Type-2 isopentenyl diphosphate isomerase, which catalyzes the interconversion of isopentenyl diphosphate and dimethylallyl diphosphate, contains a tightly bound molecule of FMN. Incubation of the active enzyme center dot FMNH2 complex with an analogue of isopentenyl diphosphate, where the methyl group has been replaced with a cyclopropane ring, results in isomerization of the analogue to the corresponding allylic isomer without inactivation of the enzyme. In contrast, the related epoxide analogue is a potent irreversible inhibitor that covalently modifies the flavin cofactor in a proton-initiated reaction. These results suggest that the mechanism for isomerization by the type-2 isopentenyl diphosphate isomerase may be similar to the protonation-deprotonation sequence of the type-1 enzyme and places limits on the lifetimes of radical intermediates in an alternative hydrogen atom addition/abstraction mechanism.