X-ray crystal structure of the Fe-only hydrogenase (Cpl) from Clostridium pasteurianum to 1.8 angstrom resolution

A three-dimensional structure for the monomeric iron-containing hydrogenase (Cpl) from Clostridium pasteurianum was determined to 1.8 angstrom resolut ion by x-ray crystallography using multiwavelength anomalous dispersion (MA D) phasing. Cpl, an enzyme that catalyzes the two-electron reduction of two protons to yield dihydrogen, was found to contain 20 gram atoms of iron pe r mole of protein, arranged into five distinct [Fe-S] clusters. The probabl e active-site cluster, previously termed the H-cluster, was found to be an unexpected arrangement of six iron atoms existing as a [4Fe-4S] cubane subc luster covalently bridged by a cysteinate thiol to a [2Fe] subcluster. The iron atoms of the [2Fe] subcluster both exist with an octahedral coordinati on geometry and are bridged to each other by three non-protein atoms, assig ned as two sulfide atoms and one carbonyl or cyanide molecule. This structu re provides insights into the mechanism of biological hydrogen activation a nd has broader implications for [Fe-S] cluster structure and function in bi ological systems.