High-resolution crystallographic analysis of Desulfovibrio fructosovorans 6NiFe9 hydrogenase

Two resolution crystal structures of an oxidised form of the [NiFe] hydrogenase of Desulfovibrio (D.) fructosovorans are reported. The high data quality allows for a detailed analysis of the active site geometry, confirming asymmetric bridging of the Ni and Fe ion by the two cysteine sulphur atoms and one oxygen atom as previously observed in the D. gigas enzyme. The CO ligand is now clearly distinguishable from the two CN− ligands, as it refines to a significantly shorter distance to the Fe. The refined structures confirm the presence of long, mainly hydrophobic cavities that most probably provide pathways for H2 diffusion between the molecular surface and the deeply buried active site. Amino acid sequence comparisons suggest that these cavities are significantly narrower in the so-called sensor hydrogenases, which may explain why this special class of enzymes is insensitive to O2.