Triose phosphate isomerase enzyme mechanism

Chapter 8, How Enzymes Work, starts with a description of the basic chemical mechanisms that are exploited by enzymes. The latter half of this chapter presents a detailed description of how three enzymes—chymotrypsin, RNase, and triose phosphate isomerase—exploit these basic mechanisms of enzyme catalysis. 

Figure 16.6. Catalytic Mechanism of Triose Phosphate Isomerase. Glutamate 165 transfers a proton between carbons with the assistance of histidine 95, which shuttles between the neutral and relatively rare negatively charged form. The latter is stabilized by interactions with other parts of the enzyme.

Enzyme Mechanisms.— Triose phosphate isomerase has been a popular enzyme recently, having been the chief example quoted in two reviews on perfection and efficiency in enzyme catalysis - and the subject of seven successive papers in one issue of Biochemistry including one on the evolution of enzyme function and the development of catalytic efficiency. During glycolysis in muscle, fructose 1,6-bisphos-... 

Figure 8.49 Mechanisms of three enzymes that utilise general acid-base catalysis as part of their mechanistic paths to successful bio-catalysis, (a) triose phosphate isomerase (TIM), (b) lysozyme, (c) RNAse A. In all cases substrates are shown in red. Lone pair donor amino acid residues are general bases, lone pair acceptor amino acid residues are general acids. Note that pK (a commonly used term) is the equivalent of p/f/ or pK (as written in this text book) as appropriate for an acidic or basic functional group.

Figure 8.58 Schematic illustration of reaction coordinate diagram of Triose Phosphate Isomerase (TIM) enzyme illustrating near perfect energy landscape pathway allowing for near perfect 1 1 1 stoichiometric equilibrium between all enzyme-bound species optimal for flux through from one enzyme-bound species to another. Enzyme turnover rate kobs is at the diffusion limit, the rate determining step is the association of dihydroxy acetone phosphate (DHAP) with the TIM catalytic site, see Fig. 8.1, hence chemistry is not rate limiting. Therefore, TIM is considered a perfect enzyme For TIM enzyme assay see Fig. 8.17 for TIM enzyme mechanism see Fig. 8.49 (illustration adapted from Knowles, 1991, Fig. 2).

An enzyme catalyzes the interconversion of dihydroxyacetone phosphate into D-phosphoglyceraldehyde in presence of NAD. Thus, triose phosphate isomerase breaks a carbon-hydrogen bond in the hydroxymethyl group of the D-phosphoglyceraldehyde to yield dihydroxyacetone phosphate. The equilibrium of that reaction favors the formation of the dihydroxyacetone phosphate. From the description of the glycolytic pathway, it is evident that dihydroxyacetone phosphate is produced in two different enzymic reactions, catalyzed by aldolase or triose phosphate isomerase. The exact mechanism of the reaction is not known, but it has ben suggested that it involves the formation of an enolate anion that is bound to the enzyme. 

Fig. 36. The Calvin cycle (black lines) and pentose phosphate cycle (red lines). PGA = 3-Phosphoglyceric acid, PGAL = 3-phosphoglyceraldehyde, Rib. = ribose-5-phosphate, Xyl = xylulose-5-phosphate, Ru-diP = ribulose-1,5-diphosphate, C4 = erythrose-4-phosphate, FDP = fructose-1,6-diphosphate. A few of the enzymes participating are encoded, 1 = carboxydismutase, 2 = triose phosphate dehydrogenase, 3 = triose phosphate isomerase, 4 = aldolase, 5 = phosphatase, 6 = phosphoglucoisomerase. Details of the conversion of glucose-6-P into ribulose-5-P are given in Fig. 43. It should be pointed out that the pentose phosphate cycle presents only here and there a true reversal of the Calvin cycle. In many instances the mechanisms and enzymes are different.

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