Structural model of the Fe-hydrogenase/cytochrome c(553) complex combiningtransverse relaxation-optimized spectroscopy experiments and soft docking calculations

Fe-hydrogenase is a 54-kDa iron-sulfur enzyme essential for hydrogen cyclin g in sulfate-reducing bacteria. The x-ray structure of Desulfovibrio desulf uricans Fehydrogenase has recently been solved, but structural information on the recognition of its redox partners is essential to understand the str ucture-function relationships of the enzyme. In the present work, we have o btained a structural model of the complex of Fe-hydrogenase with its redox partner, the cytochrome c(553), combining docking calculations and NMR expe riments. The putative models of the complex demonstrate that the small subu nit of the hydrogenase has an important role in the complex formation with the redox partner; 50% of the interacting site on the hydrogenase involves the small subunit. The closest contact between the redox centers is observe d between Cys-38, a ligand of the distal cluster of the hydrogenase and Cys -10, a ligand of the heme in the cytochrome. The electron pathway from the distal cluster of the Fe-hydrogenase to the heme of cytochrome c(553) was i nvestigated using the software Greenpath and indicates that the observed cy steine/cysteine contact has an essential role. The spatial arrangement of t he residues on the interface of the complex is very similar to that already described in the ferredoxin-cytochrome c(553) complex, which therefore, is a very good model for the interacting domain of the Fe-hydrogenase-cytochr ome c(553).