Identification of Significant Residues for Homoallylic Substrate Binding of Micrococcus luteus B-P 26 Undecaprenyl Diphosphate Synthase

Abstract

The primary structure of cis-prenyltransferase is totally different from those of trans-prenyltransferases (Shimizu, N., Koyama, T., and Ogura, K. (1998) J. Biol. Chem. 272, 19476 -19481). To better understand the molecular mechanism of enzymatic cis-prenyl chain elongation, we selected seven charged residues in the con- Prenyltransferases, also referred to as prenyl diphosphate synthases, are enzymes catalyzing the sequential condensation of isopentenyl diphosphate (IPP) 1 with allylic diphosphates to produce linear prenyl diphosphates in the biosynthetic pathway of isoprenoid compounds, most of which are essential components of the cellular machinery, such as cholesterol, carotenoids, prenyl quinones, prenyl proteins, and dolichols. Although these condensation reactions are similar in terms of chemical mechanism, there are a number of enzymes having different specificities with respect to the chain length and double-bond stereochemistry of its final product. These enzymes can be classified into two major subgroups (cis and trans types) according to the geometry of the products and are extremely interesting from an enzymological viewpoint in which the reactions are regulated to proceed consecutively and terminate precisely at definite chain lengths depending on the specificities of individual enzymes (1, 2). To date, the structural genes for many types of trans-prenyltransferases have been cloned and characterized. Multiple alignments of the deduced amino acid sequences of these transprenyltransferases showed the presence of several conserved regions in the primary structures (3, 4). The conserved regions include two characteristic aspartate-rich motifs (DDXXD), which have been shown to be essential for the catalytic function as well as substrate binding by site-directed mutational analysis (5-8). Tarshis et al. (9) determined the crystal structure of chicken FPP synthase, in which most of the conserved regions are found in a large central cavity. and Tarshis et al. (15) have intensively investigated the product chain length determination mechanisms of short chain transprenyltransferases such as FPP synthase from Bacillus stearothermophilus or chicken and geranylgeranyl diphosphate (GGPP) synthase from Sulfolobus acidocaldarius.On the other hand, cis-prenyltransferases catalyze cis-prenyl chain elongation to produce prenyl diphosphates with E,Zmixed stereochemistry. In bacteria, sequential cis addition of IPP onto FPP as an allylic primer to give undecaprenyl diphosphate (UPP, C 55 ) is catalyzed by UPP synthase. UPP is the direct precursor of glycosyl carrier lipid in the biosynthesis of bacterial cell wall polysaccharide components such as peptidoglycan and lipopolysaccharide. In eukaryotic cells, dehydrodolichyl diphosphate synthase responsible for cis-prenyl chain elongation catalyzes much longer chain elongation than does the bacterial enzyme. Dehydrodolichyl diphosphate is an essential precursor of carbohydrate carrier lipid in the biosynthesis of N-linked glycoprotein or glycosylphosphatidylinositolan...

Catalytic Mechanism Revealed by the Crystal Structure of Undecaprenyl Pyrophosphate Synthase in Complex with Sulfate, Magnesium, and Triton

“…This structural P-loop is supposed to interact with the pyrophosphate of the allylic substrate FPP. A second binding site for pyrophosphate of the homoallylic substrate IPP was also proposed (10,16 A and B, two orthogonal views of the enzyme with bound sulfate, magnesium ions, and Triton X-100 molecules. The left monomer, A, is colored in red and green for ␣-helices and ␤-strands, respectively, whereas the right monomer, B, is in magenta and cyan, respectively.…”

Mechanism of Product Chain Length Determination and the Role of a Flexible Loop in Escherichia coliUndecaprenyl-pyrophosphate Synthase Catalysis

“…2B shows the detailed arrangement of these amino acids. This region has been suggested as the FPP-and IPP-binding site based on site-directed mutagenesis studies (24,36).…”

Polyprenols Are Synthesized by a Plastidial cis-Prenyltransferase and Influence Photosynthetic Performance

“…GPP, FPP, as well as GGPP all proved to serve as substrates for AtCPT7 and exhibited Michaelian kinetics at saturating concentrations of 14 C-IPP ( Figure 3C). However, steady state kinetic analysis revealed that the enzyme had a 10-fold preference for GGPP and FPP compared with GPP (Table 1), with kinetic constants that fell within the range reported for other plant and bacterial CPTs (Kharel et al, 2001;Schulbach et al, 2001;Guo et al, 2005;Schilmiller et al, 2009;Kera et al, 2012;Demissie et al, 2013). This point was further clarified by structural analysis ( 1 H NMR) of Pren-10 (the dominating polyprenol in leaf tissue; Figure 1C) isolated from the leaves of wild-type Arabidopsis (Supplemental Figure 9).…”