The crystal structure of a reduced [NiFeSe] hydrogenase provides an image of the activated catalytic center

Abstract

The heterolytic cleavage of molecular hydrogen seems to be mediated by the nickel center and the selenocysteine residue. Beside modifying the catalytic properties of the enzyme, the selenium ligand might protect the nickel atom from oxidation. We conclude that the putative oxo ligand is a signature of inactive 'unready' [NiFe] hydrogenases.

Modulation of the electronic structure and the Ni–Fe distance in heterobimetallic models for the active site in [NiFe]hydrogenase

“…[NiFe]hydrogenases are particularly interesting because of their heterobinuclear active site and have been studied extensively (3)(4)(5)(6)(7)(8)(9)(10)(11)(12). Thiolate-bridged heterobimetallic Ni-Fe complexes, therefore, have also received considerable attention because of their importance as structural, spectroscopic, and functional models for the active site of the enzyme (13)(14)(15).…”

Molecular Biology of Microbial Hydrogenases

“…The core enzyme consists of an αβ heterodimer with the large subunit (α-subunit) of ca 60 kDa hosting the bimetallic active site and the small subunit (β-subunit) of ca 30 kDa, the Fe-S clusters. Crystal structures of Desulfovibrio H 2 ases have revealed the general fold and the nature of the binuclear NiFe active site; they have shown that the two subunits interact extensively through a large contact surface and form a globular heterodimer (Volbeda et al, 1995(Volbeda et al, , 1996Higuchi et al, 1997Higuchi et al, , 1999Garcin et al, 1999;Matias et al, 2001). The bimetallic NiFe center is deeply buried in the large subunit; it is coordinated to the protein by four cysteines.…”

“…Active sites The X-ray crystallographic studies of [NiFe]-H 2 ases isolated from Desulfovibrio gigas (Volbeda et al, 1995(Volbeda et al, , 1996, Desulfovibrio vulgaris Miyazaki (Higuchi et al, 1997(Higuchi et al, , 1999, Desulfovibrio fructosovorans , Desulfomicrobium norvegium (formerly Desulfomicrobium baculatum) (Garcin et al, 1999) and Desulfovibrio desulfuricans ATCC 27774 (Matias et al, 2001) have revealed the unique dinuclear [NiFe] active site of these enzymes ( Figure 3). The nickel atom is coordinated by four cysteinate-sulfur atoms, two of which bridge to the iron atom (in the D. norvegium enzyme, a selenocysteine instead of a cysteine coordinates the Ni).…”

“…The nickel atom is coordinated by four cysteinate-sulfur atoms, two of which bridge to the iron atom (in the D. norvegium enzyme, a selenocysteine instead of a cysteine coordinates the Ni). In the aerobically isolated inactive form of the enzyme, there is an additional µ-oxo or hydroxo (Garcin et al, 1999;Volbeda et al, 2002) or sulfi do group (Higuchi et al, 1997;Matias et al, 2001) bridging the Ni and Fe atoms. In addition, as demonstrated by crystallography and spectroscopy, the iron atom is bound to non-protein diatomic ligands, normally poisonous molecules, two CN -and one CO (Volbeda et al, 1996;Happe et al, 1997;Pierik et al, 1999), or SO, CO and CN -in D. vulgaris (Higuchi et al, 1997(Higuchi et al, , 2000.…”

“…Bruschi et al, 2002) may contribute to the identifi cation of factors indispensable for effi cient intramolecular electron transfer, stability and high turnover of the metallocenter in its supramolecular protein framework. (Cammack et al, 1987;Roberts and Lindahl, 1994;Volbeda et al, 1996;De Lacey et al, 1997), kinetics measurements De Lacey et al, 2000a) and from the crystal structures of oxidized (Volbeda et al, 1995(Volbeda et al, , 1996 and reduced (Garcin et al, 1999;Higuchi et al, 1999) forms of [NiFe]-H 2 ases. The oxidized inactive form of the enzyme yields the Ni u -A state, unready to catalyze H 2 activation (i.e.…”