Document Type

Article

Publication Date

10-25-2010

Journal or Book Title

The Journal of Physical Chemistry B

Volume

114

Issue

46

First Page

15389

Last Page

15393

DOI

10.1021/jp107886e

Abstract

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.

Comments

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.

Copyright Owner

American Chemical Society

Language

en

File Format

application/pdf

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