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Biosynthesis of Polysaccharides01:26

Biosynthesis of Polysaccharides

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Enhanced GDP-d-mannose 4-epimerization and dynamic insights into NDP-sugar 4-epimerase substrate specificity.

Carlos Josué Alvarez Quispe1, Denis Smyshliaev2, Rodrigo Gallegos Dextre1

  • 1Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, Coupure Links 653, Ghent, 9000, Belgium.

Archives of Biochemistry and Biophysics
|July 9, 2026
PubMed
Summary

Nucleotide sugar 4-epimerases (NS-4Es) exhibit diverse substrate specificities. This study expands their classification and reveals that active site dynamics, not just steric factors, determine specificity, offering new insights into carbohydrate metabolism.

Keywords:
GDP-MannoseGatekeeperHeptagonal box modelMolecular dynamicsNucleotide sugar 4-epimerasesSubstrate specificityUDP-Galactose 4-epimerase

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Area of Science:

  • Biochemistry
  • Enzymology
  • Carbohydrate Metabolism

Background:

  • UDP-galactose 4-epimerase (Gal4E) is crucial for galactose metabolism.
  • Homologous enzymes (NS-4Es) process various nucleotide sugars, vital for diverse metabolic pathways.
  • Existing models for NS-4E specificity, focusing on steric constraints and conserved motifs, have limitations.

Purpose of the Study:

  • To investigate the substrate specificity of NS-4Es.
  • To propose an expanded classification of NS-4Es.
  • To elucidate the molecular determinants of NS-4E substrate specificity.

Main Methods:

  • Sequence similarity networks
  • Site saturation mutagenesis
  • Molecular dynamics simulations

Main Results:

  • An expanded NS-4E classification into seven groups, including novel groups for GDP-sugars, UDP-D-xylose, UDP-D-galacturonic acid, and dTDP-L-rhamnose.
  • Mutagenesis of a GDP-hexose 4-epimerase gatekeeper enhanced GDP-D-Mannose activity.
  • Specificity is influenced by gatekeeper size/polarity and altered active site interactions.
  • Molecular dynamics revealed dynamic networks and clamping mechanisms in the active site.

Conclusions:

  • NS-4E specificity is more complex than previously thought, influenced by dynamic interactions.
  • The expanded classification provides a refined framework for understanding NS-4E diversity.
  • Active site dynamics are key determinants of substrate specificity across NS-4Es.