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Mechanism of Xylobiose Hydrolysis by GH43 β-Xylosidase
The Journal of Physical Chemistry B
  • Ian J. Barker, Iowa State University
  • Luis Petersen, Iowa State University
  • Peter J. Reilly, Iowa State University
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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 byGeobacillus 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 2,5B-type transition state with significant oxacarbenium ion character.

Posted with permission from The Journal of Physical Chemistry B, 114, no. 46 (2010): 15389–15393, doi:10.1021/jp107886e. Copyright 2010 American Chemical Society.

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American Chemical Society
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Ian J. Barker, Luis Petersen and Peter J. Reilly. "Mechanism of Xylobiose Hydrolysis by GH43 β-Xylosidase" The Journal of Physical Chemistry B Vol. 114 Iss. 46 (2010) p. 15389 - 15393
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