Structure of Cytochrome P450 PimD Suggests Epoxidation of the Polyene Macrolide Pimaricin Occurs via a Hydroperoxoferric Intermediate

SummaryWe present the X-ray structure of PimD, both substrate-free and in complex with 4,5-desepoxypimaricin. PimD is a cytochrome P450 monooxygenase with native epoxidase activity that is critical in the biosynthesis of the polyene macrolide antibiotic pimaricin. Intervention in this secondary metabolic pathway could advance the development of drugs with improved pharmacologic properties. Epoxidation by P450 typically includes formation of a charge-transfer complex between an oxoferryl π-cation radical species (Compound I) and the olefin π-bond as the initial intermediate. Catalytic and structural evidence presented here suggest that epoxidation of 4,5-desepoxypimaricin proceeds via a hydroperoxoferric intermediate (Compound 0). The oxygen atom of Compound 0 distal to the heme iron may insert into the double bond of the substrate to make an epoxide ring. Stereoelectronic features of the putative transition state suggest substrate-assisted proton delivery.

Graphical AbstractFigure optionsDownload high-quality image (253 K)Download as PowerPoint slideHighlights
► Binding mode of polyene macrolide to P450 PimD is revealed by X-ray crystallography
► Epoxidation of 4,5-deepoxipimaricin via Compound 0 is suggested
► Steric and stereoelectric factors drive epoxidation down the less favorable pathway