The zinc metalloenzyme protein farnesyltransferase (FTase) catalyzes the transfer of a 15-carbon farnesyl moiety from farnesyl diphosphate (FPP) to a cysteine residue near the C-terminus of a protein substrate. Several crystal structures of inactive FTase.FPP.peptide complexes indicate that K164alpha interacts with the alpha-phosphate and that H248beta and Y300beta form hydrogen bonds with the beta-phosphate of FPP [Strickland, C. L., et al. (1998) Biochemistry 37, 16601-16611]. Mutations K164Aalpha, H248Abeta, and Y300Fbeta were prepared and analyzed by single turnover kinetics and ligand binding studies. These mutations do not significantly affect the enzyme affinity for FPP but do decrease the farnesylation rate constant by 30-, 10-, and 500-fold, respectively. These mutations have little effect on the pH and magnesium dependence of the farnesylation rate constant, demonstrating that the side chains of K164alpha, Y300beta, and H248beta do not function either as general acid-base catalysts or as magnesium ligands. Mutation of H248beta and Y300beta, but not K164alpha, decreases the farnesylation rate constant using farnesyl monophosphate (FMP). These data suggest that, contrary to the conclusions derived from analysis of the static crystal structures, the transition state for farnesylation is stabilized by interactions between the alpha-phosphate of the isoprenoid substrate and the side chains of Y300beta and H248beta. These results suggest an active substrate conformation for FTase wherein the C1 carbon of the FPP substrate moves toward the zinc-bound thiolate of the protein substrate to react, resulting in a rearrangement of the diphosphate group relative to its ground state position in the binding pocket.

X-ray absorption spectroscopy has been used to determine the structure of the Zn site in protein farnesyltransferase. Extended X-ray absorption fine structure (EXAFS) data are consistent with a Zn site that is ligated to three low-Z (oxygen or nitrogen) ligands and one cysteine sulfur, as predicted from the crystal structures that are available for farnesyltransferase. However, in contrast with the crystallographic results the EXAFS data do not show evidence for significant distortions in the Zn-ligand distances. The average Zn-(N/O) and Zn-S distances are 2.04 and 2.31 A, respectively. Addition of a farnesyl diphosphate analogue causes no detectable change in the structure of the Zn site. However, addition of peptide substrate causes a change in ligation from ZnS(N/O)(3) to ZnS(2)(N/O)(2), consistent with ligation of the C-terminal cysteine to the Zn. There is no significant change in Zn-ligand distances when a substrate binds, demonstrating that the Zn remains four-coordinate. Addition of both peptide and farnesyl diphosphate to give the product complex causes the Zn to return to ZnS(N/O)(3) ligation, indicating that the product thioether is not tightly coordinated to the Zn. These spectroscopic experiments provide insight into the catalytic mechanism of FTase.