Structural Model of the Fe-Hydrogenase/Cytochromec 553 Complex Combining Transverse Relaxation-optimized Spectroscopy Experiments and Soft Docking Calculations

Abstract

Fe-hydrogenase is a 54-kDa iron-sulfur enzyme essential for hydrogen cycling in sulfate-reducing bacteria. The x-ray structure of Desulfovibrio desulfuricans Fehydrogenase has recently been solved, but structural information on the recognition of its redox partners is essential to understand the structure-function relationships of the enzyme. In the present work, we have obtained a structural model of the complex of Fe-hydrogenase with its redox partner, the cytochrome c 553 , combining docking calculations and NMR experiments. The putative models of the complex demonstrate that the small subunit 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 observed 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 investigated using the software Greenpath and indicates that the observed cysteine/cysteine contact has an essential role. The spatial arrangement of the residues on the interface of the complex is very similar to that already described in the ferredoxincytochrome c 553 complex, which therefore, is a very good model for the interacting domain of the Fe-hydrogenase-cytochrome c 553 .

Transient complexes of redox proteins: structural and dynamic details from NMR studies

“…The lysine distribution on the surface of Cc 553 , in conjunction with studies of ionic strength dependence for complex formation, suggests that electrostatic interactions play an important role in the formation of the complexes between the cytochrome and FDH (SebbanKreuzer et al, 1998b) or FeHase (Morelli et al, 2000a). The solution structure of DvH Cc 553 is available Blackledge et al, 1995;PDB entry 1dvh) and was used in the docking studies reported hereafter.…”

A further investigation of the cytochrome b 5–cytochrome c complex

“…A recently developed computer program [21] allowed us to use the NMR data to provide a model of the interaction. In a similar approach, heteronuclear NMR and docking calculations were used for building structural models of the cytochrome c 553 -ferredoxin complex and a combination of TROSY experiments and docking calculations were used for the study of the [Fe]-hydrogenase-cytochrome c 553 complex [22,23]. Other, more recent, applications of similar strategies include the cytochrome b 5 -myoglobin [24] and the cytochrome ccytochrome f [25] complexes.…”

Unusual activation during peroxidase reaction of a cytochrome c variant

“…4). The propionate rotation has been observed in others proteins, such as cytochromes and haloperoxidases [47][48][49][50]. In the crystal structure of dehaloperoxidase of Amphitrite ornata (pdb code 3DR9) there are water molecules at hydrogen bond distance (2.2-2.9Å) next to the switched A ring propionate group.…”