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Eur. J. Biochem. 269, 3339–3354 (2002) FEBS 2002 doi:10.1046/j.1432-1033.2002.03014.x REVIEW ARTICLE Structure, mechanism and function of prenyltransferases Po-Huang Liang, Tzu-Ping Ko and Andrew H.-J. Wang Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan In this review, we summarize recent progress in studying three main classes of prenyltransferases: (a) isoprenyl pyrophosphate synthases (IPPSs), which catalyze chain elongation of allylic pyrophosphate substrates via consecutive condensation reactions with isopentenyl pyrophosphate (IPP) to generate linear polymers with defined chain lengths; (b) protein prenyltransferases, which catalyze the transfer of an isoprenyl pyrophosphate (e.g. farnesyl pyrophosphate) to a protein or a peptide; (c) prenyltransferases, which catalyze the cyclization of isoprenyl pyrophosphates. The prenyltransferase products are widely distributed in nature and serve a variety of important biological functions. The catalytic mechanism deduced from the 3D structure and other biochemical studies of these prenyltransferases as well as how the protein functions are related to their reaction mechanism and structure are discussed. In the IPPS reaction, we focus on the mechanism that controls product chain length and the reaction kinetics of IPP condensation in the cis-type and trans-type enzymes. For protein prenyltransferases, the structures of Ras farnesyltransferase and Rab geranylgeranyltransferase are used to elucidate the reaction mechanism of this group of enzymes. For the enzymes involved in cyclic terpene biosynthesis, the structures and mechanisms of squalene cyclase, 5-epi-aristolochene synthase, pentalenene synthase, and trichodiene synthase are summarized. Isoprenoids are an extensive group of natural products with diverse structures consisting of various numbers of fivecarbon isopentenyl pyrophosphate (IPP) units [1,2]. The more than 23 000 isoprenoid compounds identified thus far serve a variety of essential biological functions in Eukarya, Bacteria and Archaea. For example, steroids are cyclic isoprenoids, which have distinct biological functions as hormones [3]. Carotenoids contain highly conjugated structures for absorption of light and are the most common accessory pigments in all green plants and many photosynthetic bacteria [4]. Retinoids are involved in morphogenesis and are the light-sensitive element in vision. Prenylated proteins including Ras and other G-proteins are involved in specific signal-transduction pathways [5,6]. Many linear isoprenoids, generally synthesized from C15 farnesyl pyrophosphate (FPP) and IPP, are found in nature [7]. The enzymes responsible for the synthesis of linear isoprenyl pyrophosphates can be classified as cis- and transisoprenyl pyrophosphate synthase (IPPS) according to the stereochemical outcome of their products [8]. As shown in Fig. 1, all-trans-geranyl pyrophosphate (GPP) and FPP are synthesized by trans-type geranyl pyrophosphate synthase (GPPS) and farnesyl pyrophosphate synthase (FPPS), respectively. Starting from FPP, a variety of differentchain-length products are generated by the corresponding synthases. The geranylgeranyl pyrophosphate synthase (GGPPS) and farnesylgeranyl pyrophosphate synthase (FGPPS) produce C20 and C25 all-trans-polyprenyl pyrophosphates to make C20–C20 and C20-C25 ether-linked lipids in archeon [9–11]. The C40 product of octaprenyl pyrophosphate synthase (OPPS) constitutes the side chain of ubiquinone in Escherichia coli [12–14]. Several cis-isoprenyl Keywords: chain elongation; isoprenoid; lipid carrier; prenyltransferase; site-directed mutagenesis; 3D structure. Correspondence to P.-H. Liang, Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan. Fax: +886 2 2788 9759, Tel.: +886 2 2785 5696 ext. 6070, E-mail: [email protected] or A.H.-J. Wang, Fax: +886 2788 2043, E-mail: [email protected] Abbreviations: FPP, farnesyl pyrophosphate; GPP, geranyl pyrophosphate; GGPP, geranylgeranyl pyrophosphate; IPP, isopentenyl pyrophosphate; UPP, undecaprenyl pyrophosphate; IPPS, isoprenyl pyrophosphate synthase; UPPS, undecaprenyl pyrophosphate synthase; DDPPS, dehydrodolichyl pyrophosphate synthase; PPPS, polyprenyl pyrophosphate synthase; GPPS, geranyl pyrophosphate synthase; FPPS, farnesyl pyrophosphate synthase; GGPPS, geranylgeranyl pyrophosphate synthase; FGPPS, farnesylgeranyl pyrophosphate synthase; HexPPS, hexaprenyl pyrophosphate synthase; HepPPS, heptaprenyl pyrophosphate synthase; OPPS, octaprenyl pyrophosphate synthase; SPPS, solanesyl pyrophosphate synthase; DPPS, decaprenyl pyrophosphate synthase; FTase, farnesyltransferases; GGTase, geranylgeranyltransferase. Enzymes: UPPS from Escherichia coli (EC 2.5.1.31); DDPPS from yeast Saccharomyces cerevisiae (EC 2.5.1.31); PPPS from Arabidopsis thaliana (EC 2.5.1.31); FPPS from E. coli (EC 2.5.1.10); GGPPS from yeast (EC 2.5.1.29); FGPPS from Aeropyrum pernix (EC 2.5.1.33); HexPPS from Bacillus stearothermophilus and yeast (EC 2.5.1.30); HepPPS from Mycobacterium tuberculosis (EC 2.5.1.30); OPPS from E. coli (EC 2.5.1.11); SPPS from Rhodobacter capsulatus (EC 2.5.1.11); DDPPS from human (EC 2.5.1.31); Ras farnesyltransferase from human (EC 2.1.1.100); Rab geranylgeranyltransferase from human (EC 2.1.1.100); squalene cyclase from Alicyclobacillus acidocaldarius (2.5.1.31); 5-epi-aristolochene synthase from Tobacco (EC 4.2.3.6); pentalenene synthase from Streptomyces UC5319 (EC 4.2.3.7); trichodiene synthase from Fusarium sporotrichioides (EC 4.2.3.6). (Received 22 March 2002, accepted 17 May 2002) FEBS 2002 3340 P.-H. Liang et al. (Eur. J. Biochem. 269) Fig. 1. Synthesis of linear all trans-isoprenyl pyrophosphates (top) and trans,cis-isoprenyl pyrophosphates (bottom) catalyzed by transIPPSs and cis-IPPSs, respectively. The stereoisomers are not specified in the nomenclature of the enzymes. Beside a trans-FPPS, a cis-type FPPS from M. tuberculosis has been shown to synthesize cis,trans-FPP. pyrophosphate synthases including solanesyl pyrophosphate synthase (SPPS) [15–17], decaprenyl pyrophosphate synthase (DPPS) [18], heptaprenyl pyrophosphate synthase (HepPPS) [19], and hexaprenyl pyrophosphate synthase (HexPPS) [20,21] are responsible for making C45, C50, C35, and C30 side chains, respectively, of ubiquinone in different species [22]. Among the cis-polyprenyl pyrophosphates, the C55 product of the bacterial undecaprenyl pyrophosphate synthase (UPPS) serves as a lipid carrier in cell wall peptidoglycan biosynthesis [23,24]. Its homologous dehydrodolichyl pyrophosphate synthase (DDPPS) in eukaryotes is responsible for making C55–C100 dolichols for glycoprotein biosynthesis, a pathway similar to that of the bacterial peptidoglycan synthesis [25,26]. An even longer C120 polymer was found as the final product of an isoprenyl pyrophosphate synthase in plant Arabidopsis thaliana with unknown function [27]. As the cis-prenyltransferases commonly synthesize long-chain products, a unique short-chain cis,trans-FPP is made by Mycobacterium tuberculosis FPPS which utilizes C10 GPP and IPP to produce a FPP with a cis double bond [28] (Fig. 1). This bacterium has a decaprenyl pyrophosphate synthase (DPPS) to produce C50 decaprenyl pyrophosphate as a lipid carrier, which is one IPP unit shorter than UPP found in other bacteria. The products of these prenyltransferases have specific chain lengths essential for their biological functions. An intriguing question is how do they achieve product chainlength specificity. In theory, restriction of the size of the enzyme active site should play a major role in determining the chain length of the final product. With the increasing numbers of 3D structures available for prenyltransferases, the mechanism of product chain-length determination has begun to be elucidated [29]. The cis-type UPPS crystal structures from Micrococcus luteus and E. coli have been solved by Fujihashi et al. [30] and Ko et al. [31], respectively, providing the first two structures of the cis-prenyltransferase family. The structure in conjunction with site-directed mutagenesis studies has revealed how cis-prenyltransferase controls its product size [31]. Protein prenyltransferases form another prenyltransferase family. This enzyme catalyzes the transfer of the carbon moiety of FPP or GGPP to a conserved cysteine residue in a CaaX motif of protein and peptide substrates [32]. This postranslational modification is essential for a number of proteins including Ras, Rab, nuclear lamins, trimeric G-protein c subunits, protein kinases, and small Ras-related GTP-binding proteins [33,34]. The addition of a farnesyl group to these proteins is required to anchor them to the cell membrane, a step required for them to function. As oncogenic forms of Ras in nearly 30% of human cancers were observed, inhibition of Ras farnesyltransferases (FTases) became a new strategy for anticancer therapy [35,36]. The crystal structure of a mammalian FTase had been determined at 2.25 Å resolution [37]. Subsequently, the structures of the enzyme in complex with FPP substrate [38] and a ternary complex of the enzyme with FPP and a CaaX peptide substrate were solved [39]. Later, a Rab geranylgeranyltransferase (GGTase) was solved at 2.0 Å resolution [40]. FPP is considered to be a branching point in the synthesis of different types of natural isoprenoids. A number of enzymes catalyze cyclization of FPP to generate natural products such as pentalenene (pentalenene synthase), 5-epiaristolochene (5-epi-aristolochene synthase) and trichodiene (trichodiene synthase). Squalene synthase catalyzes the cyclization of squalene which is synthesized by the coupling of two FPP molecules. The crystal structures of these enzymes have been solved and provide insights into the catalytic mechanism of terpenoid cyclization [41–44]. This review summarizes these recent advances in the structural and mechanistic studies of the above three families of prenyltransferases with emphasis on IPPS, which has essential biological functions (Table 1). A general mechanism of product chain-length determination and the reaction kinetics derived from a pre-steady-state kinetic analysis for trans-IPPS and cis-IPPS are described. CLASS I: ISOPRENYL PYROPHOSPHATE SYNTHASES (IPPSs) Structure and active site of trans-IPPS Over the past decade, many trans-IPPSs have been purified and their genes cloned [45,46]. The deduced amino-acid sequences of these enzymes show amino-acid sequence homology and two common DDxxD motifs [47], suggesting that they evolved from the same origin (Fig. 2) [48,49]. These Asp-rich motifs were recognized from the 3D structure [50] and site-directed mutagenesis studies [51–56] to be involved in substrate binding and catalysis via chelation with Mg2+, a cofactor required for enzyme activity. The first crystal structure of a trans-prenyltransferase reported is that of avian FPPS [50]. As shown in Fig. 3A, this 2.6-Å-resolution structure contains 13 a helices, 10 of them surrounding the large central cavity. Two conserved DDxxD sequences are located in this deep cleft, which FEBS 2002 Structure, mechanism and function of prenyltransferases (Eur. J. Biochem. 269) 3341 7 Table 1. The biological functions and three-dimensional structures of prenyltransferases presented in this review. Prenyltransferases Biological functions 3D structure [ref] trans-FPPS Precursor of steroids, cholesterol, sesquiterpenes, farnesylated proteins, heme, and vitamin K12 Precursor of carotenoids, retinoids, diterpenes, geranylgeranylated chlorophylls, and archaeal ether linked lipids Archaeal ether linked lipids Ubiquinone side chains [50,57] Lipid carrier for peptidoglycan synthesis Lipid carrier for glycoprotein synthesis Farnesylated Ras for signal transduction Geranylgeranylated Rab for signal transduction Precursor of cholesterol Precursor of antifungal phytoalexin capsidol Precursor of pentalenolactone antibiotics Precursor of antibiotics and mycotoxins [30,31] trans-GGPPS trans-GFPPS trans-HexPPS –DPPS cis-UPPS cis-DDPPS Ras FTase Rab GGTase Squalene cyclase epi-Aristolochene synthase Pentalenene synthase Trichodiene synthase forms the substrate-binding pocket. In site-directed mutagenesis studies of yeast FPPS, substitution of Asp with Ala in the first negatively charged DDxxD motif decreased kcat by 4–5 orders of magnitude [53]. In the second DDxxD motif of yeast FPPS, the first and second Asp to Ala Fig. 2. Sequence alignment of trans-prenyltransferases. The sequence-related proteins including FPPS from E. coli, GGPPS from yeast, FGPPS from E. coli, HexPPS from yeast, HepPPS from B. subtilis, OPPS from E. coli, SPPS from M. luteus, and DPPS from human are shown. Black and gray outlines indicate identical and similar amino acid residues, respectively. The two DDxxD motifs are conserved in all proteins. The 5th amino acid upstream from the first DDxxD is a large residue (Leu, Phe, or Tyr) for FPPS and GGPPS, and is small amino acid (Ala) for FGPPS, HexPPS, HepPPS, OPPS, SPPS, and DPPS. [37–39] [40] [41] [42] [43] [44] mutations resulted in kcat values 4–5 orders of magnitude smaller [53]. However, when the third Asp was mutated to Ala, there was a less pronounced effect ( 100-fold smaller kcat) [53]. A 104)105 lower activity was observed for the FPPS from Bacillus stearothermophilus when the first 3342 P.-H. Liang et al. (Eur. J. Biochem. 269) FEBS 2002 Fig. 3. (A) Crystal structure of trans-type FPPS and (B) schematic representation of the active site with FPP (product) and IPP bound. (A) The model of avian FPPS is shown using a ribbon diagram. Two identical subunits are associated into a dimer by forming a four-layer helix bundle. The N-terminal a helical hairpins in the outer layers are shown in blue and red for the two individual subunits, while the eight helices in the inner layers are shown in cyan and magenta. Two small peripheral domains are colored green and yellow. The locations of the active sites are indicated by red arrows, where the aspartate side chains of the two DDxxD motifs in each subunits are also shown in red. The phenylalanine side chains of F112 and F113, which are involved in product length control, are shown in green. (B) The 5th amino acid (shown as a filled black circle) before the first DDxxD motif in the sequence is located next to the tail of FPP. The large amino acid at this position can block further chain elongation of the product and represents a mechanism to control the product chain length. and second Asp of the second DDxxD motif were replaced with Ala [55]. In contrast, the third Asp seems to be less important to catalysis as its mutation to Ala only resulted in 6–16 times lower kcat values, but with a 10-fold increased IPP Km value [55]. For rat FPPS, replacement of the second and third Asp with Glu in the first Asp-rich motif decreased kcat by 1000-fold [52]. However, no significant change in the Km values for IPP and GPP were observed. In the second DDxxD motif of rat FPPS, substituting the first Asp with Glu decreased kcat 90-fold and increased IPP Km 26-fold, whereas GPP Km remained unchanged [51]. On the other hand, mutation of the third Asp resulted in no change in the kinetic parameters. These results indicate that all the Asp residues in the two DDxxD motifs except the last one in the second motif are important for catalysis. In addition, the second motif is essential for IPP binding. These results are consistent with the cocrystal structure of avian FPP in complex with GPP and IPP [57]. The structure of FPPS clearly shows that the first DDxxD is bound to the allylic substrate GPP and the second motif is the binding site of the homoallylic substrate IPP. Site-directed mutagenesis of other amino acids around the two DDxxD motifs was also performed to show their effects in substrate binding and catalysis [54,56]. Amino-acid residues essential to product chain-length determination of trans-prenyltransferases In parallel with the site-directed mutagenesis studies, a random chemical mutagenesis approach was used to select FPPS mutants induced by NaNO2 treatment that could synthesize longer-chain products. FPPS was converted into GGPPS which synthesizes a C20 product by generating mutations at position 81, 34 and 157 of FPPS from B. stearothermophilus [58]. The Y81H mutant was the most effective at increasing the production of GGPP (C20) compared with FPP (C15) [58]. The subsequent site-directed mutagenesis study in which Y81 was systematically replaced with each of the other 19 amino-acid residues showed that Y81A, Y81G and Y81S are capable of making hexaprenyl pyrophosphate (C30) [59]. The final products of Y81C, Y81H, Y81I, Y81L, Y81N, Y81T and Y81V are C25 geranylfarnesyl pyrophosphate. On the other hand, Y81D, Y81E, Y81F, Y81K, Y81M, Y81Q, and Y81R cannot synthesize products larger than GGPP (C20). It appears that this residue, located at the fifth position before the first DDxxD motif, is the key residue in determining product chain length. Predicted from the secondary structure of FPPS, this residue is located at a distance of 12 Å from the first Asp-rich motif, which is similar to the length of the hydrocarbon moiety of FPP [59]. The chain length of the product catalyzed by these mutants is inversely proportional to the accessible surface volume of the substituted aminoacid residue in the first DDxxD. Also in archaebacterial GGPPS, mutation of Phe77, which is upstream from the first DDxxD, led to a change in product [60]. For instance, replacement of this large residue with the smaller Ser resulted in the production of C25 rather than C20. There was a similar finding in avian FPPS, in which replacement of aromatic Phe112 and Phe113 with smaller amino acids resulted in the product specificity shifting from 1 C15 (FPP) to C20 (GGPP) (F112A), C25 geranylfarnesyl pyrophosphate (F113S) and longer products (F112A/ F113S double mutant) [57]. These two residues are located in the fifth and sixth position before the first DDxxD FEBS 2002 Structure, mechanism and function of prenyltransferases (Eur. J. Biochem. 269) 3343 motif. The X-ray crystal structure of the enzyme reveals that the first DDxxD is near a large hydrophobic pocket which contains the mutated Phe112 and Phe113 residues (Fig. 3A). It is proposed that this pocket binds the growing hydrocarbon tail of the product, and the first DDxxD is responsible for the binding of its pyrophosphate moiety. An enlarged active site of the mutant enzymes is probably related to increased product size based on the 3D structures of the FPPS in the apo state and to the allylic substrate bound. Accordingly, an increase of 5.8 Å in the depth of the hydrophobic pocket agrees with the 5.2 Å difference of an extra IPP unit between FPP (C15) and GGPP (C20). The role of F113 in controlling the product chain length is further supported by the fact that GGPPS from Methanobacterium thermoautotrophicum contains phenylalanine and serine at the positions corresponding to Phe112 and Phe113 in avian FPPS. From the X-ray crystal structure and the sequence alignment of a variety of polyprenyl pyrophosphate synthases (PPPSs), which generate C15, C20 and larger products, the importance of Phe112 and Phe113 in the mechanism of product chainlength determination is evident. In conclusion, the large amino-acid residue located before the first DDxxD motif provides the ÔfloorÕ to block further elongation of the product (Fig. 3B). Once this residue is replaced with a smaller one, elongation can continue. In addition to the 5th and 6th amino-acid residues, the roles of the 8th and/or the 11th positions before the first DDxxD in the control of product specificity of archaeal GGPPS and FPPS were also examined [61]. The single mutant (F77S, 5th amino acid residue before the first Asprich motif), double mutant (L74G/F77G) and triple mutant (I71G/74G/F77G) of GGPPS mainly produce C25, C35 and C40, respectively [61]. FPPS mutants display a similar pattern. This indicates that replacing amino acids near the 5th amino acid with smaller ones can further increase production of longer polymers. Conversely, replacement of a small amino acid with a larger one shortens the chain length of the product. The avian FPPS mutants A116W and N114W produce C10 GPP instead of C15 FPP synthesized by the wild-type enzyme [62]. These residues are also located in the hydrophobic pocket of the allylic substrate site, as revealed by docking dimethylallyl pyrophosphate into the crystal structure of FPPS. Dimethylallyl pyrophosphate is an isomer of IPP and its condensation with IPP produces GPP. The mutations A116W and N114W could fill in the bottom of the activesite cavity, forcing the synthesis of shorter GPPs. Steadystate kinetic measurements indicate that the two mutant enzymes have larger kcat values with dimethylallyl pyrophosphate as substrate and binding of GPP is therefore shifted to the allylic site because of the smaller internal space of the active site. Structure and active site of cis-IPPS UPPS has been partially purified from Lactobacillus plantarum and characterized [63]. Subsequently, the UPPS encoding gene cloned from M. luteus is the first cisprenyltransferase gene identified, and the deduced aminoacid sequence shows no sequence similarity to those of trans-prenyltransferases [64]. The sequence comparison with UPPS allows the identification of many cis-type IPPSs in bacteria, plant and animals as a family [65]. Several regions of conserved sequences can be identified (Fig. 4). Broadly grouped, they are (with the amino-acid sequence shown in parentheses): region I (20–32), region II (42–46), region III (66–88), region IV (142–154) and region V (190–224). Most of the fully conserved amino acids are involved in catalysis, substrate binding, or structural interactions as revealed later by the crystal structures and mutagenesis studies. Unlike the trans-type enzymes, cis-prenyltransferases lack the DDxxD motifs, although they require Mg2+ for activity. Earlier site-directed mutagenesis studies examined the conserved Asp and Glu of E. coli UPPS and revealed the importance of Asp26, Asp150 and Glu213 in substrate binding and catalysis [66]. Replacement of Asp26 with Ala results in 103-fold smaller kcat without any significant change in FPP and IPP Km values. Mutagenesis of Asp150 to alanine leads to a 50 times larger IPP Km but no change in FPP Km and kcat values. If Glu213 is replaced with Ala, there is a 70-fold increase in IPP Km and a 100-fold decrease in kcat. The subsequent 3D structure of UPPS from M. luteus suggests that Asp29 (equivalent to Asp26 in E. coli UPPS) is located in a p-loop, a conserved motif for the pyrophosphate-binding site in many phosphatebinding proteins such as nucleotide triphosphate hydrolase, phosphofructokinase, cAMP-binding domain, and sugar phosphatase [67]. Site-directed mutagenesis studies on M. luteus UPPS have also identified Glu216 (equivalent to Glu213 in the E. coli enzyme) as being responsible for IPP binding via Mg2+ [68]. A hydrophobic cleft in the enzyme with four positively charged Arg residues located at the entrance of the cleft and the hydrophobic residues covering the interior is proposed as the site for substrate recognition [30]. The E. coli UPP structure reveals a larger hydrophobic tunnel surrounded by two a helices (a2 and a3) and four b strands (bB, bA, bD, and bC) as shown in Fig. 5A. In contrast with the symmetric structure of M. luteus UPPS, two protein conformations (open and closed forms) are seen in the two subunits of E. coli UPPS, implicating a closed/open conformational change mechanism in substrate binding and product release [31]. The difference between the two conformers is mainly in the position of the a3 helix. On the basis of site-directed mutagenesis studies [31], the flexible loop with amino acids 72–83 connected to the a3 helix has been suggested to serve as a hinge for the interconversion of two conformers. This study also suggested a role for a Trp residue in the loop for FPP binding and catalysis [69]. Fluorescent stopped-flow technology and steady-state spectrophotometer have recently been used to directly observe a Trp fluorescence intensity change due to the change in protein conformation during catalysis [70]. When Trp91, which is located in the a3 helix, is mutated to Phe, the fluorescence quenching upon addition of FPP is abolished, suggesting that the a3 helix moves toward the active site during substrate binding [70]. Thus the change in UPPS conformation to a closed form results in better interaction between the enzyme and the substrates and intermediates. After the reaction, the UPPS structure shifts to an open form for product release, triggered by crowding of the prenyl chain of the product because the large amino-acid residues seal the bottom of the tunnel-shaped active site. 3344 P.-H. Liang et al. (Eur. J. Biochem. 269) FEBS 2002 Fig. 4. Alignment of the cis-type IPPSs. These include, in turn, E. coli UPPS, yeast DDPPS Rer2, Yeast DDPPS Srt1, M. tuberculosis FPs Rv1086, M. tuberculosis DPPS Rv2361c, Arabidopsis thaliana PPPS and human DDPPS. The numbers and secondary-structural elements shown above the sequences are for the UPPS from E. coli, based on PROCHECK analysis of the crystal structure. The green arrows denote the locations of b-strands, and the cylinders in red, magenta and cyan are for a helices, 310 helices and turns, respectively. In the aligned sequences, several conserved regions including (I) residues 20–32, (II) 42–46, (III) 66–88, (IV) 142–154, and (V) 190–224 can be identified, which probably also have corresponding secondary structures in common. Mechanism of product chain-length determination in cis-IPPS E. coli UPPS has a hydrophobic tunnel formed by two a helices and four b strands, which is sufficiently large to accommodate the whole UPP (Fig. 5A). Large amino acids including I62, L137, V105, and H103 are located on the bottom of the tunnel [31]. Among the mutants produced by replacing these residues with the smaller Ala, L137A synthesizes C70 and C75 as major products, which are longer than the C55 product of the wild-type enzyme [31]. Ko et al. [31] proposed that this residue plays an essential role in determining the product chain length by blocking further product elongation, analogous to the above amino-acid residue located upstream from the first DDxxD motif in the trans-type enzyme (Fig. 5B). This residue may represent a common residue in the mechanism of product chain-length determination among cis-prenyltransferases. From their sequence homology, yeast Rer2, which synthesizes longerchain C70–C80 products, has an Ala residue at this position. The single UPPS mutation, L137A, has converted UPPS into DDPPS in terms of product specificity. V105 may also play a role in blocking chain elongation, as its mutation increases the proportion of C60, C65 and C70 in the absence of Triton, but it is not as critical as L137. All cis-prenyltransferases so far identified have products of chain length at least C55, except a short-chain FPPsynthesizing enzyme recently identified from M. tuberculosis. When the amino-acid sequence of UPPS is compared with that of the short-chain FPPS, the A69 and A143 in E. coli UPPS correspond to the large L84 and V156 in M. tuberculosis FPPS, respectively. Substitution of Leu for A69 in E. coli UPPS indeed leads to production of a greater amount of C30 intermediate which is longer lived, suggesting that this residue interferes with the chain elongation of the C30 product. From the structure, it is reasonable to assume that A69 is located midway in FPP elongation to the C55 product. The conclusion derived from the changes in product specificity in E. coli UPPS mutants needs to be confirmed when the structures of the other cis-prenyltransferases are available. Reaction mechanism and kinetics of trans-IPPS and cis-IPPS An ionization–condensation–elimination mechanism has been proposed for the trans-prenyltransferase reaction. As shown below in Fig. 9A, the carbocation resulting from the dissection of the pyrophosphate group from GPP is proposed as the intermediate during the FPPS-catalyzed condensation reaction of IPP with allylic pyrophosphate substrate [1]. This conclusion is based on the finding that the enzyme, which normally catalyzes the addition of a GPP to IPP, is able to catalyze the hydrolysis of GPP [71]. Hydrolysis carried out in H218 O or with (1S)-[1-3H]GPP shows that the C–O bond is broken, and the chirality of the C1 carbon of GPP is inverted in the process. Furthermore, the trifluoromethyl substituent at the C3 position or the fluoro atom at the C2 position of the allylic substrate destabilizes the carbocation and retards the enzyme reaction [72]. FEBS 2002 Structure, mechanism and function of prenyltransferases (Eur. J. Biochem. 269) 3345 Fig. 5. (A) Two orthogonal views of the ribbon representation of an E. coli UPPS dimer and (B) the proposed active site of the E. coli UPPS located in a tunnel-like crevice surrounded by a2, a3, bD, bB, bA, and bC. (A) The top view is perpendicular to, and the bottom view is parallel to, the molecular dyad axis. The seven a helices and six b strands are shown in red and green, respectively, for subunit A, and in magenta and cyan for subunit B, and they are labelled separately. The blue arrows indicate locations of the active sites, each having a substrate-binding tunnel formed by helices a2, a3 and the central b-sheet. (B) The substrate site is located on the top of the hydrophobic tunnel with D26 and D213 playing a significant role in substrate binding and catalysis. A69 is in the midle of FPP chain elongation to the product. The large amino acid L137 on the bottom of the tunnel is essential for determination of product chain length by blocking further elongation of UPP. A tertiary carbocation on the C3 carbon of the IPP part is proposed to form during the 1¢-4 condensation. The aza analogues with nitrogen replacing the cationic carbon to mimic the transition state have previously been demonstrated to strongly inhibit enzymes in isoprenoid biosynthesis where the carbocation transition state is presumably formed during catalysis [73]. An aza analogue of the transition state, 3-azageranylgeranyl diphosphate, is also a potent inhibitor of GGPPS [74,75]. In the elimination step, a hydrogen is removed from C2 of IPP with simultaneous formation of a C¼C double bond between C2 and C3. The formation of the trans or cis double bond during the IPPS reaction depends on the spatial arrangement of the IPP relative to the elongating oligoprenyl substrate. In the trans-prenyltransferases, the allylic substrate is added to the si face of the double bond of the IPP, and the pro-R proton is removed from the methylene group next to the double bond, with the concomitant formation of a new trans double bond [72]. The amino acid involved in the hydrogen removal of IPP in prenyltransferase has not yet been reported. However, several important amino acids, including the nucleophilic His309 responsible for the removal of the pro-R hydrogen, have been proposed from analysis of the crystal structure of pentalenene synthase, which catalyzes cyclization of FPP initiated by the cleavage of its pyrophosphate moiety and formation of a carbocation intermediate (see below for details) [43]. The active-site residues Phe77 and Asn219 have been implicated in the stabilization of the carbocation intermediate [43]. In UPPS, there are several conserved hydrophilic amino acids in the vicinity of Asp26, including Asn28, Arg30, His43, Phe70, Ser71, Arg194 and Glu198. It is conceivable that some of them may play roles analogous to those of His309, Phe77 and Asn219 in pentalenene synthase. However, to form a cis double bond in UPPS, the position of the requisite nucleophile (possibly His43) will need to be close to the pro-S proton of IPP. The reaction mechanism of the cis-prenyltransferases is less well understood. The hydrolysis of the allylic substrate by cis-prenyltransferases has not been observed. Analogously to the two DDxxD motifs in the trans-prenyltransferases, site-directed mutagenesis studies of UPPS indicate that Asp and Glu play a significant role in IPP binding and 3346 P.-H. Liang et al. (Eur. J. Biochem. 269) FEBS 2002 activity probably through co-ordination with Mg2+. The IPP condensation kinetics for UPPS, DDPPS (cis-type) and OPPS (trans-type) had been measured for comparison of IPP condensation catalyzed by cis-IPPS and trans-IPPS [76–78]. These experiments were performed under the enzyme single-turnover condition using a rapid-quench instrument, because the slow release of the large hydrophobic product limits IPPS catalysis under steady-state conditions. The IPP condensation rate constant in the UPPS reaction is similar to that of OPPS (2.5 s)1 vs. 2.0 s)1) derived from the time course data simulated by the Kinsim program (Fig. 6). This suggests that the chemical environment of the active site in the two types of enzyme may be similar, despite the completely different primary sequence. Moreover, Triton could facilitate product release and increase the UPPS steady-state rate by 190-fold by switching the rate-limiting step from product release to IPP condensation. However, OPPS activity is only slightly increased (threefold) by Triton. Also determined from these studies, the bond-forming or bond-breaking step during IPP condensation must be rate limiting because the first reaction of C15 to C20, in which UPPS or OPPS is preincubated with FPP so that the pyrophosphate dissociation and the relocation of the intermediate are not involved in the reaction, has the same rate as the subsequent steps [76]. Product distribution of cis-prenyltransferases and trans-prenyltransferases In the UPPS reaction, significant amounts of intermediates are yielded as products under the conditions of 50 lM FPP and 50 lM IPP, whereas the C55-UPP is synthesized with 5 lM FPP and 50 lM IPP. In contrast, OPPS produces no intermediate products under these conditions [77]. Another trans-prenyltransferase, SPPS from M. luteus, shows a similar pattern of product distribution in which no intermediate is displaced from the active site at high concentration of FPP [15]. As OPPS and UPPS have similar FPP and IPP Km values, OPPS and SPPS (trans-type) apparently have higher affinities for intermediates compared with UPPS (cis-type). At a fixed concentration of allylic substrate, the increased ratio of IPP to FPP results in the synthesis of longer-chain products. As shown for a UPPS from the Archaeon Sulfolobus acidocaldarius, the enzyme mainly generates C50 and C55 when IPP is present in excess of GGPP (or FPP), but decreasing the concentration of IPP results in larger amounts of short-chain products [79]. This could be due to the low affinity of IPP for the enzyme. In the presence of Triton, UPPS mainly synthesizes C55 product. In contrast, under conditions in which product release is slow, chain elongation beyond normal can occur. Therefore, in the absence of Triton, UPPS could produce C55–C75 polymers [76]. For the microsomal DDPPS of rat liver, the chain length of products shifted downward from C90 and C95 with increasing concentration of detergent [80]. The trans-type OPPS could also generate C40–C60 compounds as the final products. Derived from pre-steady-state kinetic studies, the rate constant for condensation of an extra IPP with C55 to produce C60 is fivefold lower than that for regular IPP condensation (e.g. C50 to C55) in the UPPS reaction (Fig. 6). On the other hand, the rate for elongation from C40 to C45 catalyzed by OPPS is 100 times slower than for elongation from C35 to C40 (Fig. 6). The trans enzyme Fig. 6. Comparison of the kinetic pathways of UPPS and OPPS. OPPS catalyzes elongation of C15 to C40, resulting in all trans double bonds, and UPPS catalyzes formation of the C55 product containing newly formed cis double bonds. The IPP condensation steps have rate constants of 2 s)1 and 2.5 s)1 for OPPS and UPPS, respectively. The similar rate constants suggest closely related reaction mechanisms and perhaps similar active-site environments. However, OPPS has higher product specificity as judged from its much lower rate of conversion into C45 extra product. seems to have a more rigid active site than the cisprenyltransferase, as shown by the higher product specificity. The most surprising observation on the product distribution of the UPPS and OPPS reactions is that, when the FEBS 2002 Structure, mechanism and function of prenyltransferases (Eur. J. Biochem. 269) 3347 concentration of the UPPS and FPP complex is in 10-fold excess over that of IPP, long-chain polymers larger than C20 (GGPP), including C55, are generated. Pan et al. [76] proposed that UPPS–intermediate complexes may have greater affinity than the UPPS–FPP complex for the limited amount of IPP, leading to the formation of product with the correct chain length. OPPS shows the same phenomenon in producing C20–C40 under the same conditions [77]. This strategy for synthesizing the desired chain length seems to be shared by both types of enzyme. CLASS II: PROTEIN PRENYL-TRANSFERASES Structure and active site of protein prenyltransferases Ras FTase is a Zn2+-dependent prenyltransferase containing a and b heterodimer, which catalyzes the farnesylation on a C-terminal CaaX motif of the Ras protein. As shown in Fig. 9B, the Zn2+-activated thiolate of Cys acts as a nucelophile to attack the ionized farnesyl group. In the 3D structure of a mammalian Ras FTase, both subunits are largely composed of a helices (Fig. 7A) [37]. The a-2 to a-15 helices in the a subunit fold into a novel helical hairpin structure, resulting in a crescent-shape domain that envelopes part of the b subunit. On the other hand, the 12 helices of the b subunit form an a–a barrel. Six additional helices connect the inner core of helices and form the outside of the helical barrel. A deep cleft surrounded by hydrophobic amino acids in the center of the barrel is proposed as the FPP-binding pocket. A single Zn2+ ion is located at the junction between the a-hydrophilic surface groove near the subunit interface and the deep cleft in the b subunit. This Zn2+ ion is pentaco-ordinated by the Asp297 and Cys299 located in the N-terminal helix 11, His362 in helix 13 of the 2 b subunit, and a water molecule as well as a bidentate ligand Asp297b. Replacement of Cys299b with Ala results in lower Zn2+ affinity and abolishes enzyme activity [81]. A nineamino-acid portion of the adjacent b subunit in the crystal lattice was found to bind in the positively charged pocket of the b subunit close to the FPP site. This observation allowed the authors to speculate that the nonapeptide mimics some aspects of normal CaaX peptide binding. This was supported by the fact that the first four residues of the peptide form a type 1 b turn which indeed is similar to the observed conformation for the natural CaaX peptide when bound to FTase [82]. Furthermore, the C-terminal residue of the nonapeptide could form hydrogen bonds with Lys164a, Arg291b, and Lys294b. Since the report of the first FTase structure, the same research group has published the structure of FTase in complex with FPP [38] as well as the structure of the ternary complex containing an inactive FPP analogue and a CaaX peptide substrate [39]. Many features of the apo-FTase structure are retained in the complexes. According to the structure of FTase in complex with FPP, the highly conserved residues Trp303b, Try251b, Trp102b, Tyr205b, and Tyr200a form hydrophobic interactions with FPP. Arg202b in the binary complex adopts a different conformation from the structure of the apoenzyme to further interact with the substrate. This residue is stabilized by Asp200b and Met193b which also adopts a different conformation. From the binary structure, two additional amino acids, Cys254b and Gly250b, participate in the binding of FPP. The diphosphate moiety of the FPP substrate is hydrogen-bonded with His248b, Arg291b, and Tyr300b. Lys164a and Lys294b are also within hydrogenbonding distance of the diphosphate. Mutations of His248b, Arg291b, Lys294b, Tyr300b, and Trp303b cause 3–15 times increased FPP Kd compared with the wild-type FTase [83], consistent with the crystal structure. On the other hand, replacement of Lys164a with Asn results in a markedly decreased kcat value, suggesting that this residue plays a catalytic role [84]. From the binary structure, Lys164 may interact with the diphosphate moiety of FPP and be involved in the transfer of Cys thiol to C1 of the substrate. As for the binding of the 5th CaaX peptide substrate, the structure of FTase complexed with a-hydroxyfarnesyl- Fig. 7. (A) Ribbon diagram of Ras FTase and (B) the molecular ruler mechanism for substrate specificity of FTase and GGTase. (A) The heterodimeric enzyme consists of two subunits, a and b, colored in cyan–blue and yellow–green, respectively. Most of the secondary structures are helices, with the a subunit comprising seven helical hairpins that surround the more compact b subunit. The peptide substrate, colored red, binds to a cleft between the two subunits, and so does the substrate analogue, colored magenta. The active site is located in the b subunit. It contains a zinc ion, shown in blue, which is bound by three residues Asp297, Cys299 and His362, shown in cyan, and also makes bonds with the substrate molecules. (B) When FPP is replaced with GGPP in the active site of FTase, the thiolate nucleophile is further away from the electrophilic carbon next to the pyrophosphate leaving group, thereby decreasing the enzyme activity. Similarly, FPP is a poor substrate for GGTase. FEBS 2002 3348 P.-H. Liang et al. (Eur. J. Biochem. 269) phosphonic acid and acetyl-Cys-Val-Ile-selenoMet-COOH reveals that it binds in a cleft located in the subunit interface, in agreement with the pervious apoenzyme structure [37]. The peptide is in contact with FPP and several amino acids of the enzyme. The Ile-Met portion interacts with the adjacent Tyr166a, and the carbonyl group of the main chain forms a hydrogen bond with Arg202b. The Cys sulfur atom of the peptide co-ordinates with a water molecule and the Zn2+ ion which is stabilized by interacting with Asp297a, Cys299b, and His362b. The N-terminal acetyl group makes no contacts with the enzyme. As revealed by the FTase structure in complex with FPP, large amino-acid residues (Trp102b and Tyr205b) are located on the bottom of the hydrophobic funnel for FPP binding. The distance from these amino acids to the bound Zn2+ ion is approximately the length of FPP from C1 to C15 (Fig. 7B). According to this model, if a C20 GGPP is within the active site, its pyrophosphate is out of the reach of Zn2+. This explains why GGPP binds competitively with FPP to FTase but only FPP serves as an effective substrate. On the other hand, FPP binds to GGTase with 330-fold less affinity than GGPP [85]. However, it still serves as a moderately effective substrate because its diphosphate moiety can be situated around the Zn2+. This hypothesis has been confirmed by the solving of the 3D structure of Rab GGTase [40]. The GGPP is bound in the central cavity of the a–a barrel in the b subunit with its diphosphate head group to the positively charged cluster composed of Arg232b, Lys235b, and L105a. The diphosphate is closed to the Zn2+, which is co-ordinated with Asp238b, Cys240 b and His290b in a similar way to that observed in FTase, and an additional His residue. The structure of Rab GGTase can be superimposed on that of Ras FTase. One of the most striking differences is that on the bottom of the GGTase active-site cavity, Ser48b and Leu99b replace the more bulky Trp102b and Tyr154b seen in FTase, thereby enlarging the active site to accommodate GGPP. This is consistent the molecular ruler mechanism (Fig. 7B) proposed in FTase for substrate specificity. Rab GGTase is unique and different from FTase and type I GGTase in that it is able to prenylate Rab only in the presence of Rab escort protein. It exclusively modifies members of a single subfamily of Ras-related small GTPase, the Rab proteins involved in the regulation of intracellular vesicular transport in the biosynthetic secretory and exocytic/endocytic pathways [86,87]. Upon binding with the protein complex, the Rab GGTase transfers two GGPPs to the two Cys residues of Rab C-terminal -CC, -CXC, -CCX, or -CCXX motif [88]. As shown in the superimposition of the GGTase and FTase structures, several residues in the peptide-binding pockets are different, reflecting their peptide substrate specificity. Reaction mechanism and kinetics of protein: prenyltransferase Kinetic analysis of the enzymatic prenylation reaction reveals a relatively fast chemical step 0.8–12 s)1 followed by rate-limiting product release (0.06 s)1) [89,90]. Substrate binding follows an ordered sequential mechanism with the formation of the FTase–FPP complex before binding of the CaaX substrate [91]. When the FPP analogue with a strong electron-withdrawing fluorine atom replacing the C3 hydrogen was used, the reaction rate was significantly decreased, suggesting formation of a carbocation at C1 during the reaction [92,93]. This phenomenon is similar to that previously observed for FPPS as described above, but the fluorinated FPP had less effect in the FTase reaction than in the FPPS reaction. The formation of the carbocation with the simultaneous separation of the pyrophosphate of FPP represents in part the rate-determining step in the FTase reaction as the metal required for co-ordination with Cys of the peptide substrate is also involved in the catalysis. The direct contact of Zn2+ with Cys thiol is evident from the crystal structure of the FTase ternary complex and the studies using the Co2+-substituted FTase [94]. The use of the more thiophilic Cd2+ to increase the thio affinity and lowering its pKa to display lower activity suggests the direct participation of a metal ion in FTase catalysis [95]. However, inclusion of high concentrations of Mg2+ in the reaction mixture increases enzyme activity 700-fold because excess Mg2+ occupies a separate site, facilitating departure of the diphosphate group [96]. Therefore, an associated character with partially positive charge at C1 of FPP and partially negative charge pyrophosphate oxygen as well as in the metal-co-ordinated thiolate was proposed as the transition state of the FTase reaction (see Fig. 9B). CLASS III: TERPENOID CYCLASES General structure and mechanism of terpenoid cyclase Terpenoid cyclases such as squalene cyclase, pentalenene synthase, 5-epi-aristolochene synthase, and trichodiene synthase are responsible for the synthesis of cholesterol, a hydrocarbon precursor of the pentalenolactone family of antibiotics, a precursor of the antifungal phytoalexin capsidiol, and the precursor of antibiotics and mycotoxins, respectively. The last three enzymes catalyze the cyclization of FPP involving: (a) ionization of FPP to an allylic cation which acts as electrophile to react with one of the p bonds of the substrate for cyclization; (b) relocalization of the carbocation via hydride transfer and Wagner-Meerwein rearrangements; (c) deprotonation or capture of an exogenous nucleophile such as water to eliminate the carbocation. On the other hand, squalene synthase catalyzes the cyclization of squalene, which is formed by coupling two FPP molecules. Like trans-type IPPSs, which make linear polymers from FPP, the four cyclases also contain conserved Asp-rich motifs, suggesting that these enzymes have similar strategies for activating FPP. In the structures of these three enzymes, the similar structural feature referred to as Ôterpenoid synthase foldÕ with 10–12 mostly antiparallel a helices is found, as also observed in IPPS and FTase (Fig. 8). The high structural similarity provides support for the hypothesis that the three families of prenyltransferases described in this review have related evolution despite their low sequence similarity. Pentalenene synthase As shown in Fig. 8A, the active site of bacterial pentalenene synthase cloned from Streptomyces UC5319 [97] is located in a hydrophobic pocket with the bottom sealed by aromatic FEBS 2002 Structure, mechanism and function of prenyltransferases (Eur. J. Biochem. 269) 3349 Fig. 8. Ribbon representation of the structures of cyclic terpenoid-synthetic enzymes pentalenene synthase (A), 5-epi-aristolochene synthase (B), trichodiene synthase (C) and squalene synthase (D). They are shown in different colors with the N-terminus and C-terminus labeled. All of these enzymes have the terpenoid synthase fold and contain a helices as their major secondary-structure elements. The homologous helices that constitute the active site are emphasized with broad ribbons. residues Phe57, Phe76, and Trp308, and aliphatic residues Leu53, Val177, Val179, Thr182, and Val301 [43]. These residues together create the necessary conformation for FPP to undergo cyclization to pentalenene. The top of the pocket is surrounded by hydrophilic amino acids, including His309, Asn219, Arg44, Arg157, Arg173, Lys226, Arg230, and particularly Asp80 and Asp84 with their carboxylate protruded into the active site to complex with Mg2+. Together they facilitate the FPP carbocation formation as shown in Fig. 9C (path a). Subsequent cyclization and carbocation rearrangement processes use a His309 catalytic residue in the active site [43]. 5-epi-Aristolochene synthase Tobacco 5-epi-aristolochene synthase adopts entirely an a-helical structure with short loops and turns (Fig. 8B). The structure folds into two domains: the N-terminal domain aligns structurally with two glycosyl hydroxylases, and its function is not known; the C-terminal domain shares the common fold with FPPS. The active site of epi-aristolochene synthase is located in the C-terminal domains containing two Mg2+-binding sites. The Asp301 and Asp305 found in the conserved DDxxD motif co-ordinate with a Mg2+ [42]. The Asp444, Thr448, Glu452 and a water molecule co-ordinate FEBS 2002 3350 P.-H. Liang et al. (Eur. J. Biochem. 269) interaction with Arg264, Arg441 and the three Mg2+ ions. The newly formed allylic carbocation is positioned near the main-chain carbonyl oxygens of residues 401 and 402 at the kink in helix G, and the C1 is near the p orbitals of the C10–C11 bond. The bond forming between C1 and C10 leaves a tertiary carbocation on C11 (see Fig. 9C, path b), which is stabilized by Tyr527. A deprotonation at C13 by Asp525 leads to the germacrene intermediate. The formation of a C–C bond between C2 and C7 of the intermediate is triggered by protonation of C6 with a proton donated by Tyr520. This leaves a positive charge on C3 to form a bicyclic eudesmane carbocation intermediate. The following rearrangement of the carbocation is facilitated by the electron-rich side chain of Trp273 to generate the final product aristolochene. Trichodiene synthase Fig. 9. The transition state for reactions of cis-IPPS and trans-IPPS (A), protein farnesyltransferase (B), and pentalenene synthase, epi-aristolochene synthase, and trichodiene synthase (C). In three cases, the carbocation intermediate at C1–C3 carbons of FPP is formed, and the negative charge developed on pyrophosphate is stabilized by co-ordination with Mg2+. The deprotonated IPP or a Zn2+-activated thiolate anion of a protein acts as a nucleophile to attack the carbocation at C1 resulting in condensation with departure of the pyrophosphate. In the cyclase reaction, the nearby C¼C bond donates electrons for ring closure. The paths a, b, and c denote the routes of electron migration from the C¼C bond to C1 with the release of pyrophosphate catalyzed by pentalenene synthase, epi-aristolochene synthase, and trichodiene synthase, respectively. with the other Mg2+. These two Mg2+ ions located in the entrance of the active-site pocket are responsible for binding to the FPP substrate. A number of hydrophobic amino acids around the FPP site were proposed to provide further hydrophobic binding interactions. The catalytic mechanism of epi-aristolochene synthase was elucidated by its structure in complex with the substrate analogue farnesyl hydroxyphosphonate. Accordingly, as a loop (residues 521–534) becomes ordered, it forms a lid that clamps down over the active-site entrance in the presence of farnesyl hydroxyphosphonate. This brings the loop containing Arg264 and Arg266 close to the C1 hydroxy group of farnesyl hydroxyphosphonate, and an additional Mg2+ site forms. In analogy, the released negatively charged diphosphate group of the FPP substrate is stabilized by The recently solved 3D structure of trichodiene synthase (Fig. 8C) reveals 17 a helices, six of which (C, D, G, H, I, and J) form the hydrophobic active-site cleft [44]. An Asprich D100DSKD motif, which is important for catalytic activity as suggested by the mutagenesis studies [98], is located in the active site at the C-terminus of helix D. Three Mg2+ ions were found in the electron map of the enzyme–pyrophosphate complex. Among them, two metal ions in the active-site region co-ordinate with Asp100 (the first residue of the conserved Asp-rich motif). The conserved Asp residues are also found in aristolochene synthase and FPPS. The other Mg2+ is located in the site of N225, S229, and E233 on helix H, which are in a consensus sequence conserved among all known terpene synthase sequences. The metal ions are bound to the enzyme in the presence of pyrophosphate, and the pyrophosphate (also probably FPP) triggers a protein conformational change, in which D101 breaks a salt link with R62 and forms a new salt bridge with R304 after pyrophosphate binding. The purpose of the protein conformational change is proposed to facilitate the departure of the pyrophosphate group of the substrate. These ligand-induced conformational changes were also observed in other terpene synthases such as 5-epi-aristolochene synthase, suggestive of divergent evolution from a common ancestor. On the basis of the structures and the mechanism of trichodiene synthase, a model of the enzyme reaction has been constructed (Fig. 9C). Path c is the initial step of the reaction; the recapture of a-phosphate oxygen by the C3 cation forms the intermediate, which then undergoes dephosphorylation and C1–C6 bond formation [44]. The resulting C7 carbocation attracts the electrons of the C10–C11 p orbital to form the C7–C11 bond. Subsequently, three carbocation-driven migrations occur to generate the final product. Squalene cyclase Squalene cyclase and 2,3-oxidosqualene synthase catalyze the cyclization reactions to give steroid compounds and have become the targets for development of anticholesteremic and antifungal drugs. Bacterial squalene synthase had been crystallized in three distinct forms, and the structure of form A solved. The enzyme is a homodimer, and the structure shows two domains in the a subunit FEBS 2002 Structure, mechanism and function of prenyltransferases (Eur. J. Biochem. 269) 3351 A large number of isoprenoids have significant biological functions in nature. The structural and mechanistic information available so far provides an initial step to understanding the functions of many other prenyltransferases and a basis for designing enzyme agonists and antagonists to treat various diseases. However, the structures and even functions of many isoprenoid-synthetic enzymes, as well as the proteins catalyzing and undergoing prenylation, are still not known. Further studies on the structure, mechanism and function of prenyltransferases are therefore required. (Fig. 8D) [41]. Domain 1 is an a6–a6 barrel of two concentric rings of parallel a helices, which is similar to the fold of FPPSs and glucanases [99]. Domain 2 forms an a–a barrel and inserts into domain 1. The active site is located in a central cavity, with two amino acids in a DxDD motif, Asp376 and Asp377, on the top of the cavity [41]. Mutagenesis of these two Asp residues abolishes enzyme activity, indicating their importance in catalysis [100]. Based on the structure, Asp376 is the catalytic acid to protonate the first C¼C double bond, resulting in a carbocation for the initiation of ring cyclization. A water molecule acts as a base to receive a proton on the other end of the squalene molecule, which is polarized by the other water in a hydrogen-bonding network formed by Glu45 and Gln262. A constriction formed by Phe166, Val174, Phe434, and Cys435 in a mobile loop may serve as a gate for substrate passage. CONCLUSION This review summarizes the 3D structures, IPP condensation kinetics and mechanism of trans-IPPS and cis-IPPS for the production of linear polyprenyl pyrophosphates, and the reaction mechanism and structures of protein prenyltransferases and isoprenyl diphosphate cyclases. As illustrated in Fig. 9, the three families of prenyltransferases have similar strategies for substrate binding and catalysis. First, they use hydrophobic interactions to bind the hydrocarbon moiety of the allylic pyrophosphate substrate. Secondly, pyrophosphtae leaving is facilitated by co-ordination of active-site amino acids such as Asp, Glu and Lys with Mg2+. Although the protein FTase was isolated with Zn2+ bound, the inclusion of Mg2+ greatly enhances enzyme activity. The carbocation character of the allylic substrate (FPP) exists during reactions of all these prenyltransferases. In the IPPS reaction, IPP with a proton abstracted attacks the carbocation of FPP. For the protein farnesyltransferase, a thiolate anion of the substrate protein or a peptide acts as the nucelophile. The FPP cyclase reaction is also initiated by the formation of an FPP carbocation which attracts a pair of electrons from the nearby C¼C double bond for the ring closure (paths a, b, and c for pentalenene synthase, 5-epi-aristolochene synthase, and trichodiene synthase, respectively). As the X-ray structure of cis-type UPPS has become available, the general mechanism for product chain-length determination of the cis and trans forms of IPPS has gradually been understood. As revealed by the 3D structures, the size of the active-site cavity apparently controls the chain length of the final product of the IPPS reaction. Several large amino acids form a floor to seal the bottom of the active site and block further elongation of the product. Site-directed substitution of key large amino acids with smaller ones extends the size of the active site, thereby allowing the formation of a longer product and vice versa. The substrate specificities of protein FTase and GGTase are controlled by the size of the substrates. The larger GGPP is more distant from the Zn2+ catalytic site when binding on FTase and hence produces lower activity. The accurately tailored active sites of FPP cyclases (pentalenene synthase, 5-epi-aristolochene synthase, and trichodiene synthase) guarantee formation of the correct cyclization products. ACKNOWLEDGEMENTS We are grateful to Yi-Kai Chen for the preparation of the sequence alignment figures. REFERENCES 3 1. Poulter, C.D. & Rilling, H.C. (1981) Prenyl transferases and isomerase. In Biosynthesis of Isoprenoid Compounds (Spurgeon, S.L., ed.), Vol. 1, pp. 161–224. John Wiley & Sons, New York. 4 2. Poulter, C.D. (1974) Model studies in terpene biosynthesis. J. Agric. Food Chem. 22, 167–173. 3. Poulter, C.D. & Rilling, H.C. (1981) Conversion of farnesyl 5 pyrophosphate to squalene. In Biosynthesis of Isoprenoid Compounds (Spurgeon, S.L., ed.), Vol. 1, pp. 225–282. John Wiley & Sons, New York. 4. Spurgeon, S.L. & Porter, J.W. (1981) Biosynthesis of caro6 tenoids. In Biosynthesis of Isoprenoid Compounds (Spurgeon, S.L., ed.), Vol. 2, pp. 1–122. John Wiley & Sons, New York. 5. Sinensky, M. 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