Carbon Monoxide Induced Decomposition of the Active Site [Ni−4Fe−5S] Cluster of CO Dehydrogenase

Abstract

During the past two years, crystal structures of Cu- and Mo-containing carbon monoxide dehydrogenases (CODHs) and Ni- and Fe-containing CODHs have been reported. The active site of CODHs from anaerobic bacteria (cluster C) is composed of Ni, Fe, and S for which crystallographic studies of the enzymes from Carboxydothermushydrogenoformans, Rhodospirillum rubrum, and Moorella thermoacetica revealed structural similarities in the overall protein fold but showed substantial differences in the essential Ni coordination environment. The [Ni−4Fe−5S] cluster C in the fully catalytically competent dithionite-reduced CODH II from C. hydrogenoformans (CODHII_Ch) at 1.6 Å resolution contains a characteristic μ₂-sulfido ligand between Ni and Fe1, resulting in a square-planar ligand arrangement with four S-ligands at the Ni ion. In contrast, the [Ni−4Fe−4S] clusters C in CO-treated CODH from R. rubrum resolved at 2.8 Å and in CO-treated acetyl-CoA synthase/CODH complex from M. thermoacetica at 2.2 and 1.9 Å resolution, respectively, do not contain the μ₂-sulfido ligand between Ni and Fe1 and display dissimilar geometries at the Ni ion. The [Ni−4Fe−4S] cluster is composed of a cubane [Ni−3Fe−4S] cluster linked to a mononuclear Fe site. The described coordination geometries of the Ni ion in the [Ni−4Fe−4S] cluster of R. rubrum and M. thermoacetica deviate from the square-planar ligand geometry in the [Ni−4Fe−5S] cluster C of CODHII_Ch. In addition, the latter was converted into a [Ni−4Fe−4S] cluster under specific conditions. The objective of this study was to elucidate the relationship between the structure of cluster C in CODHII_Ch and the functionality of the protein. We have determined the CO oxidation activity of CODHII_Ch under different conditions of crystallization, prepared crystals of the enzyme in the presence of dithiothreitol or dithionite as reducing agents under an atmosphere of N₂ or CO, and solved the corresponding structures at 1.1 to 1.6 Å resolutions. Fully active CODHII_Ch obtained after incubation of the enzyme with dithionite under N₂ revealed the [Ni−4Fe−5S] cluster. Short treatment of the enzyme with CO in the presence of dithiothreitol resulted in a catalytically competent CODHII_Ch with a CO-reduced [Ni−4Fe−5S] cluster, but a prolonged treatment with CO caused the loss of CO-oxidizing activity and revealed a [Ni−4Fe−4S] cluster, which did not contain a μ₂-S. These data suggest that the [Ni−4Fe−4S] cluster of CODHII_Ch is an inactivated decomposition product originating from the [Ni−4Fe−5S] cluster.