Structural basis of mevalonate pathway regulation by feedback inhibition of mevalonate kinase

The mevalonate pathway diverts acetyl-CoA from central metabolism to produce isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP), the universal precursors to all steroids and isoprenoids in biology. Mevalonate kinase (MK) catalyzes a key regulatory step of mevalonate pathway in many eukaryotes, in which several downstream isoprenoid pyrophosphates act as feedback inhibitors. Known MK inhibitors vary widely in size, including IPP and DMAPP (five carbons, C₅), geranyl pyrophosphate (GPP, C₁₀), farnesyl pyrophosphate (FPP, C₁₅), and geranylgeranyl pyrophosphate (GGPP, C₂₀). These inhibitors compete for binding at a single site, yet how the enzyme is able to accommodate inhibitors of such varying sizes remains unknown. In this work, we first characterized the inhibition kinetics of all five of these inhibitors using MK from Saccharomyces cerevisiae (ScMK), revealing an inhibition potency that ranges approximately two orders of magnitude. We then solved X-ray crystal structures of ScMK bound to all five inhibitors as well as the structure of apo ScMK to shed light on how inhibitors of such varying sizes may all bind to the same site. In all, this suite of inhibitor-bound MK structures provides the first comprehensive structural depiction of MK feedback inhibition, a key regulatory mechanism of the mevalonate pathway of steroid and isoprenoid precursor biosynthesis.