More than 100 proteins necessary for eukaryotic cell growth, differentiation, and morphology require posttranslational modification by the covalent attachment of an isoprenoid lipid (prenylation). Prenylated proteins include members of the Ras, Rab, and Rho families, lamins, CENPE and CENPF, and the g subunit of many small heterotrimeric G proteins. This modification is catalyzed by the protein prenyltransferases: protein farnesyltransferase (FTase), protein geranylgeranyltransferase type I (GGTase-I), and GGTase-II (or RabGGTase). In this review, we examine the structural biology of FTase and GGTase-I (the CaaX prenyltransferases) to establish a framework for understanding the molecular basis of substrate specificity and mechanism. These enzymes have been identified in a number of species, including mammals, fungi, plants, and protists. Prenyltransferase structures include complexes that represent the major steps along the reaction path, as well as a number of complexes with clinically relevant inhibitors. Such complexes may assist in the design of inhibitors that could lead to treatments for cancer, viral infection, and a number of deadly parasitic diseases.-Lane, K. T., and L. S. Beese. More than 100 proteins necessary for eukaryotic cell growth, differentiation, and morphology require posttranslational modification by the covalent attachment of an isoprenoid lipid (prenylation) (1). This modification is catalyzed by three protein prenyltransferases: protein farnesyltransferase (FTase) and protein geranylgeranyltransferase type I (GGTase-I), collectively termed the CaaX prenyltransferases, as well as protein GGTase-II (or RabGGTase) [reviewed in this series in (2)], whose substrates are limited to members of the Rab subfamily of G proteins. FTase and GGTase-I transfer a 15 or 20 carbon isoprenoid [donated by farnesyl diphosphate (FPP) or geranylgeranyl diphosphate (GGPP)], respectively, to the cysteine of a C-terminal CaaX motif, defined by a cysteine (C) residue, followed by two small, generally aliphatic (a) residues, and the X residue, which contributes significantly to specificity (Fig. 1) (3-9). Kinetic assays and analysis of lipidated CaaX proteins purified from the cell demonstrate the general preference of FTase for methionine, serine, glutamine, or alanine and the preference of GGTase-I for leucine or phenylalanine in the X position. Here, we review the structural biology of FTase and GGTase-I; the biochemical properties of these enzymes have been reviewed extensively elsewhere (1, 10-15).After covalent attachment of the isoprenoid in the cytoplasm, most CaaX proteins undergo two further prenylation-dependent processing steps at the endoplasmic reticulum (1): proteolytic removal of the aaX tripeptide by the CaaX protease Ras and a-factor-converting enzyme (Rce1), and carboxymethylation of the prenylcysteine residue by the enzyme Isoprenylcysteine carboxyl methyltransferase (Icmt). The fully processed proteins exhibit high affinity for cellular membranes and present a unique structure at thei...