Stereochemical Studies of the Type II Isopentenyl Diphosphate–Dimethylallyl Diphosphate Isomerase Implicate the FMN Coenzyme in Substrate Protonation

The interconversion of isopentenyl diphosphate (IPP, 1) and dimethylallyl diphosphate (DMAPP, 2) by isopentenyl diphosphate:dimethylallyl diphosphate isomerase (IDI) is a key reaction in the synthesis of the building blocks for isoprenoid compounds.[1] Two structurally unrelated types of IDI have been identified. The type I enzyme (IDI-1) is a zinc metalloprotein that also requires Mg2+ for activity.[2] It employs appropriate active site amino acid residues as general acid and base catalysts to carry out the isomerization reaction.[2g, 3] In contrast, the type II IDI (IDI-2), discovered in 2001,[4] is a flavoprotein that requires a reduced flavin mononucleotide (FMNred, 3) coenzyme in addition to Mg2+ for activity.[5] The reaction catalyzed by IDI-2 is unusual in that it utilizes the redox active FMN coenzyme to perform a reaction that does not involve a change in the redox state of the substrate/product. This observation raises questions as to the exact role of the flavin coenzyme in the catalytic mechanism. In addition, several human pathogens, such as Staphylococcus aureus, rely exclusively on IDI-2 for the initiation of long-chain isoprenoid biosynthesis, whereas humans employ the structurally unrelated IDI-1. Thus, IDI-2 is a potential target for new antimicrobial agents.