Isopentenyl isomerase

As part of the extensive studies by Cornforth and co-workers of squalene biosynthesis, the stereochemistry of the last step has now been elucidated. This concerns the stereochemistry of proton addition to isopentenyl pyrophosphate with formation of the new methyl group of dimethylallyl pyrophosphate under the influence of isopentenyl isomerase (EC 5.3.3.2). The investigation hinged on the generation of a chiral methyl. CHDT. [2- C,2R- H,3R]- and [2- C,2S- H,3/ ]-mevalonic acid were separately converted in the presence of... 

Wallach proposed that one isoprene (2-methyl-l, 3-butadiene) unit of five carbon atoms could serve as this function. This idea was eventually elaborated on by Ruzicka and Bloch into the isoprene rule. Eventually, as we will see, the family of terpenes (Cio), sesquiterpenes (C15), diterpenes (C20), sesterpenes (C25), triter-penes (C30), and truly large compounds (polymers) found in latex and gutta-percha comprises tens of thousands of individual, unique compounds all of which may be considered as derived from isoprene (2-methyl-l,3-butadiene) and that the pair of C5 isomers, isopentenyl diphosphate and dimethylallyl diphosphate, compounds linked by interconversion (Scheme 11.41) under the influence of the isopentenyl isomerase (EC 5.3.3.1) serve as the biochemical parents to the family. ... 

The stereochemistry of the formation of the double bonds in abscisic acid (36), biosynthesized by avocado fruit, has been studied using (2R)-[2- H]-, (2S)-[2- H]-, and (5S)-[5- H]-mevalonates. The anticipated stereochemistry of the hydrogen atoms derived from C-2 and C-5 of mevalonate is shown in (37). The C-3 and C-4 hydrogen atoms of abscisic acid (36) were derived from a 2-pro-R-mevalonoid hydrogen atom. The hydrogen atom at C-5 of abscisic acid is derived from a 5-pro-S-mevalonoid hydrogen. The presence of some label at positions 3 and 4 when (2S)-[2- H]mevalonic acid was the precursor was attributed to the action of isopentenyl isomerase. 

The isomerization of isopentenyl diphosphate to dimethylally diphos phate is catalyzed by JPP isomerase and occurs through a carbocation pathway Protonation of the IPP double bond by a hydrogen-bonded cysteine residue ir the enzyme gives a tertiary carbocation intermediate, which is deprotonated b a glutamate residue as base to yield DMAPP. X-ray structural studies on the enzyme show that it holds the substrate in an unusually deep, well-protectec pocket to shield the highly reactive carbocation from reaction with solvent 01 other external substances. 

KAJIWARA s, FRASER p D, KONDO K and MISAWA N (1997) Expressiou of an exogenous isopentenyl diphosphate isomerase gene enhances isoprenoid biosynthesis in Escherichia coli Biochem J, 324, 421-6. 

Shelton, D.A., Leach, D.N., and Henry, R.J., Isopentenyl pyrophosphate isomerases from Melaleuca altemifolia (Cheel) and their role in isoprenoid biosynthesis, J. Hort. 

Cunningham, EX. Jr. and Gantt, E., Identification of multi-gene families encoding isopentenyl diphosphate isomerase in plants by heterologous complementation in Escherichia coli. Plant Cell Physiol. 41, 119, 2000. 

Figure 73. The carotenoid biosynthetic pathway. Enzymes are named according to the designation of their genes Ccs, capsanthin-capsorubin synthase CrtL-b, lycopene-b-cyclase CrtL-e, lycopene-e-cyclase CrtR-b, b-ring hydroxylase, CrtR-e, e-ring hydroxylase DMADP, dimethylallyl diphosphate GGDP, geranylgeranyl diphosphate Ggps, geranylgeranyl-diphosphate synthase IDP, isopentenyl diphosphate Ipi, IDP isomerase Pds, phytoene desaturase Psy, phytoene synthase Vde, violaxanthin de-epoxidase Zds, z-carotene desaturase Zep, zeaxanthin epoxidase. (From van den Berg and others 2000.)...

Figure 9.4 Monoterpene biosynthesis in peppermint oil gland secretory cells. The enzymes involved in this pathway are (1) 1-deoxy-D-xylulose 5-phosphate synthase, (2) 2-C-methyl-D-erythritol 4-phosphate reductoisomerase, (3) 2-C-methyl-D-erythritol 4-phosphate cytidyltransferase, (4) 4-(cytidine 5 -diphospho)-2-C-methyl-D-erythritol kinase, (5) 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase, (6) isopentenyl diphosphate isomerase, (7) geranyl diphosphate synthase, (8)...

The CPPase substrate DMAPP (15) is formed from isopentenyl pyrophosphate (IPP) (14) via the IPP isomerase reaction. It had been assumed that IPP was generated only via mevalonic acid (12) (Fig. 2), but Rohmer discovered another route, 2-C-methyl-D-erythritol 4-phosphate (13) (MEP) pathway (Fig. 2) [22, 23]. A key step in the MEP pathway is the reaction catalyzed by 1-deoxy-D-xylulose 5-phosphate synthase (DXS), which combines hydroxyethyl thiamine pyrophosphate (hydroxyethyl TPP) generated from pyruvic acid (17) and TPP with glyceral-dehyde 3-phosphate (18) to yield 1-deoxy-D-xylulose 5-phosphate (19) containing five carbons. The mevalonate pathway operates in the cytosol of plants and animals, whereas the MEP pathway is present in the plastid of plants or in eubacteria [24-27]. 

Isopentenyl diphosphate isomerase catalyzes the isomerization of isopentenyl diphosphate to dimethylallyl diphosphate (Equation (6)) " ... 

Figure 28 Active site of the isopentenyl diphosphate isomerase enzyme from E. coli. In the crystals studied by Bonanno et al. the bidentate glutamate is monodentate and the Mn has a distorted square pyramidal geometry.

Phytoene synthase [EC 2.5.1.32] (also known as gera-nylgeranyl-diphosphate geranylgeranyltransferase and prephytoene-diphosphate synthase) catalyzes the reaction of two geranylgeranyl diphosphate to produce pyrophosphate (or, diphosphate) and prephytoene diphosphate. Isopentenyl pyrophosphate isomerase [EC 5.3.3.2] catalyzes the interconversion of isopentenyl diphosphate and dimethylallyl diphosphate. See also Geranylgeranyl Diphosphate Geranylgeranyltransferase... 

Prenylation, the key step in terpene biosynthesis, is catalyzed by prenyltransferases. These enzymes are responsible for the condensation of isopentenyl pyrophosphate (IPP) with an allyl pyrophosphate, thus yielding isoprenoids. Numerous studies have been performed with fluorinated substrates in order to determine the mechanism of the reactions that involve these enzymes prenyltransferases, farnesyl diphosphate synthase (FDPSase), famesyltransferase (PFTase), and IPP isomerase. These studies are based on the potential ability of fluorine atoms to destabilize cationic intermediates, and then slow down S l type processes in these reactions. 

Recently Fujiwara et al. reported on the in vitro polymerization of trans-polyisoprene using the enzymes isopentenyl diphosphate isomerase (IDI) and fra 3-isoprenyl diphosphate synthase (IDS) [271]. IDI catalyzes the interconversion of IPP and DMAPP. IDS can now catalyze the polymerization of IPP from DMAPP as outlined above for the synthesis of natural rubber, and as outlined in Fig. 13a. However, the condensation process is inhibited due to hydrophobic interaction between IDS and hydrocarbon of the longer products. The hydrophobic chain of the elongating product does not readily protrude into the aqueous phase and it tends to interact with the enzyme. To achieve an efficient in vitro synthesis, the authors used an organic-aqueous two-liquid phase system to successfully synthesize (low molecular weight) fran.y-polyisoprene (see Fig. 13b). 

As a general comment, the cations that have been implicated in such biosyntheses are of the type for which analogues have been observed in superacids. However, many of these cations, (e.g., 106 and 109) would have a questionable existence as a free cation in an aqueous solution. This finding raises an interesting question whether they do have more than a fleeting existence within the active site of the enzyme. Does the enzyme provide some form of stabilization, such as that suggested when 106 is formed in the active site of isopentenyl diphosphate dimethylallyl diphosphate isomerase ... 

Some isopentenyl pyrophosphate is converted to the isomer dimethylallyl pyrophosphate, by an isomerase that produces a mixture, isopentenyl pyrophosphate dimethylallyl pyrophosphate. From this point on, the carbon chain-length of the intermediates progressively increase this is followed by reduction to squalene, which has 30 carbon atoms in a folded chain and no oxygen atoms (Chap. 6). The conversion of isopentenyl pyrophosphate to squalene is shown in Fig. 13-22. 

Blanc, V.M. and Pichersky, E. (1995) Nucleotide sequence of a Clarkia breweri cDNA clone of ipil, a gene encoding isopentenyl pyrophosphate isomerase. Plant Physiol, 108, 855-6. 

Dogbo, O. and Camara, B. (1987) Rurification of isopentenyl pyrophosphate isomerase and geranylgeranyl pyrophosphate synthase from Capsicum chromoplasts by affinity chromatography. Biochim. Biophys. Acta, 920, 140-8. 

Phillips, M.A., D Auria, J.C., Gershenzon, J. and Pichersky, E. (2008) The Arabidopsis thaliana type I Isopentenyl Diphosphate Isomerases are targeted to multiple sub-cellular compartments and have overlapping functions in isoprenoid biosynthesis. Plant Cell, 20, 677-96. 

Ramosvaldivia, A.C., Vanderheijden, R. and Verpoorte, R. (1997a) Elicitor-mediated induction of anthraquinone biosynthesis and regulation of isopentenyl diphosphate isomerase and famesyl diphosphate synthase activities in cell suspension cultures of Cinchona robusta How. Planta, 203, 155-61. 

Spurgeon, S.L., Sathyamoorthy, N. and Porter, J.W. (1984) Isopentenyl pyrophosphate isomerase and prenyltransferase from tomato fruit plastids. Arc/ . Biochem. Biophys., 230, 446-54. 

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