Structural study of the activation mechanism of dihydrogen at the Ni-Fe active site of [NiFe] hydrogenase

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Hydrogenases catalyze the reversible oxidation of molecular hydrogen and play a key role in hydrogen metabolism in various bacteria. Dihydrogen, the substrate and product of hydrogenases, is a good candidate for fuel in the future, since fossil fuels are a limited resource and considered to cause environmental disruption. The reaction mechanism of dihydrogen production by hydrogenases is potentially useful for development of new chemical engineering processes for hydrogen fuels, whereas that of dihydrogen consumption is potentially applicable for new types of fuel cells. While various lines of evidence indicated that the extrinsic CO interacts with the Ni atom of [NiFe]hydrogenase, they were not entirely conclusive, given the hetero-binulcear nature of the active site and the intimate communication between the two metals. In this study, we present the first direct evidence of CO coordination to the Ni atom of D.V.Miyazaki [NiFe]hydrogenase by X-ray crystallography.The carbon monoxide c … More omplex of [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki F has been characterized by X-ray crystallography and absorption and resonance Raman spectroscopy. Nine crystal structures of the [NiFe] hydrogenase in the CO-bound and CO-liberated forms were determined at 1.2-1.4 Å resolution. The exogenously added CO was assigned to be bound to the Ni atom at the Ni-Fe active site. Distinct changes were observed in the electron density distribution of the Ni and Sγ(Cys546) atoms between the CO-bound and CO-liberated structures for all the crystals tested. The novel structural features found near the Ni and Sγ(Cys546) atoms suggest that these two atoms at the Ni-Fe active site play a role during the initial H2-binding process.[NiFe] hydrogenase has two different oxidized states, Ni-A (unready) and Ni-B (ready). We have succeeded in converting Ni-B to Ni-A with the use of Na_2S and O_2, and determination of the high resolution crystal structures of the both states. Ni-B possesses a monatomic non-protein bridging ligand at the Ni-Fe active site, whereas Ni-A has a diatomic species. The terminal atom of the bridging species of Ni-A occupies a similar position as C of the exogenous CO in the CO complex (inhibited state). The common features of the enzyme structures at the resting (Ni-A) and inhibited (CO complex) states are proposed. These findings provide useful information on the design of new systems of biomimetic dihydrogen production and fuel cell devices. Less