Novel substrates of a ribose-5-phosphate isomerase from Clostridium thermocellum

Yoon, Ran-Young; Yeom, Soo‐Jin; Kim, Hye-Jung; Oh, Deok‐Kun

doi:10.1016/j.jbiotec.2008.09.012

Cited by 36 publications

(28 citation statements)

References 29 publications

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“…S1 in the supplemental material). Because these isomerases are involved in the isomerization of phosphosugars, they can also catalyze the isomerization of various monosaccharides owing to their broad substrate specificity (15)(16)(17)(18)(19) (Fig. 1).…”

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confidence: 99%

Development of Novel Sugar Isomerases by Optimization of Active Sites in Phosphosugar Isomerases for Monosaccharides

Yeom

Kim

2013

Appl Environ Microbiol

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Phosphosugar isomerases can catalyze the isomerization of not only phosphosugar but also of monosaccharides, suggesting that the phosphosugar isomerases can be used as sugar isomerases that do not exist in nature. Determination of active-site residues of phosphosugar isomerases, including ribose-5-phosphate isomerase from Clostridium difficile (CDRPI), mannose-6-phosphate isomerase from Bacillus subtilis (BSMPI), and glucose-6-phosphate isomerase from Pyrococcus furiosus (PFGPI), was accomplished by docking of monosaccharides onto the structure models of the isomerases. The determinant residues, including Arg133 of CDRPI, Arg192 of BSMPI, and Thr85 of PFGPI, were subjected to alanine substitutions and found to act as phosphatebinding sites. R133D of CDRPI, R192 of BSMPI, and T85Q of PFGPI displayed the highest catalytic efficiencies for monosaccharides at each position. These residues exhibited 1.8-, 3.5-, and 4.9-fold higher catalytic efficiencies, respectively, for the monosaccharides than the wild-type enzyme. However, the activities of these 3 variant enzymes for phosphosugars as the original substrates disappeared. Thus, R133D of CDRPI, R192 of BSMPI, and T85Q of PFGPI are no longer phosphosugar isomerases; instead, they are changed to a D-ribose isomerase, an L-ribose isomerase, and an L-talose isomerase, respectively. In this study, we used substrate-tailored optimization to develop novel sugar isomerases which are not found in nature based on phosphosugar isomerases.

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Development of Novel Sugar Isomerases by Optimization of Active Sites in Phosphosugar Isomerases for Monosaccharides

Yeom

Kim

2013

Appl Environ Microbiol

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“…(9), an L-arabinose isomerase mutant from Escherichia coli (4), a D-xylose isomerase mutant from Actinoplanes missouriensis (14), and a D-lyxose isomerase from Cohnella laeviribosi (3), indicating that L-ribose can be produced from L-ribulose by these enzymes. However, the enzymatic production of L-ribulose is slow, and the enzymatic production of L-ribose from L-ribulose has been not reported.Sugar phosphate isomerases, such as ribose-5-phosphate isomerase, glucose-6-phosphate isomerase, and galactose-6-phosphate isomerase, work as general aldose-ketose isomerases and are useful tools for producing rare sugars, because they convert the substrate sugar phosphates and the substrate sugars without phosphate to have a similar configuration (11,12,21,22). L-Ribose isomerase from an Acinetobacter sp.…”

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“…Sugar phosphate isomerases, such as ribose-5-phosphate isomerase, glucose-6-phosphate isomerase, and galactose-6-phosphate isomerase, work as general aldose-ketose isomerases and are useful tools for producing rare sugars, because they convert the substrate sugar phosphates and the substrate sugars without phosphate to have a similar configuration (11,12,21,22). L-Ribose isomerase from an Acinetobacter sp.…”

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Substrate Specificity of a Mannose-6-Phosphate Isomerase from Bacillus subtilis and Its Application in the Production of l -Ribose

Yeom

Kim

et al. 2009

Appl Environ Microbiol

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The uncharacterized gene previously proposed as a mannose-6-phosphate isomerase from Bacillus subtilis was cloned and expressed in Escherichia coli. The maximal activity of the recombinant enzyme was observed at pH 7.5 and 40°C in the presence of 0.5 mM Co 2؉ . The isomerization activity was specific for aldose substrates possessing hydroxyl groups oriented in the same direction at the C-2 and C-3 positions, such as the D and L forms of ribose, lyxose, talose, mannose, and allose. The enzyme exhibited the highest activity for L-ribulose among all pentoses and hexoses. Thus, L-ribose, as a potential starting material for many L-nucleoside-based pharmaceutical compounds, was produced at 213 g/liter from 300-g/liter L-ribulose by mannose-6-phosphate isomerase at 40°C for 3 h, with a conversion yield of 71% and a volumetric productivity of 71 g liter ؊1 h ؊1 .L-Ribose is a potential starting material for the synthesis of many L-nucleoside-based pharmaceutical compounds, and it is not abundant in nature (5, 19). L-Ribose has been produced mainly by chemical synthesis from L-arabinose, L-xylose, Dglucose, D-galactose, D-ribose, or D-mannono-1,4-lactone (2,17,23). Biological L-ribose manufacture has been investigated using ribitol or L-ribulose. Recently, L-ribose was produced from ribitol by a recombinant Escherichia coli containing an NAD-dependent mannitol-1-dehydrogenase (MDH) with a 55% conversion yield when 100 g/liter ribitol was used in a 72-h fermentation (18). However, the volumetric productivity of L-ribose in the fermentation is 28-fold lower than that of the chemical method synthesized from L-arabinose (8). L-Ribulose has been biochemically converted from L-ribose using an Lribose isomerase from an Acinetobacter sp. (9), an L-arabinose isomerase mutant from Escherichia coli (4), a D-xylose isomerase mutant from Actinoplanes missouriensis (14), and a D-lyxose isomerase from Cohnella laeviribosi (3), indicating that L-ribose can be produced from L-ribulose by these enzymes. However, the enzymatic production of L-ribulose is slow, and the enzymatic production of L-ribose from L-ribulose has been not reported.Sugar phosphate isomerases, such as ribose-5-phosphate isomerase, glucose-6-phosphate isomerase, and galactose-6-phosphate isomerase, work as general aldose-ketose isomerases and are useful tools for producing rare sugars, because they convert the substrate sugar phosphates and the substrate sugars without phosphate to have a similar configuration (11,12,21,22). L-Ribose isomerase from an Acinetobacter sp. (9) and D-lyxose isomerase from C. laeviribosi (3) had activity with L-ribose, D-lyxose, and D-mannose. Thus, we can apply mannose-6-phosphate (EC 5.3.1.8) isomerase to the production of L-ribose, because there are no sugar phosphate isomerases relating to L-ribose and D-lyxose. The production of the expensive sugar L-ribose (bulk price, $1,000/kg) from the rare sugar L-ribulose by mannose-6-phosphate isomerase may prove to be a valuable industrial process, because we have produced Lribulose from the ch...

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“…Sugar phosphate isomerases, such as ribose-5-phosphate isomerase (Park et al 2007a;Yoon et al 2009a), galactose-6-phosphate isomerase (Park et al 2007b), mannose-6-phosphate isomerase (Yeom et al 2009), and glucose-6-phosphate isomerase (Yoon et al 2009b), work as general aldose-ketose isomerases. These isomerases are useful for converting monosaccharides because they can isomerize monosaccharide substrates that exhibit similar configurations to monosaccharide phosphate substrates.…”

Section: Introductionmentioning

confidence: 99%

“…These isomerases are useful for converting monosaccharides because they can isomerize monosaccharide substrates that exhibit similar configurations to monosaccharide phosphate substrates. Due to of its broad substrate specificity, RpiB has been used to convert D-psicose to D-allose, which is a potential medical sugar (Hossain et al 2000), D-talose to D-tagatose, and D-ribose to D-ribulose (Park et al 2007a;Yoon et al 2009a). Despite the many reports describing the substrate specificity of sugar phosphate isomerases, comparison of the substrate specificity in sugar phosphate isomerases of different strains for monosaccharides have not yet been published.…”

Section: Introductionmentioning

confidence: 99%

Substrate specificity of ribose-5-phosphate isomerases from Clostridium difficile and Thermotoga maritima

et al. 2010

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The activity of ribose-5-phosphate isomerases (RpiB) from Clostridium difficile for D-ribose isomerization was optimal at pH 7.5 and 40 degrees C, while that from Thermotoga maritima for L-talose isomerization was optimal at pH 8.0 and 70 degrees C. C. difficile RpiB exhibited activity only with aldose substrates possessing hydroxyl groups oriented in the right-handed configuration (Fischer projections) at the C2 and C3 positions, such as D-ribose, D-allose, L-talose, L-lyxose, D-gulose, and L-mannose. In contrast, T. maritima RpiB displayed activity only with aldose substrates possessing hydroxyl groups configured the same direction at the C2, C3, and C4 positions, such as the D- and L-forms of ribose, talose, and allose.

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Novel substrates of a ribose-5-phosphate isomerase from Clostridium thermocellum

Cited by 36 publications

References 29 publications

Development of Novel Sugar Isomerases by Optimization of Active Sites in Phosphosugar Isomerases for Monosaccharides

Development of Novel Sugar Isomerases by Optimization of Active Sites in Phosphosugar Isomerases for Monosaccharides

Substrate Specificity of a Mannose-6-Phosphate Isomerase from Bacillus subtilis and Its Application in the Production of l -Ribose

Substrate specificity of ribose-5-phosphate isomerases from Clostridium difficile and Thermotoga maritima

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