Theoretically exploring the key role of the Lys412 residue in the conversion of N2O to N2 by nitrous oxide reductase from Achromobacter cycloclastes

Abstract

Density functional theory (DFT) calculations have been performed to investigate the N₂O reduction reaction mechanism catalyzed by the μ₄-sulfide-bridged tetranuclear Cu_Z cluster of nitrous oxide reductase from Achromobacter cycloclastes. Our calculations showed that the active site Cu_Z cluster can provide strong back-donation to N₂O, facilitating N–O bond cleavage. In addition, the Lys412 residue near the Cu_I/Cu_IV edge of the Cu_Z cluster is considered as a suitable proton donor and plays a key role in the reduction reaction. The predicted activation barrier of N–O bond dissociation for the energetically favorable pathway with the terminal nitrogen atom of N₂O coordinated to the Cu_I center is only 14.6 kcal mol⁻¹ in the protein environment. The barrier is significantly lower than the barrier in the absence of the Lys412 residue and Cu_Z cluster. The relatively low barrier is ascribed to the N–O bond cleavage coupled with the oxygen-atom protonation of the coordinated N₂O. Present calculations provide significant insights into the mode of substrate coordination, activation, reduction and catalysis.