Unraveling the Mechanism of the Oxidative C–C Bond Coupling Reaction Catalyzed by Deoxypodophyllotoxin Synthase

Abstract

Deoxypodophyllotoxin synthase (DPS), a nonheme Fe(II)/2-oxoglutarate (2OG)-dependent oxygenase, is a key enzyme that is involved in the construction of the fused-ring system in (−)-podophyllotoxin biosynthesis by catalyzing the C−C coupling reaction. However, the mechanistic details of DPScatalyzed ring formation remain unclear. Herein, our quantum mechanics/molecular mechanics (QM/MM) calculations reveal a novel mechanism that involves the recycling of CO 2 (a product of decarboxylation of 2OG) to prevent the formation of hydroxylated byproducts. Our results show that CO 2 can react with the Fe III − OH species to generate an unusual Fe III −bicarbonate species. In this way, hydroxylation is avoided by consuming the OH group. Then, the C−C coupling followed by desaturation yields the final product, deoxypodophyllotoxin. This work highlights the crucial role of the CO 2 molecule, generated in the crevice between the iron active site and the substrate, in controlling the reaction selectivity.