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Expanding the enzyme repertoire for sugar nucleotide epimerization : the CDP-tyvelose 2-epimerase from Thermodesulfatator atlanticus for glucose/mannose interconversion

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Abstract
Epimerization of sugar nucleotides is central to the structural diversification of monosaccharide building blocks for cellular biosynthesis. Epimerase applicability to carbohydrate synthesis can be limited, however, by the high degree of substrate specificity exhibited by most sugar nucleotide epimerases. Here, we discovered a promiscuous type of CDP-tyvelose 2-epimerase (TyvE)-like enzyme that promotes C-2 epimerization in all nucleotide (CDP, UDP, GDP, ADP, and TDP)-activated forms of D-glucose. This new epimerase, originating from Thermodesulfatator atlanticus, is a functional homodimer that contains one tightly bound NAD(+)/subunit and shows optimum activity at 70 degrees C and pH 9.5. The enzyme exhibits a k(cat) with CDP-D-glucose of -1.0 min(-1) (pH 7.5 and 60 degrees C). To characterize the epimerase kinetically and probe its substrate specificity, we developed chemoenzymatic synthesis for CDP-D-mannose, CDP-D-deoxy-D-glucose, CDP-3-deoxy-o-glucose, and CDP-6-deoxy-D-xylo-hexopyranos-4-ulose. Attempts to obtain CDP-D-paratose and CDP-D-tyvelose were not successful. Using high-resolution carbohydrate analytics and in situ nuclear magnetic resonance (NMR) to monitor the enzymatic conversions (60 degrees C and pH 7.5), we show that the CDP-D-mannose/CDP-D-glucose ratio at equilibrium is 0.67 (+/- 0.1), determined from the kinetic Haldane relationship and directly from the reaction. We further show that deoxygenation at sugar C-6 enhances the enzyme activity 5-fold compared to CDP-D-glucose, whereas deoxygenation at C-3 renders the substrate inactive. Phylogenetic analysis places the T. atlanticus epimerase into a distinct subgroup within the sugar nucleotide epimerase family of SDRs (short-chain dehydrogenases/reductases), for which the current study now provides functional context. Collectively, our results expand an emerging toolbox of epimerase-catalyzed reactions for sugar nucleotide synthesis. IMPORTANCE Epimerases of the sugar nucleotide-modifying class of enzymes have attracted considerable interest in carbohydrate (bio)chemistry for the mechanistic challenges and the opportunities for synthesis involved in the reactions catalyzed. The discovery of new epimerases with an expanded scope of sugar nucleotide substrates used is important to promote mechanistic inquiry and can facilitate the development of new enzyme applications. Here, a CDP-tyvelose 2-epimerase-like enzyme from Thermodesulfatator atlanticus is shown to catalyze sugar C-2 epimerization in CDP-glucose and other nucleotide-activated forms of D-glucose. The reactions are new to nature in the context of enzymatic sugar nucleotide modification. The current study explores the substrate scope of the discovered C-2 epimerase and, based on modeling, suggests structure-function relationships that may be important for specificity and catalysis.
Keywords
Biotechnology, Food Science, Ecology, Applied Microbiology and Biotechnology, CDP-glucose, carbohydrate synthesis, catalytic mechanism, epimerase, multistep enzyme catalysis, short-chain dehydrogenase/reductase (SDR), specificity, sugar nucleotide, CYTIDINE DIPHOSPHATE 3, 6-DIDEOXYHEXOSES, UDP-GALACTOSE 4-EPIMERASE, SUBSTRATE-SPECIFICITY, CRYSTAL-STRUCTURE, YERSINIA-PSEUDOTUBERCULOSIS, CARBOHYDRATE EPIMERASES, STRUCTURAL-ANALYSIS, BIOSYNTHESIS, PURIFICATION, REDUCTASE

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MLA
Rapp, Christian, et al. “Expanding the Enzyme Repertoire for Sugar Nucleotide Epimerization : The CDP-Tyvelose 2-Epimerase from Thermodesulfatator Atlanticus for Glucose/Mannose Interconversion.” APPLIED AND ENVIRONMENTAL MICROBIOLOGY, vol. 87, no. 4, 2021, doi:10.1128/aem.02131-20.
APA
Rapp, C., Van Overtveldt, S., Beerens, K., Weber, H., Desmet, T., & Nidetzky, B. (2021). Expanding the enzyme repertoire for sugar nucleotide epimerization : the CDP-tyvelose 2-epimerase from Thermodesulfatator atlanticus for glucose/mannose interconversion. APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 87(4). https://doi.org/10.1128/aem.02131-20
Chicago author-date
Rapp, Christian, Stevie Van Overtveldt, Koen Beerens, Hansjörg Weber, Tom Desmet, and Bernd Nidetzky. 2021. “Expanding the Enzyme Repertoire for Sugar Nucleotide Epimerization : The CDP-Tyvelose 2-Epimerase from Thermodesulfatator Atlanticus for Glucose/Mannose Interconversion.” APPLIED AND ENVIRONMENTAL MICROBIOLOGY 87 (4). https://doi.org/10.1128/aem.02131-20.
Chicago author-date (all authors)
Rapp, Christian, Stevie Van Overtveldt, Koen Beerens, Hansjörg Weber, Tom Desmet, and Bernd Nidetzky. 2021. “Expanding the Enzyme Repertoire for Sugar Nucleotide Epimerization : The CDP-Tyvelose 2-Epimerase from Thermodesulfatator Atlanticus for Glucose/Mannose Interconversion.” APPLIED AND ENVIRONMENTAL MICROBIOLOGY 87 (4). doi:10.1128/aem.02131-20.
Vancouver
1.
Rapp C, Van Overtveldt S, Beerens K, Weber H, Desmet T, Nidetzky B. Expanding the enzyme repertoire for sugar nucleotide epimerization : the CDP-tyvelose 2-epimerase from Thermodesulfatator atlanticus for glucose/mannose interconversion. APPLIED AND ENVIRONMENTAL MICROBIOLOGY. 2021;87(4).
IEEE
[1]
C. Rapp, S. Van Overtveldt, K. Beerens, H. Weber, T. Desmet, and B. Nidetzky, “Expanding the enzyme repertoire for sugar nucleotide epimerization : the CDP-tyvelose 2-epimerase from Thermodesulfatator atlanticus for glucose/mannose interconversion,” APPLIED AND ENVIRONMENTAL MICROBIOLOGY, vol. 87, no. 4, 2021.
@article{8693374,
  abstract     = {{Epimerization of sugar nucleotides is central to the structural diversification of monosaccharide building blocks for cellular biosynthesis. Epimerase applicability to carbohydrate synthesis can be limited, however, by the high degree of substrate specificity exhibited by most sugar nucleotide epimerases. Here, we discovered a promiscuous type of CDP-tyvelose 2-epimerase (TyvE)-like enzyme that promotes C-2 epimerization in all nucleotide (CDP, UDP, GDP, ADP, and TDP)-activated forms of D-glucose. This new epimerase, originating from Thermodesulfatator atlanticus, is a functional homodimer that contains one tightly bound NAD(+)/subunit and shows optimum activity at 70 degrees C and pH 9.5. The enzyme exhibits a k(cat) with CDP-D-glucose of -1.0 min(-1) (pH 7.5 and 60 degrees C). To characterize the epimerase kinetically and probe its substrate specificity, we developed chemoenzymatic synthesis for CDP-D-mannose, CDP-D-deoxy-D-glucose, CDP-3-deoxy-o-glucose, and CDP-6-deoxy-D-xylo-hexopyranos-4-ulose. Attempts to obtain CDP-D-paratose and CDP-D-tyvelose were not successful. Using high-resolution carbohydrate analytics and in situ nuclear magnetic resonance (NMR) to monitor the enzymatic conversions (60 degrees C and pH 7.5), we show that the CDP-D-mannose/CDP-D-glucose ratio at equilibrium is 0.67 (+/- 0.1), determined from the kinetic Haldane relationship and directly from the reaction. We further show that deoxygenation at sugar C-6 enhances the enzyme activity 5-fold compared to CDP-D-glucose, whereas deoxygenation at C-3 renders the substrate inactive. Phylogenetic analysis places the T. atlanticus epimerase into a distinct subgroup within the sugar nucleotide epimerase family of SDRs (short-chain dehydrogenases/reductases), for which the current study now provides functional context. Collectively, our results expand an emerging toolbox of epimerase-catalyzed reactions for sugar nucleotide synthesis.

IMPORTANCE Epimerases of the sugar nucleotide-modifying class of enzymes have attracted considerable interest in carbohydrate (bio)chemistry for the mechanistic challenges and the opportunities for synthesis involved in the reactions catalyzed. The discovery of new epimerases with an expanded scope of sugar nucleotide substrates used is important to promote mechanistic inquiry and can facilitate the development of new enzyme applications. Here, a CDP-tyvelose 2-epimerase-like enzyme from Thermodesulfatator atlanticus is shown to catalyze sugar C-2 epimerization in CDP-glucose and other nucleotide-activated forms of D-glucose. The reactions are new to nature in the context of enzymatic sugar nucleotide modification. The current study explores the substrate scope of the discovered C-2 epimerase and, based on modeling, suggests structure-function relationships that may be important for specificity and catalysis.}},
  articleno    = {{e02131-20}},
  author       = {{Rapp, Christian and Van Overtveldt, Stevie and Beerens, Koen and Weber, Hansjörg and Desmet, Tom and Nidetzky, Bernd}},
  issn         = {{0099-2240}},
  journal      = {{APPLIED AND ENVIRONMENTAL MICROBIOLOGY}},
  keywords     = {{Biotechnology,Food Science,Ecology,Applied Microbiology and Biotechnology,CDP-glucose,carbohydrate synthesis,catalytic mechanism,epimerase,multistep enzyme catalysis,short-chain dehydrogenase/reductase (SDR),specificity,sugar nucleotide,CYTIDINE DIPHOSPHATE 3,6-DIDEOXYHEXOSES,UDP-GALACTOSE 4-EPIMERASE,SUBSTRATE-SPECIFICITY,CRYSTAL-STRUCTURE,YERSINIA-PSEUDOTUBERCULOSIS,CARBOHYDRATE EPIMERASES,STRUCTURAL-ANALYSIS,BIOSYNTHESIS,PURIFICATION,REDUCTASE}},
  language     = {{eng}},
  number       = {{4}},
  pages        = {{14}},
  title        = {{Expanding the enzyme repertoire for sugar nucleotide epimerization : the CDP-tyvelose 2-epimerase from Thermodesulfatator atlanticus for glucose/mannose interconversion}},
  url          = {{http://dx.doi.org/10.1128/aem.02131-20}},
  volume       = {{87}},
  year         = {{2021}},
}

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