Insights from the computational studies on the oxidized as-isolated state of [NiFeSe] hydrogenase from D. vulgaris Hildenborough

Abstract

A density functional theory study of the active site structure and features of the oxygen tolerant [NiFeSe] Hase in the oxidized as-isolated state of the enzyme D. vulgaris Hildenborough (DvH) is reported here. The three conformers reported to be present in the X-ray structure (PDB ID: 2WPN) have been studied. The novel bidentate interchalcogen ligand (S–Se) in Conf-I of the [NiFeSe] Hase reported for the first time in hydrogenases (Hase) is found to be of donor–acceptor type with an uneven η² L → M σ-bond. The symmetry mismatch at the sp orbital of Se and at the d_z² orbital of Ni has been identified to be the reason for the inability of Conf-II to convert to Conf-I. NBO analysis shows that the sulfinate ligand peculiar to the state stabilizes the active site through n → π* interactions. The results reveal that the isolated oxidized state of the [NiFeSe] Hase is significantly different from the well-known [NiFe] Hase.