Acta Phys. -Chim. Sin. ›› 2015, Vol. 31 ›› Issue (6): 1169-1178.doi: 10.3866/PKU.WHXB201504151

• BIOPHYSICAL CHEMISTRY • Previous Articles     Next Articles

Molecular Dynamics Simulation of Active-Sites of Retaining and Inverting β-Xylosidases

ZHANG Jun-Wei1, ZHOU Jun-Gang1, Lü Hong1,2, HUANG Qiang1,2   

  1. 1 State Key Laboratory of Genetic Engineering, School of Life Sciences, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai 200433, P. R. China;
    2 Shanghai Collaborative Innovation Center for Biomanufacturing Technology, Shanghai 200237, P. R. China
  • Received:2015-02-16 Revised:2015-04-13 Published:2015-06-05
  • Contact: ZHOU Jun-Gang, HUANG Qiang;
  • Supported by:

    The project was supported by the Shanghai Natural Science Foundation, China (13ZR1402400) and National Natural Science Foundation of China (31200022).


Xylans are important as potential renewable energy sources. In recent years, there has therefore been interest in improving their degradation efficiencies. β-Xylosidases are key enzymes for xylan degradation; these enzymes are classified, based on their hydrolysis mechanisms, as retaining or inverting enzymes. Although much research has been devoted to understanding retaining and inverting mechanisms, little is known about their differences in solution. We used molecular dynamics (MD) simulations with explicit solvent representation to study the dynamic behaviors of the active-sites of four typical β-xylosidases by analyzing the distances between two catalytic amino acids and the pKa values of proton-donor amino acids. The results show that the distance between the catalytic amino acids with inverting enzymes is about 0.8-1.0 nm, which is greater than that for retaining enzymes, i.e., 0.5-0.6 nm. This is consistent with previous results based on the crystal structures of glycosidases. We found that the pKa of the retaining proton donors are modulated by interactions with neighboring amino acids, enabling switching between low and high values. Such a pKa switch is needed for the double-displacement mechanism of retaining enzymes. In contrast, inverting proton donors, modulated by interactions with neighboring glutamic acids, have only high pKa values. This may be important in proton capture from the solvent by donors, and may facilitate the single-displacement mechanism of inverting enzymes. This study provides new insights into the hydrolysis mechanisms of β-xylosidases, and will therefore be useful in improving the efficiency and applications of β-xylosidases.

Key words: β-Xylosidase, Catalytic mechanism, Molecular modelling, Proton donor, pKa value


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