, and catalysis involves H2 binding on the vacant coordination site of an iron centre. Here, we show that the reversible oxidative inactivation of this enzyme results from the binding of H2 to coordination positions that are normally blocked by intrinsic CO ligands. This flexibility of the coordination sphere around the reactive iron centre confers on the enzyme the ability to avoid harmful reactions under oxidizing conditions, including exposure to O2. The versatile chemistry of the diiron cluster in the natural system might inspire the design of novel synthetic catalysts for H2 oxidation.

Structural basis for a [4Fe-3S] cluster in the oxygen-tolerant membrane-bound [NiFe]-hydrogenase

Membrane-bound respiratory [NiFe]-hydrogenase (MBH), a H(2)-uptake enzyme found in the periplasmic space of bacteria, catalyses the oxidation of dihydrogen: H(2) → 2H(+) + 2e(-) (ref. 1). In contrast to the well-studied O(2)-sensitive [NiFe]-hydrogenases (referred to as the standard enzymes), MBH has an O(2)-tolerant H(2) oxidation activity; however, the mechanism of O(2) tolerance is unclear. Here we report the crystal structures of Hydrogenovibrio marinus MBH in three different redox conditions at resolutions between 1.18 and 1.32 Å. We find that the proximal iron-sulphur (Fe-S) cluster of MBH has a [4Fe-3S] structure coordinated by six cysteine residues--in contrast to the [4Fe-4S] cubane structure coordinated by four cysteine residues found in the proximal Fe-S cluster of the standard enzymes--and that an amide nitrogen of the polypeptide backbone is deprotonated and additionally coordinates the cluster when chemically oxidized, thus stabilizing the superoxidized state of the cluster. The structure of MBH is very similar to that of the O(2)-sensitive standard enzymes except for the proximal Fe-S cluster. Our results give a reasonable explanation why the O(2) tolerance of MBH is attributable to the unique proximal Fe-S cluster; we propose that the cluster is not only a component of the electron transfer for the catalytic cycle, but that it also donates two electrons and one proton crucial for the appropriate reduction of O(2) in preventing the formation of an unready, inactive state of the enzyme.

Probing intermediates in the activation cycle of [NiFe] hydrogenase by infrared spectroscopy: the Ni-SIr state and its light sensitivity

The [NiFe] hydrogenase from the sulphate-reducing bacterium Desulfovibrio vulgaris Miyazaki F is reversibly inhibited in the presence of molecular oxygen. A key intermediate in the reactivation process, Ni-SI_r, provides the link between fully oxidized (Ni-A, Ni-B) and active (Ni-SI_a, Ni-C and Ni-R) forms of hydrogenase. In this work Ni-SI_r was found to be light-sensitive (T ≤ 110 K), similar to the active Ni-C and the CO-inhibited states. Transition to the final photoproduct state (Ni-SL) was shown to involve an additional transient light-induced state (Ni-SI₁₉₆₁). Rapid scan kinetic infrared measurements provided activation energies for the transition from Ni-SL to Ni-SI_r in protonated as well as in deuterated samples. The inhibitor CO was found not to react with the active site of the Ni-SL state. The wavelength dependence of the Ni-SI_r photoconversion was examined in the range between 410 and 680 nm. Light-induced effects were associated with a nickel-centred electronic transition, possibly involving a change in the spin state of nickel (Ni²⁺). In addition, at T ≤ 40 K the CN⁻ stretching vibrations of Ni-SL were found to be dependent on the colour of the monochromatic light used to irradiate the species, suggesting a change in the interaction of the hydrogen-bonding network of the surrounding amino acids. A possible mechanism for the photochemical process, involving displacement of the oxygen-based ligand, is discussed.

Enzymatic activity mastered by altering metal coordination spheres

Metalloenzymes control enzymatic activity by changing the characteristics of the metal centers where catalysis takes place. The conversion between inactive and active states can be tuned by altering the coordination number of the metal site, and in some cases by an associated conformational change. These processes will be illustrated using heme proteins (cytochrome c nitrite reductase, cytochrome c peroxidase and cytochrome cd1 nitrite reductase), non-heme proteins (superoxide reductase and [NiFe]-hydrogenase), and copper proteins (nitrite and nitrous oxide reductases) as examples. These examples catalyze electron transfer reactions that include atom transfer, abstraction and insertion.

Proton pathways in a [NiFe]-hydrogenase: A theoretical study

We present here a theoretical study to investigate possible proton pathways in the [NiFe]-hydrogenase from Desulfovibrio gigas. The approach used in this study consists of a combination of Poisson-Boltzmann and Monte Carlo simulations together with a distance-based network analysis to find possible groups involved in the proton transfer. Results obtained at different pH values show a reasonable number of proton active residues distributed by the protein interior and surface, with a concentration around the metal centres. The electrostatic interactions in this protein are strong, as shown by the unusual shape of the titration curves of several sites. Some residue pairs show strongly correlated protonations, indicating the sharing and probably exchange of a proton between them. The conjugation of the PB and MC simulations with the distance-based analysis allows a detailed characterization of the possible proton pathways. We discuss previous suggestions and propose a new complete pathway for the proton transfer between the active site and the surface. This pathway is mainly composed of histidines and glutamic acid residues.

The strength of EPR and ENDOR techniques in revealing structure-function relationships in metalloproteins

Recent technological and methodological advances have strongly increased the potential of electron paramagnetic resonance (EPR) and electron nuclear double resonance (ENDOR) techniques to characterize the structure and dynamics of metalloproteins. These developments include the introduction of powerful pulsed EPR/ENDOR methodologies and the development of spectrometers operating at very high microwave frequencies and high magnetic fields. This overview focuses on how valuable information about metalloprotein structure-function relations can be obtained using a combination of EPR and ENDOR techniques. After an overview of the historical development and a limited theoretical description of some of the key EPR and ENDOR techniques, their potential will be highlighted using selected examples of applications to iron-, nickel-, cobalt-, and copper-containing proteins. We will end with an outlook of future developments.

Characterization of the active site of catalytically inactive forms of [NiFe] hydrogenases by density functional theory

The inactive forms, unready (Ni-A, Ni-SU) and ready (Ni-B), of NiFe hydrogenases are modeled by examining the possibility of hydroxo, oxo, hydroperoxo, peroxo, and sulfenate groups in active-site models and comparing predicted IR frequencies and g tensors with those of the enzyme. The best models for Ni-A and Ni-SU have hydroxo (mu-OH) bridges between Fe and Ni and a terminal sulfenate [Ni-S(=O)Cys] group, although a hydroperoxo model for Ni-A is also quite viable, whereas the best model for Ni-B has only a mu-OH bridge. In addition, a mechanism for the activation of unready hydrogenase is proposed on the basis of the relative stabilities of sulfenate models versus peroxide models.

Pathways of H2 toward the active site of [NiFe]-hydrogenase

Hydrogenases catalyze the reversible oxidation of molecular hydrogen (H(2)), but little is known about the diffusion of H(2) toward the active site. Here we analyze pathways for H(2) permeation using molecular dynamics (MD) simulations in explicit solvent. Various MD simulation replicates were done, to improve the sampling of the system states. H(2) easily permeates hydrogenase in every simulation and it moves preferentially in channels. All H(2) molecules that reach the active site made their approach from the side of the Ni ion. H(2) is able to reach distances of <4 A from the active site, although after 6 A permeation is difficult. In this region we mutated Val-67 into alanine and perform new MD simulations. These simulations show an increase of H(2) inside the protein and at lower distances from the active site. This valine can be a control point in the H(2) access to the active center.

Density functional study of the catalytic cycle of nickel–iron [NiFe] hydrogenases and the involvement of high-spin nickel(II)

In light of recent experiments suggesting high-spin (HS) Ni(II) species in the catalytic cycle of [NiFe] hydrogenase, a series of models of the Ni(II) forms Ni-SI(I,II), SI-CO and Ni-R(I,II,III) were examined in their high-spin states via density functional calculations. Because of its importance in the catalytic cycle, the Ni-C form was also included in this study. Unlike the Ni(II) forms in previous studies, in which a low-spin (LS) state was assumed and a square-planar structure found, the optimized geometries of these HS Ni(II) forms resemble those observed in the crystal structures: a distorted tetrahedral to distorted pyramidal coordination for the NiS4. This resemblance is particularly significant because the LS state is 20-30 kcal/mol less stable than the HS state for the geometry of the crystal structure. If these Ni(II) forms in the enzyme are not high spin, a large change in geometry at the active site is required during the catalytic cycle. Furthermore, only the HS state for the CO-inhibited form SI-CO has CO stretching frequencies that match the experimental results. As in the previous work, these new results show that the heterolytic cleavage reaction of dihydrogen (where H2 is cleaved with the metal acting as a hydride acceptor and a cysteine as the proton acceptor) has a lower energy barrier and is more exothermic when the active site is oxidized to Ni(III). The enzyme models described here are supported by a calibrated correlation of the calculated and measured CO stretching frequencies of the forms of the enzyme. The correlation coefficient for the final set of models of the forms of [NiFe] hydrogenase is 0.8.

How are the ready and unready states of nickel–iron hydrogenase activated by H2? A density functional theory study

We have explored possible mechanisms for the formation of the catalytically active Ni(a)-S state of the enzyme, nickel iron hydrogenase, from the Ni*(r) (ready) or Ni*(u) (unready) state, by reaction with H(2), using density functional theory calculations with the BP86 functional in conjunction with a DZVP basis set. We find that for the reaction of the ready state, which is taken to have an -OH bridge, the rate determining step is the cleavage of H(2) at the Ni(3+) centre with a barrier of approximately 15 kcal mol(-1). We take the unready state to have a -OOH bridge, and find that reaction with H(2) to form the Ni(r)-S state can proceed by two possible routes. One such path has a number of steps involving electron transfer, which is consistent with experiment, as is the calculated barrier of approximately 19 kcal mol(-1). The alternative pathway, with a lower barrier, may not be rate determining. Overall, our predictions give barriers in line with experiment, and allow details of the mechanism to be explored which are inaccessible from experiment.

Structural differences between the ready and unready oxidized states of [NiFe] hydrogenases

[NiFe] hydrogenases catalyze the reversible heterolytic cleavage of molecular hydrogen. Several oxidized, inactive states of these enzymes are known that are distinguishable by their very different activation properties. So far, the structural basis for this difference has not been understood because of lack of relevant crystallographic data. Here, we present the crystal structure of the ready Ni-B state of Desulfovibrio fructosovorans [NiFe] hydrogenase and show it to have a putative mu-hydroxo Ni-Fe bridging ligand at the active site. On the other hand, a new, improved refinement procedure of the X-ray diffraction data obtained for putative unready Ni-A/Ni-SU states resulted in a more elongated electron density for the bridging ligand, suggesting that it is a diatomic species. The slow activation of the Ni-A state, compared with the rapid activation of the Ni-B state, is therefore proposed to result from the different chemical nature of the ligands in the two oxidized species. Our results along with very recent electrochemical studies suggest that the diatomic ligand could be hydro-peroxide.

Relativistic DFT calculation of the reaction cycle intermediates of [NiFe] hydrogenase: a contribution to understanding the enzymatic mechanism

Structures and spectroscopic observables of the paramagnetic intermediates of the enzymatic reaction cycle of the metalloenzyme [NiFe] hydrogenase were calculated using relativistic density functional theory (DFT) within the zero-order regular approximation (ZORA). By comparing experimental and calculated magnetic resonance parameters (g- and hyperfine tensors) for the states Ni-A, Ni-B, Ni-C, Ni-L, and Ni-CO the details of the atomic composition of these paramagnetic intermediates could be elucidated that are mostly not available from X-ray structure analysis. In general, good agreement between calculated and experimental observables could be obtained. A detailed picture of the changes of the active center during the catalytic cycle was deduced from the obtained structures. Based on these results, a consistent model for the sequence of redox states including protonation steps is proposed which is important for understanding the mechanism of the [NiFe] hydrogenase.

An orientation-selected ENDOR and HYSCORE study of the Ni-C active state of Desulfovibrio vulgaris Miyazaki F hydrogenase

Electron nuclear double resonance (ENDOR) and hyperfine sublevel correlation spectroscopy (HYSCORE) are applied to study the active site of catalytic [NiFe]-hydrogenase from Desulfovibrio vulgaris Miyazaki F in the reduced Ni-C state. These techniques offer a powerful tool for detecting nearby magnetic nuclei, including a metal-bound substrate hydrogen, and for mapping the spin density distribution of the unpaired electron at the active site. The observed hyperfine couplings are assigned via comparison with structural data from X-ray crystallography and knowledge of the complete g-tensor in the Ni-C state (Foerster et al. (2003) J Am Chem Soc 125:83-93). This is found to be in good agreement with density functional theory calculations. The two most strongly coupled protons (a(iso)=13.7, 11.8 MHz) are assigned to the beta-CH(2) protons of the nickel-coordinating cysteine 549, and a third proton (a(iso)=8.9 MHz) is assigned to a beta-CH(2) proton of cysteine 546. Using D(2)O exchange experiments, the presence of a hydride in the bridging position between the nickel and iron-recently been detected for a regulatory hydrogenase (Brecht et al. (2003) J Am Chem Soc 125:13075-13083)-is experimentally confirmed for the first time for catalytic hydrogenases. The hydride exhibits a small isotropic hyperfine coupling constant (a(iso)=-3.5 MHz) since it is bound to Ni in a direction perpendicular to the z-axis of the Ni (3d(z)(2)) orbital. Nitrogen signals that belong to the nitrogen N(epsilon) of His-88 have been identified. This residue forms a hydrogen bond with the spin-carrying Ni-coordinated sulfur of Cys-549. Comparison with other hydrogenases reveals that the active site is essentially the same in all proteins, including a regulatory hydrogenase.

High-spin Ni(II), a surprisingly good structural model for [NiFe] hydrogenase

The first density functional calculations on high-spin (HS) Ni(II) models for the active site of the [NiFe] hydrogenases predict a ligand arrangement about Ni that is in better agreement with the crystal structures than previous predictions for low-spin (LS) Ni(II) models. With the crystal structures' geometry, the HS form is approximately 20 kcal/mol lower in energy than the LS one.

Modeling the active sites of metalloenzymes. 4. Predictions of the unready states of [NiFe] Desulfovibrio gigas hydrogenase from density functional theory

Density functional theory has been used to predict the structures of a variety of active site models for the unready states, Ni-A and Ni-SU, of the [NiFe] hydrogenase from Desulfovibrio gigas. By comparing available experimental results on Ni-A, Ni-SU, and Ni-SI with the computational results on these model complexes, we have been able to identify the most likely formulas and structures for the active sites of Ni-A and Ni-SU. Ni-A is predicted to be a Ni(III)-Fe(II) species with the bridging hydroxo ligand, rather than the expected oxo ligand, while Ni-SU is predicted to be a Ni(II)-Fe(II) species with a water molecule coordinated to the Fe center. Both have one of the terminal S atoms (cysteines) protonated.

Construction of multicomponent catalytic films based on avidin-biotin technology for the electroenzymatic oxidation of molecular hydrogen

Two methods based on the avidin-biotin technology were developed for the multimonolayer immobilization of Desulfovibrio gigas hydrogenase on glassy carbon or gold electrodes. In both methods the molecular structure of the modified interface was the result of a step-by-step process. The first method alternates monolayers of avidin and biotinylated hydrogenase, the mediator (methyl viologen) being free to diffuse in the structure. In the second method, the avidin monolayers were used to immobilize both the biotinylated enzyme and a long-chain biotinylated viologen derivative. The viologen head of this hydrophilic arm shuttles the electrons between the electrode and the enzyme. The modified electrodes were evaluated for the electroenzymatic oxidation of molecular hydrogen, which has interest for the development of enzymatic fuel cells. The parameters that affect the current density of mediated oxidation of H(2) at the modified electrodes was studied. The second structure, which has given typical catalytic currents of 25 microA per cm(2) for 10 monolayers, was found clearly less efficient than the first structure (500 microA per cm(2) for 10 monolayers). In both methods the catalytic currents increased linearly with the number of monolayers of hydrogenase immobilized, which indicates that the multilayer structures are spatially ordered.

Purification and characterization of membrane-bound hydrogenase from Hydrogenobacter thermophilus strain TK-6, an obligately autotrophic, thermophilic, hydrogen-oxidizing bacterium

A membrane-bound hydrogenase was purified to electrophoretic homogeneity from the cells of Hydrogenobacter thermophilus strain TK-6, an obligately autotrophic, thermophilic, hydrogen-oxidizing bacterium. Solubilization and purification were done aerobically in the presence of Triton X-100. Three chromatography steps were done for purification; Butyl-Sepharose, Mono-Q, and Superose 6, in this order. Purification was completed with 6.73% yield of total activity and with 21.4-fold increase of specific activity when compared with the values for the membrane fraction. The purified hydrogenase was shown to be a tetramer with alpha2beta2 structure, with a molecular mass of 60,000 Da for the large subunit and 38,000 Da for the small subunit. The purified hydrogenase directly reduced methionaquinone with an apparent Km of around 300 microM and with a turnover number around 2900 (min(-1)). Metal analysis and EPR properties of the hydrogenase have shown that the enzyme is one of the [NiFe]-hydrogenases. Also, optimum pH and temperature for reaction, thermal stability, and electron acceptor specificity were reported. Finally, a model is presented for energy and central metabolism of H. thermophilus strain TK-6.

Biochemical and molecular characterization of the [NiFe] hydrogenase from the hyperthermophilic archaeon, Thermococcus litoralis

Thermococcus litoralis is a hyperthermophilic archaeon that grows at temperatures up to 98 degrees C by fermentative metabolism and reduces elemental sulfur (S0) to H2S. A [NiFe] hydrogenase, responsible for H2S or H2 production, has been purified and characterized. The enzyme is composed of four subunits with molecular mass 46, 42, 34 and 32 kDa. Elemental analyses gave approximate values of 22 Fe, 22 S and 1 Ni per hydrogenase. EPR spectra at 70 and 5 K indicated the presence of four or five [4Fe-4S] and one [2Fe-2S] type clusters. The optimal temperature for both H2 evolution and oxidation, using artificial electron carriers, was around 80 degrees C. The operon encoding the T. litoralis enzyme is composed of four genes forming one transcriptional unit, and transcription is not regulated by S0. An unusual transcription-initiation site is located 139 bp upstream from the translational start point. Sequence analyses indicated the presence of new putative nucleotide-binding domains. Upstream from the hydrogenase operon, ORFs probably encoding a molybdopterin oxidoreductase enzyme have been identified. Based on sequence, biochemical and biophysical analyses, a model of the enzyme and the pathway of electron flow during catalysis is proposed.

Desulfovibrio desulfuricans iron hydrogenase: the structure shows unusual coordination to an active site Fe binuclear center

BACKGROUND

Many microorganisms have the ability to either oxidize molecular hydrogen to generate reducing power or to produce hydrogen in order to remove low-potential electrons. These reactions are catalyzed by two unrelated enzymes: the Ni-Fe hydrogenases and the Fe-only hydrogenases.

RESULTS

We report here the structure of the heterodimeric Fe-only hydrogenase from Desulfovibrio desulfuricans - the first for this class of enzymes. With the exception of a ferredoxin-like domain, the structure represents a novel protein fold. The so-called H cluster of the enzyme is composed of a typical [4Fe-4S] cubane bridged to a binuclear active site Fe center containing putative CO and CN ligands and one bridging 1, 3-propanedithiol molecule. The conformation of the subunits can be explained by the evolutionary changes that have transformed monomeric cytoplasmic enzymes into dimeric periplasmic enzymes. Plausible electron- and proton-transfer pathways and a putative channel for the access of hydrogen to the active site have been identified.

CONCLUSIONS

The unrelated active sites of Ni-Fe and Fe-only hydrogenases have several common features: coordination of diatomic ligands to an Fe ion; a vacant coordination site on one of the metal ions representing a possible substrate-binding site; a thiolate-bridged binuclear center; and plausible proton- and electron-transfer pathways and substrate channels. The diatomic coordination to Fe ions makes them low spin and favors low redox states, which may be required for catalysis. Complex electron paramagnetic resonance signals typical of Fe-only hydrogenases arise from magnetic interactions between the [4Fe-4S] cluster and the active site binuclear center. The paucity of protein ligands to this center suggests that it was imported from the inorganic world as an already functional unit.

[3Fe-4S] to [4Fe-4S] cluster conversion in Desulfovibrio fructosovorans [NiFe] hydrogenase by site-directed mutagenesis

The role of the high potential [3Fe-4S]1+,0 cluster of [NiFe] hydrogenase from Desulfovibrio species located halfway between the proximal and distal low potential [4Fe-4S]2+,1+ clusters has been investigated by using site-directed mutagenesis. Proline 238 of Desulfovibrio fructosovorans [NiFe] hydrogenase, which occupies the position of a potential ligand of the lacking fourth Fe-site of the [3Fe-4S] cluster, was replaced by a cysteine residue. The properties of the mutant enzyme were investigated in terms of enzymatic activity, EPR, and redox properties of the iron-sulfur centers and crystallographic structure. We have shown on the basis of both spectroscopic and x-ray crystallographic studies that the [3Fe-4S] cluster of D. fructosovorans hydrogenase was converted into a [4Fe-4S] center in the P238 mutant. The [3Fe-4S] to [4Fe-4S] cluster conversion resulted in a lowering of approximately 300 mV of the midpoint potential of the modified cluster, whereas no significant alteration of the spectroscopic and redox properties of the two native [4Fe-4S] clusters and the NiFe center occurred. The significant decrease of the midpoint potential of the intermediate Fe-S cluster had only a slight effect on the catalytic activity of the P238C mutant as compared with the wild-type enzyme. The implications of the results for the role of the high-potential [3Fe-4S] cluster in the intramolecular electron transfer pathway are discussed.

Activation of methyl-SCoM reductase to high specific activity after treatment of whole cells with sodium sulfide

Here, we report a method to generate the active form of methyl-SCoM reductase (MCR) from Methanosarcina thermophila. The protocol involves adding sodium sulfide to a growing cell culture prior to harvest to yield a "ready" (MCRox1) state of the enzyme. This method can also generate a ready state of the Methanobacterium thermoautotrophicum (strain Marburg) MCR. Experiments using sodium 35S-labeled sulfide indicate the ready state that is generated involves a Ni-S adduct. As was shown earlier for the Mb. thermoautotrophicum MCRox1 [Goubeaud, M., Schreiner, G. and Thauer, R. K. (1997) Eur. J. Biochem. 17, 2374-2377], this ready state is converted to the highly active MCRred1 form by reductive activation with Ti(III) citrate. The reduction of MCRox1 to MCRred1 with concomitant increase in activity demonstrated that MCRred1 is the active form of MCR from Ms. thermophila. We also observed the loss of the 35S-sulfide label from the enzyme when MCRox1 was converted to MCRred1. Other states of MCR could be generated in the whole cells by adding different potential ligands to the cell medium; for example, the MCRox2 state was generated by treating cells with sodium sulfite or sodium dithionite.