The electron transfer complex between nitrous oxide reductase and its electron donors

Identifying redox partners and the interaction surfaces is crucial for fully understanding electron flow in a respiratory chain. In this study, we focused on the interaction of nitrous oxide reductase (N₂OR), which catalyzes the final step in bacterial denitrification, with its physiological electron donor, either a c-type cytochrome or a type 1 copper protein. The comparison between the interaction of N₂OR from three different microorganisms, Pseudomonas nautica, Paracoccus denitrificans, and Achromobacter cycloclastes, with their physiological electron donors was performed through the analysis of the primary sequence alignment, electrostatic surface, and molecular docking simulations, using the bimolecular complex generation with global evaluation and ranking algorithm. The docking results were analyzed taking into account the experimental data, since the interaction is suggested to have either a hydrophobic nature, in the case of P. nautica N₂OR, or an electrostatic nature, in the case of P. denitrificans N₂OR and A. cycloclastes N₂OR. A set of well-conserved residues on the N₂OR surface were identified as being part of the electron transfer pathway from the redox partner to N₂OR (Ala495, Asp519, Val524, His566 and Leu568 numbered according to the P. nautica N₂OR sequence). Moreover, we built a model for Wolinella succinogenes N₂OR, an enzyme that has an additional c-type-heme-containing domain. The structures of the N₂OR domain and the c-type-heme-containing domain were modeled and the full-length structure was obtained by molecular docking simulation of these two domains. The orientation of the c-type-heme-containing domain relative to the N₂OR domain is similar to that found in the other electron transfer complexes.