Isopentenyl-diphosphate A-isomerase

Liitzow, M., Beyer, P. The isopentenyl diphosphate A-isomerase and its relation to the phytoene synthase complex in daffodil chromoplasts BBA 959 (1988) 118-126... 

Isopentenyl diphosphate (IPP) isomerase (EC 5.3.3.2) catalyses the interconversion of IPP and dimethylallyl diphosphate (DMAPP). During a growth cycle of a suspension culture of C. roseus, relatively highest IPP isomerase activity was found between 4 and 6 days after subculture about 20 pkat/mg protein. By Western blot analysis, using purified polyclonal antibodies raised against IPP isomerase from Capsicum annuum chloroplasts, two isoforms of IPP isomerase were detected in the C. roseus extracts [13]. 

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. 

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.

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 ... 

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. 

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]. 

A. C. Ramos-Valdivia. Characterization of isopentenyl diphosphate isomerase. A regulatory enzyme in Cinchona isoprenoid biosynthesis. Ph.D. Thesis. Leiden University, 1996. 

Gresh N, Audiffren N, Piquemal JP, de Ruyck J, Ledecq M, Wouters J (2010) Analysis of the interactions taking place in the recognition site of a bimetallic Mg(II)-Zn(II) enzyme, isopentenyl diphosphate isomerase. A parallel quantum-chemical and polarizable molecular mechanics study. J Phys Chem B 114 4884... 

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. 

IPP and DMAPP are interconverted by isopentenyl-di-phosphate D-isomerase (isopentenyl pyrophosphate dimethylallyl pyrophosphate isomerase isopentenyl pyrophosphate A -A -isomerase EC 5.3.3.2). This enzyme has been isolated from a number of plant sources, such as pumpkin, orange peel, and pine seedlings. Isopenenyl-diphosphate d-isomerase (from the fungus Claviceps) has a molecular weight of 35,000, a requirement for Mg, and an pH optimum of 6.0-8.5, and it is inhibited by geranyl and famesyl diphosphate. 

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. 

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]. 

Berthelot, K., Estevez., and A., Deffieux. 2012. Isopentenyl diphosphate isomerase A checkpoint to isoprenoid biosynthesis . Biochimie. 94(8) 1621-34. 

However, our different incubation data show, that the first enzyme of the phytoene synthase complex in daffodil chromoplasts, the isopentenyl diphosphate isomerase, works independently and maintains with high efficiency a pool of free DMAPP/IPP. On the other hand the consecutive enzymes, the prenyltransferase and the phytoene-synthase utilized this pool in an effective way for the formation of phytoene. Whether this conclusions can be extrapolated to the in vivo situation remains uncertain. The complicated situation is daffodil chromo-... 

---