Isopentenyl diphosphate isomerization

The conversion of isopentenyl diphosphate (IPP) to terpenoids begins with its isomerization to dimethylallyl diphosphate, abbreviated DMAPP and formerly called dimethylallyl pyrophosphate. These two C5 building blocks then combine to give the C10 unit geranyl diphosphate (GPP). The corresponding alcohol, geraniol, is itself a fragrant terpenoid that occurs in rose oil. 

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. 

Isopentenyl diphosphate is isomerized by a shift of the double bond to form dimethylallyl diphosphate, then condensed with another molecule of isopentenyl diphosphate to form the ten-carbon intermediate ger-anyl diphosphate (Figure 26-2). A further condensation with isopentenyl diphosphate forms farnesyl diphosphate. Two molecules of farnesyl diphosphate condense at the diphosphate end to form squalene. Initially, inorganic pyrophosphate is eliminated, forming presqualene diphosphate, which is then reduced by NADPH with elimination of a further inorganic pyrophosphate molecule. 

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

Formation of squalene. Isopentenyl diphosphate undergoes isomerization to form dimethylallyl diphosphate. The two C5 molecules condense to yield geranyl diphosphate, and the addition of another isopentenyl diphosphate produces farnesyl diphosphate. This can then undergo dimerization, in a head-to-head reaction, to yield squalene. Farnesyl diphosphate is also the starting-point for other polyisoprenoids, such as doli-chol (see p. 230) and ubiquinone (see p. 52). 

A second example is isomerization of isopentenyl diphosphate to dimethylallyl diphosphate (Eq. 13-56) 304-307 The stereochemistry has been investigated using the 3H-labeled compound shown in Eq. 13-56. The pro-R proton is lost from C-2 and a proton is added to the re face at C-4. When the reaction was carried out in 2H20 a chiral methyl group was produced as shown.304 A concerted proton addition and abstraction is also possible, the observed trans stereochemistry being expected for such a mechanism. However, the... 

Before polymer formation begins, one molecule of isopentenyl diphosphate must be isomerized to dime-thylallyl diphosphate (Fig. 22-1, step e, Eq. 13-... 

All isoprenoids are biosynthesized from two isomeric 5-carbon compounds, isopentenyl diphosphate (IPP, 86) and dimethylallyl diphosphate (DMAPP, 87) (Fig. 11). The mammalian pathway for the biosynthesis of these key biosynthetic precursors from three acetyl-CoA units (83) via mevalonate (85) had been elucidated in the 1950s (51). In the wake of that pioneering work, it became established dogma that all terpenoids are invariably of mevalonate origin, even in the face of significant aberrant findings. 

Isopentenyl diphosphate isomerase (IPI E.C. 5.3.3.2) catalyzes the isomerization of isopentenyl diphosphate (IPP) to dimethylallyl diphosphate (DMADP), a previous and mandatory step to create the electrophilic allylic diphosphates needed for the condensation reaction generating geranyl diphosphate, Fig. (6). Thus, IPI is an essential enzyme in organisms which synthesize IPP through the mevalonic acid pathway as archaea, eukaryota and some Gram-positive bacteria [275, 305]. 

The isoprenoids are derived from mevalonic acid (MVA), which is formed from three molecules of acetyl-CoA (Fig. 3). Two molecules of acetyl-CoA are condensed, yielding acetoacetyl-CoA. Subsequently, this product is coupled with another molecule of acetyl-CoA to yield 35-hydroxy-3-methylglutaryl-CoA (HMG-CoA). By reduction of HMG-CoA MVA is obtained. MVA is further converted in some steps to yield the Cs-unit isopentenyl diphosphate (IPP), which is then isomerized to dimethy-lallyl diphosphate (DMAPP), the starter molecule of the isoprenoid pathway. Coupling of DMAPP with one or more IPP molecules yields the basic structures which form the backbone of terpenoid biosynthesis. A number of reviews on the early steps in the terpenoid biosynthesis have been published (70-77). 

In the presence of the enzyme isopentenyl diphosphate isomerase, isopentenyl diphosphate is converted to dimethylallyl diphosphate. The isomerization involves two successive proton transfers one from an acidic site of the enzyme (Enz—H) to the double bond to give a tertiary carbocation the other is deprotonation of the carbocation by a basic site of the enzyme to generate the double bond of dimethylallyl diphosphate. 

The early stages of carotenoid biosynthesis are common to the biosynthesis of all isoprenoids. The characteristic isoprenoid precursor, mevalonic acid (MVA) is converted into the C5 compound isopentenyl diphosphate (IDP), some of which is isomerized to dimethyallyl diphosphate (DMADP). The isoprenoid chain is then built from these precursors by means of prenyl transferase enzymes to give, successively, the Ciq geranyl... 

The isomerization of isopentenyl diphosphate to dimethylallyl diphosphate is catalyzed by the enzyme isopentenyl pyrophosphate isomerase. In this process, the 2R hydrogen is lost and another hydrogen is picked up on the opposite face. Thus, the original methyl group is now cis or (Z)- to the methylene bearing the diphosphate group, that is. 

Then (Scheme 11.41) mevalonate [(l )-3,5-dihydroxy-3-methylpentanoic acid] is phosphorylated by the enzyme mevalonate kinase (EC 2.7.1.36) at the primary hydroxyl. The phosphate that is added is obtained (an addition-elimination reaction or a displacement reaction) from the terminal phosphate group of ATP forming ADP in turn. Another phosphorylation, again using ATP yields mevalonate diphosphate, this time by the enzyme phosphomevalonate kinase (EC 2.7.4.2) and then, after one more phosphorylation, this time on the tertiary hydroxyl, decarboxylation and dehydration co-occur, catalyzed by the enzyme mevalonate diphosphate decarboxylase (EC 4.1.1.43). The products are inorganic phosphate, carbon dioxide, and isopentenyl diphosphate (diphosphoric acid mono[3-methylbut-3-enyl] ester). Isopentenyl diphosphate isomerase (EC S.3.3.2) catalyzes the isomerization, via loss of the C2 pro-R hydrogen, between isopentenyl diphosphate and dimethylallyl diphosphate. 

Scheme 11.41. The enzyme-catalyzed phosphorylation (ATP -y ADP) and decarboxylation (with elimination of inorganic phosphate) of (i )-mevalonate [(i )-3,5-dihydroxy-3-methylpentanoic acid] to isopentenyl diphosphate (diphosphoric acid mono-[3-methylbut-3-enyl] ester) and the isomerization of the latter to dimethylallyl diphosphate (EC 5.3.3.2). It is important to note that the isomerization involves the specific removal of the pro-R hydrogen of C2 of the former. EC numbers and some graphic materials provided in this scheme have been taken with permission from appropriate links in a URL starting with http // www.chem.qmul.ac.uk/iubmb/enzyme/.

A central role in the biosynthesis of isoprenoids is filled by the isopentenyl diphosphate-dimethylallyl diphosphate isomerase (IDl) that catalyzes the interconversion of IPP and DMAPP. The necessity for such an enzyme was suggested in the 1950s when only IPP was known as a monomeric isoprenoid precursor, but an allylic diphosphate such as DMAPP was assumed to have the higher intrinsic reactivity for polyisoprenoid synthesis [22, 88, 89]. The first enzymatic isomerization of IPP to DMAPP was observed in 1959 from a cell-free extract of baker s yeast [90, 91]. Two types of IDI with essentially no amino acid sequence or structural similarities are able to catalyze this interconversion by completely different enzyme mechanisms. The well-known IDI-I have been identified in animals, plants, fungi, and bacteria, whereas the IDI-II can be found mainly in archaea but also in some bacteria [92, 93]. 

Briefly, three acetyl-CoAs provide the carbons for the synthesis of five-carbon isopentenyl diphosphate which may undergo isomerization to yield dimethylallyl diphosphate. Head-to-tail interaction between isopentenyl diphosphate and dimethylallyl... 

Isopentenyl pyrophosphate is potentially a bifunctional molecule. Its terminal vinyl group gives a nucleophilic character whereas when it isomerizes to 3,3-dimethylallyl diphosphate, the latter is electrophilic. Thus, longer-chain polyprenyls are formed by a favourable condensation of isopentenyl pyrophosphate first with dimethylallyl pyrophosphate and later with other allylic diphosphates. The initial interconversion of isopentenyl diphosphate and dimethylallyl diphosphate is promoted by an isomerase. The successive condensations yield the Cio compound geranyl diphosphate and then the C15 farnesyl diphosphate. The two molecules of famesyl diphosphate condense to form presqualene pyrophosphate which is reduced by NADPH to give the C30 open chain terpenoid squalene. The condensation reactions with IPP are a rather novel method of C-C bond formation since in the formation of other types of natural products (peptides, sugars, fatty acids, etc.) the reactions involve Claisen- or aldol-type condensations. 

Although, terpenoids show enormous chemical and structural diversity, their backbones are synthesized from only two universal precursors isopentenyl pyrophosphate (IPP) and its highly electrophilic allyUc isomer dimethylaUyl pyrophosphate (DMAPP) [25]. IPP is isomerized to DMAPP by the enzyme isopentenyl pyrophosphate isomerase. The mevalonate pathway for the biosynthesis of terpenoids has been illustrated in Fig. 86.3. To summarize, the active isoprene unit (IPP) is repetitively added to DMAPP or a prenyl diphosphate in sequential head-to-tail... 

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