Mechanistic insights into the selective oxidation of D-arginine by the nonheme iron-dependent viomycin biosynthesis enzyme VioC

VioC, a nonheme iron enzyme, catalyzes different reactions with D- and L-arginine, hydroxylating L-arginine at C3 and oxidatively deaminating D-arginine. Combining molecular dynamics with quantum mechanics/molecular mechanics (QM/MM) simulations, we reveal that the chirality of D-arginine positions its C2-H bond in proximity to the Fe(IV)-oxo intermediate and optimizes the geometry for enhanced σ-orbital alignment, thereby guiding the initial hydrogen atom transfer (HAT) from C2. Subsequent reactivity favors HAT from the ammonium group over alternative Glu-mediated proton coupled electron transfer pathway, driving C2-N desaturation to form a cationic imine intermediate. Both the C2-hydroxylation and C2-C3 desaturation pathways were ruled out due to their higher energy barriers. The cationic imine intermediate then hydrolyzes to yield the final ketone product. These findings demonstrate how substrate stereochemistry controls reactive site accessibility, providing mechanistic understanding of reaction bifurcation in Fe/2OG-dependent oxygenases.