Ribulose isomerase

Ribulose 5-phosphate is capable of a reversible isomerization to other pentose phosphates-xylulose 5-phosphate and ribose 5-phosphate. These reactions are catalyzed by two respective enzymes, viz., pentose-phosphate epimerase and pentose-phosphate isomerase, according to the scheme below ... 

A true xylose isomerase, that did not require arsenate for its activity, was found in strains of Lactobacillus, especially L. brevis (25). In this study, it was found that the activity of isomerization of glucose and xylose were essentialfy equal, and that ribose was isomerized to ribulose at a reduced rate 24). The xylose isomerases from this strain, like those from other species, requires divalent cations for activity. In this case, Mn and Co were found to be required for activity. In other studies, Co has been found to increase xylose isomerase stability 25,26,21. ... 

L-Fucose isomerase catalyzes the interconversion of L-fucose to L-fuculose and o-arabinose to D-ribulose. It has neither sequence nor structural similarity with the other aldose-ketose isomerases. A crystal structure of the E. coli enzyme with an L-fucitol bound in the active site shows that the active site is located in a 20 A deep pocket, at the bottom of which is a single Mn ion. Mn is bound to Oi and O2 of L-fucitol the side chains of a monodentate Glu-337, a bidentate Asp-361 (with long bonds to both oxygens), His-528 and a water molecule. ... 

Arabinose isomerase [EC 5.3.1.3] catalyzes the interconversion of D-arabinose and D-ribulose. The enzyme will also utilize L-fucose and more slowly utilize L-galactose and D-altrose as substrates. L-Arabinose isomerase [EC 5.3.1.4] catalyzes the interconversion of L-arabinose and L-ribulose. 

This enzyme [EC 4.1.1.48] catalyzes the conversion of l-(2-carboxyphenylamino)-l-deoxy-D-ribulose 5-phos-phate to generate l-(indol-3-yl)glycerol 3-phosphate, carbon dioxide, and water. 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 (/.e., anthranilate synthase, anthranilate phosphoribosyltransferase, tryptophan synthase, and phosphoribosylanthranilate isomerase). 

The product of the PNP enzyme, FDRP 9 has been purified and characterised. The evidence suggests that FDRP 9 is then isomerised to 5-fluoro-5-deoxyribulose-1-phosphate 10, acted upon by an isomerase (Scheme 7). Such ribulose phosphates are well-known products of aldolases and a reverse aldol reaction will clearly generate fluoroacetaldehyde 11. Fluoroacetaldehyde 11 is then converted after oxidation to FAc 1. We have also shown that there is a pyridoxal phosphate (PLP)-dependent enzyme which converts fluoroacetaldehyde 11 and L-threonine 12 to 4-FT 2 and acetaldehyde in a transaldol reaction as shown in Scheme 8. Thus, all of the biosynthetic steps from fluoride ion to FAc 1 and 4-FT 2 can be rationalised as illustrated in Scheme 7. 

These enzymes vary widely in secondary and tertiary structure.1273 Mannose-6-phosphate isomerase is a 45 kDa Zn2+-containing monomer. The larger 65 kDa L-fucose isomerase, which also acts on D-arabinose, is a hexameric Mn2+-dependent enzyme.1273 L-Arabinose isomerase of E. coli, which interconverts arabinose and L-ribulose, is a hexamer of 60-kDa subunits128 while the D-xylose isomerase of Streptomyces is a tetramer of 43-kDa subunits.129 The nonenzymatic counterpart of the isomerization catalyzed by the enzyme is the base-catalyzed Lobry deBruyn-Alberda van Ekenstein transformation (Eq. 13-25).130... 

Ribulose 5-phosphate 3-epimerase UDP-glucose 4-epimerase D-Glyceraldehyde 3-phosphate ketol isomerase... 

Alternatively, ribulose (D-eryt/iro-pentulose) 5-phosphate may be iso-merized to ribose 5-phosphate with pentose phosphate isomerase, but the same isomerase will convert D-ribose 5-phosphate into D- ryt/zro-pentulose 5-phosphate, the equilibrium being displaced by phosphorylation to the diphosphate (involving three enzyme systems). 

Ribulose-5-phosphate (3.13) can be converted to ribose-5-phosphate (3.14) and xylulose 5-phosphate (3.15), by the enzymes ribose-5-phosphate isomerase and ribulose 5-phosphate 3-epimerase, respectively. The two pentose-phosphate molecules, 3.14 and 3.15, are converted to a C3 and a C7 sugar-phosphate, glyceraldehyde 3-phosphate (3.4) and sedoheptulose-7-phosphate (3.16), respectively, via the action of atransketolase. 

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).

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. 

PFACRI N -[(5 -phosphoribosyl)formimino]-5-aminoimidazole-4-carboxamide ribonucleotide isomerase ImGPS imidazole 3-glycerol phosphate synthase OMPDC orotidine 5 -phosphate decarboxylase R5PE ribulose 5-phosphate epimerase HUMPS hex-3-ulose monophosphate... 

The ribulose 5-phosphate is now converted to ribose 5-phosphate by isomerization, a reaction catalyzed by phosphopentose isomerase ... 

The 5-carbon sugar phosphates are interconverted by the action of epimerase and isomerase to yield ribulose-5-phosphate, which is phosphorylated by the enzyme ribulose phosphate kinase to make RuBP, the acceptor of C02. 

L-arabinose isomerase, which interconverts L-arabinose and L-ribulose araB, L-ribulokinase, which uses ATP to phosphorylate L-ribulose at C-5 araD, L-ribulose 5-phosphate epimerase, which interconverts L-ribulose 5-phosphate and L-xylulose 5-phosphate talB, transaldolase and tktA, transketolase. 

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

Finally, ribose-5-phosphate is converted into ribulose 5-phosphate by phosphopentose isomerase while xylulose 5-phosphate is converted into ribulose 5-phosphate by phosphopentose epimerase. Ribulose 5-phosphate is converted into ribulose 1,5-bisphosphate through the action of phosphoribulose kinase (Figure 20,11). The sum of these reactions is... 

Ribulose 5-phosphate ribose 5-phosphate Phosphopentose isomerase... 

A recurring intermediate. Phosphopentose isomerase interconverts the aldose ribose 5-phosphate and the ketose ribulose 5-phosphate. Propose a mechanism. 

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