Mechanism of xylobiose hydrolysis by GH43 β-xylosidase

J Phys Chem B. 2010 Nov 25;114(46):15389-93. doi: 10.1021/jp107886e. Epub 2010 Oct 25.


Glycoside hydrolases cleave the glycosidic linkage between two carbohydrate moieties. They are among the most efficient enzymes currently known. β-Xylosidases from glycoside hydrolase family 43 hydrolyze the nonreducing ends of xylooligomers using an inverting mechanism. Although the general mechanism and catalytic amino acid residues of β-xylosidases are known, the nature of the reaction's transition state and the conformations adopted by the glycon xylopyranosyl ring along the reaction pathway are still elusive. In this work, the xylobiose hydrolysis reaction catalyzed by XynB3, a β-xylosidase produced by Geobacillus stearothermophilus T-6, was explicitly modeled using first-principles quantum mechanics/molecular mechanics Car-Parrinello metadynamics. We present the reaction's free energy surface and its previously undetermined reaction pathway. The simulations also show that the glycon xylopyranosyl ring proceeds through a (2,5)B-type transition state with significant oxacarbenium ion character.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Bacterial Proteins / chemistry
  • Bacterial Proteins / metabolism*
  • Catalytic Domain
  • Disaccharides / chemistry
  • Disaccharides / metabolism*
  • Geobacillus stearothermophilus / enzymology*
  • Hydrolysis
  • Models, Molecular
  • Molecular Dynamics Simulation
  • Molecular Structure
  • Protein Conformation
  • Xylosidases / chemistry
  • Xylosidases / metabolism*


  • Bacterial Proteins
  • Disaccharides
  • Xylosidases
  • exo-1,4-beta-D-xylosidase
  • xylobiose