Computational study into the oxidative ring‐closure mechanism during the biosynthesis of deoxypodophyllotoxin

The nonheme iron dioxygenase deoxypodophyllotoxin synthase performs an oxidative ring-closure reaction as part of natural product synthesis in plants. How the enzyme enables the oxidative ring-closure reaction of (-)-yatein and avoids substrate hydroxylation remains unknown. To gain insight into the reaction mechanism and understand the details of the pathways leading to products and byproducts we performed a comprehensive computational study. The work shows that substrate is bound tightly into the substrate binding pocket with the C7’−H bond closest to the iron(IV)-oxo species. The reaction proceeds with hydrogen atom abstraction from the C7’−H position followed by ring-closure and a final hydrogen transfer to form iron(II)-water and deoxypodophyllotoxin. Alternative mechanisms including substrate hydroxylation and an electron transfer pathway were explored but found to be higher in energy. The mechanism is guided by electrostatic perturbations of charged residues in the second-coordination sphere that prevent alternative pathways.