D-Ribulose 5-phosphate

Similar to DHAP aldolases, the 3-hexulose 6-phosphate aldolase found in Methylomonas Ml 5 is highly specific for the aldol donor component D-ribulose 5-phosphate, but accepts a wide variety of aldehydes as replacement for formaldehyde as the acceptor. With propanal,... 

This enzyme [EC 5.3.1.13] catalyzes the interconversion of D-arabinose 5-phosphate to D-ribulose 5-phosphate. 

This enzyme [EC 5.3.1.24], also known as /V-(5 -phos-phoribosyl)anthranilate isomerase, catalyzes the interconversion of /V-(5-phospho-/3-D-ribosyl)anthranilate and l-(2-carboxyphenylammo)-l-deoxy-D-ribulose 5-phosphate. In some organisms, this enzyme is part of a multifunctional protein, together with one or more components of the system for the biosynthesis of tryptophan (anthranilate phosphoribosyltransferase, indole-3-glycerol-phosphate synthase, anthranilate synthase, and tryptophan synthase). 

This enzyme [EC 1.1.1.137] catalyzes the reaction of d-ribitol 5-phosphate with NAD(P)+ to produce D-ribulose 5-phosphate and NAD(P)H. 

This enzyme [EC 5.1.3.1] (also known as phosphoribu-lose epimerase, erythrose-4-phosphate epimerase, and pentose-5-phosphate 3-epimerase) catalyzes the interconversion of D-ribulose 5-phosphate and D-xylulose 5-phosphate. The enzyme can also act on D-erythrose 4-phosphate. 

The Calvin cycle is completed by the phosphorylation of D-ribulose 5-phosphate with ATP. The resulting D-ribulose 1,5-diphosphate then is used to start the cycle again by combining with carbon dioxide. There is one sixth more fructose generated per cycle than is used to reform the ribulose 1,5-diphosphate. This fructose is used to build other carbohydrates, notably glucose, starch, and cellulose. 

Like the DHAP aldolases, the class II 3-hexulose 6-phosphate aldolase from a unique formaldehyde-fixing system of the methylotrophic bacterium Methyl-omonas Ml5 utilizes a ketose phosphate, i.e. D-ribulose 5-phosphate (128), as the aldol donor component for which it has a stringent requirement [374], On the... 

Enzymes of KDO Synthesis and Metabolism and Their Inhibition. The KDO pathway can be thought of as a minor branched pathway in carbohydrate metabolism initiating with the key intermediate in the hexose-monophosphate shunt, D-ribulose-5-phosphate. As shown in Figure 2 the biosynthesis and utilization are known to involve at least five sequential reactions ... 

Figure 2. Expanded pathway for the synthesis and use of KDO. The pathway initiates with D-giucose-6-phosphate, shows the branch point whereby D-ribulose-5-phosphate can be used to synthesize either D-arabinose-5-phosphate or D-ribose-5-phosphate and terminates with the transfer of KDO to the lipid A precursor. The numbers in parenthesis below the various enzymes correspond to their specific activities (nmoles per minute per...

D-Arabinose-5-phosphate isomerase, the first key enzyme in the synthesis of KDO, catalyzes the interconversion of D-ribulose-5-phosphate and D-arabinose-5-phosphate. This enzyme was briefly studied by Volk (18) and later by Lim and Cohen (19). Due to the instability of the enzyme, we have only purified this enzyme 100-fold. The reversible reaction is readily monitored by measuring the formation of the keto-sugar from the aldo-sugar by the method of Dische and Borenfreund (20). The K values for D-ribulose-5-phojsphate and D-arabinose-5-phosphate are 0.9 to 1.5 and 1 to 3 x 10 M, respectively. 

Figure 3. Plausible mechanism for the conversion of D-ribulose-5-phosphate isomerase to n-arabinose-5-phosphate by n-arabinose-5-phosphate isomerase. It is a least-motion model consistent with the mechanisms of similar enzymes (21-23).

In vivo measurements of lipopolysaccharide synthesis in E. coli B have indicated that two nanomoles of KDO must be synthesized per minute per mg of protein in order to meet the cellular requirement for LPS synthesis under the normal conditions of growth on glucose-minimal medium (27). We have measured the specific activities of the enzymes involved in KDO synthesis in crude extracts of E. coli B including those enzymes responsible for the synthesis of D-ribulose-5-phosphate, the precursor of D-arabinose-5-phosphate. D-Ribulose-5-phosphate is a key intermediate in carbohydrate metabolism as shown in Figure 2, since it is the direct precursor of both D-ribose-5-phosphate and D-arabinose-5-phosphate... 

Measurements of the crude specific activity (mmoles of product synthesized per minute per mg of protein in the supernatant after a 50,000 x g centrifugation) of the two isomerases in E. coli indicated that the conversion of D-ribulose-5-phosphate to D-ri-bose-5-phosphate was approximately 20- to 30-fold greater than the conversion of D-ribulose-5-phosphate to D-arabinose-5-phosphate. This rate of reaction strongly pulls the reaction substrate to D-ribose-5-phosphate, since the isomerase reaction at equilibrium strongly favors the formation of the aldo-sugar over the key intermediate D-ribulose-5-phosphate. 

The third step in the pathway yields a C5 sugar, D-ribulose 5-phosphate, and concomitantly reduces another molecule of NADP+. This is catalyzed by 6-phosphogluconate dehydrogenase ... 

D-Ribulose 5-phosphate then undergoes an isomerization by ribose-5-phosphate isomerase to o-ribose 5-phosphate (Step 4) ... 

Of the two D-tetroses, only 4-phospho-D-erythrose is found in any quantity, as an intermediate in the photo synthetic reactions. Of the four pentoses, only D-ribose and D-xylose occur to any extent. The phospho- z/J6>-D-pentoses, D-ribose-5-phosphate and D-xylose-5-phosphate, are found in the photo synthetic reactions. Three phospho- t6>-D-pentoses are also found as intermediates in the photosynthetic reactions D-ribulose-5-phosphate, D-xylulose-5-phosphate, and D-ribulose-l,5-bis-phosphate, the latter carbohydrate being directly involved in the fixing of C02in photosynthesis. 

The pentose phosphate pathway also catalyzes the interconversion of three-, four-, five-, six-, and seven-carbon sugars in a series of non-oxidative reactions. All these reactions occur in the cytosol, and in plants part of the pentose phosphate pathway also participates in the formation of hexoses from CO2 in photosynthesis. Thus, D-ribulose 5-phosphate can be directly converted into D-ribose 5-phosphate by phosphopentose isomerase, or to D-xylulose 5-phosphate by phosphopentose epimerase. D-Xylulose 5-phosphate can then be combined with D-ribose 5-phosphate to give rise to sedoheptulose 7-phosphate and glyceraldehyde-3-phosphate. This reaction is a transfer of a two-carbon unit catalyzed by transketolase. Both products of this reaction can be further converted into erythrose 4-phosphate and fructose 6-phosphate. The four-carbon sugar phosphate erythrose 4-phosphate can then enter into another transketolase-catalyzed reaction with the D-xylulose 5-phosphate to form glyceraldehyde 3-phosphate and fructose 6-phosphate, both of which can finally enter glycolysis. 

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. 

Aldol condensation of D-ribulose 5-phosphate with formaldehyde (0.082 mol- Is" )... 

ATP -I- D-ribulose = ADP + D-ribulose 5-phosphate (<1> random bi bi reaction mechanism [2])... 

---