Interplay of isoprenoid and peptide substrate specificity in protein farnesyltransferase

Protein farnesyltransferase (FTase) catalyzes the post-translational modification of many important cellular proteins, and is a potential anticancer drug target. Crystal structures of the FTase ternary complex illustrate an unusual feature of this enzyme, the fact that the isoprenoid substrate farnesyl diphosphate (FPP) forms part of the binding site for the peptide substrate. This implies that changing the structure of FPP could alter the specificity of the FPP-FTase complex for peptide substrates. We have found that this is the case; a newly synthesized FPP analogue, 3-MeBFPP, is a substrate with three peptide cosubstrates, but is not an effective substrate with a fourth peptide (dansyl-GCKVL). Addition of this analogue also inhibits farnesylation of dansyl-GCKVL by FPP. Surprisingly, the differential substrate abilities of these four peptides with FPP-FTase and 3-MeBFPP-FTase complexes do not correlate with their binding affinities for these isoprenoid-enzyme complexes. The possible mechanistic rationales for this observation, along with its potential utility for the study of protein prenylation, are discussed.