Ribulose-5-phosphate epimerization

The first of the interconversions features xylulose 5-phosphate and ribose 5-phosphate. Because transketolase has the specific requirement that the hydroxyl group at C-3 must be in the xylulose configuration, xylulose 5-phosphate is produced from ribulose 5-phosphate by epimerization involving the enzyme, ribulose-phosphate 3-epimerase. Epimers are sugars which differ only in the configuration of the hydroxyl group on one specific chiral carbon atom (Section 3.2), in this case C-3, hence the name of the enzyme. Carbon atoms 1 and 2 of xylulose 5-phosphate are transferred to ribose 5-phosphate to synthesize sedoheptulose 7-phosphate which, under the influence of transaldo-... 

In tissues that require primarily NADPH, the pentose phosphates produced in the oxidative phase of the pathway are recycled into glucose 6-phosphate. In this nonoxidative phase, ribulose 5-phosphate is first epimerized to xylulose 5-phosphate ... 

Epimerization changes the stereochemistry at one of the chiral centres, e.g. the interconversion of ribulose 5-phosphate and xylulose 5-phosphate (Figure 8.3). This reaction involves epimerization adjacent to a carbonyl group and probably proceeds through a common enol tautomer, but some other epimerizations are... 

L-Ribulose-5-phosphate 4-epimerase catalyzes epimerization at the C4 position of L-ribulose-5-phosphate to form D-xylulose-5-phosphate, allowing bacteria to utilize arabi-nose as an energy source in the pentose phosphate pathway ". The enzyme from E. coli is comprised of four equal 25.5 kDa subunits and shows very close resemblance to the... 

Another group of sugar epimerases, which uses a metal cofactor instead of NADH/NAD+, takes an entirely different approach to epimerization. L-ribulose 5-phosphate 4-epimerase, which is involved in the bacterial metabolism of arabinose, performs a retro-aldol cleavage of a C-C bond to yield a metal-stabilized enolate of dihydroxyacetone and glycoaldehyde phosphate, similar to the reaction catalyzed by class II aldolases [77-79]. The glycoaldehyde phosphate is thought to rotate, such that addition of the enolate generates the isomeric product. 

There are a number of cofactor independent carbohydrate epimerases that act on activated substrates, such as keto-sugars and keto-sugar nucleotides, although there is a paucity of details about their mechanisms. D-ribulose-5-phosphate 3-epimerase catalyzes the stereoinversion of substrate about the C-3 carbon to form D-xylulose 5-phosphate (as in Fig. 7.15) [102, 103]. Solvent hydron is completely incorporated into the product at the C-3 carbon, during epimerization in the d-xylulose 5-phosphate to o-ribulose 5-phosphate direction [102], This was taken as evidence for a two-base mechanism. 

Fig. 29.7. Ribulose 5-phosphate is epimerized (to xyulose 5-phosphate) and isomerized (to ribose 5-phosphate).

Perhaps the key reaction in this chapter was the aldol condensation in Section 22.2. Although it is not mentioned in the discussion, the aldol reaction is reversible under certain circumstances. Enzymes known as aldolases can catalyze both the forward and reverse aldol reactions. An example is the retro-aldol/ aldol mechanism employed by the enzyme l-ribulose-5-phosphate-4-epimerase, found in both prokaryotes and eukaryotes, to invert the stereochemistry of the hydroxyl-bearing carbon in 150 to that in 153. In other words, 1-ribulose-5-phosphate is epimerized to give d-xylulose-5-phosphate (see Chapter 28, Section 28.1, for a discussion of these carbohydrates). 

The first step is a retro-aldol of the Zn+ -coordinated l-ribulose-5-phosophate (150) induced by the enzyme to give the aldehyde 151A (glycoaldehyde phosphate) and the zinc-coordinated enolate anion 152 (dihydroxyacetone enolate). Before the aldol reaction occurs, there is a bond rotation to generate a different rotamer of the aldehyde, 151B (see Chapter 8, Section 8.1, for a discussion of rotamers). The aldehyde unit is not positioned differently, such that an aldol reaction will give the aldolate 153, but rather with a different absolute stereochemistry (Chapter 9, Section 9.3). The overall enzyme process leads to epimerization of the hydroxyl-bearing carbon. 

Scheme 11.12. A representation of the interconversion of ribulose 5-phosphate and xylulose 5-phosphate through the common enol and their subsequent hydrolysis and epimerization (or vice versa) to ribose and arabinose on the one hand and xylose and lyxose on the other.

Briefly, two of the five glyceraldehyde 3-phosphates are isomerized to glycerone phosphate, one of which reacts with a third glyceraldehyde 3-phosphate under the influence of fructose-bisphosphate aldolase (Section 11.2) to yield fructose 1,6-bis-phosphate which is dephosphorylated.to fructose 6-phosphate (Section 11.7). Transketolase catalyses a two-carbon unit transfer between fructose 6-phosphate and a fourth glyceraldehyde 3-phosphate to yield erythrose 4-phosphate and xylulose 5-phosphate. An aldol condensation of erythrose 4-phosphate with the second glycerone phosphate, catalyst by fructose-bisphosphate aldolase, produces sedoheptulose 1,7-bisphosphate which on dephosphorylation yields sedoheptulose 7-phos-phate. A second transketolase reaction utilizes sedoheptulose 7-phosphate and a flfth glyceraldehyde 3-phosphate to produce xylulose 5-phosphate and ribose 5-phosphate. The epimerization of both xylulose 5-phosphates and the isomerization of ribose 5-phosphate (Section 11.9) produces ribulose 5-phosphates which are phosphorylated to regenerate three ribulose 1,5-bisphosphate molecules. 

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