Dey Protyusha, Bairagya Hridoy R, Roy Amit
Department of Biotechnology, Visva-Bharati University, Santiniketan, West Bengal 731 235, India.
J Biosci. 2018 Jun;43(2):339-349.
Fungal endo-1,4-beta-xylanases (EC3.2.1.8), because of their widespread industrial applications have become one of the most researched industrial enzymes in recent times. Despite its significance, the role of conserved water molecules in the catalytic activities and structural stability of these enzymes from the fungi have not been studied to a great extent. Our computational structural bioinformatics and MD simulation studies have identified the existence of seven invariant water molecules (IW1- IW7) and reveals the stereo-chemical and electronic consequences of those conserved water molecules in G-xylanase enzyme from eight different fungi. The buried water molecules IW1 and IW2 may have decisive roles in catalysis and may also be associated with ligand binding process of the enzyme, whereas IW3, IW4, IW5, IW6 and IW7 may be involved in stabilizing the important (H144/R145) residues through H-bonds. Possibly they are also involved in the stabilization of secondary structures and anchor to maintain its stereo-chemical architecture. Moreover, a distorted 'W' shaped signature geometry that is observed at the surface of the enzyme can be used to identify the hydrophilic centers in the electron density map of other unknown members of the family G xylanases. The results from this computational investigation could be of interest to a large number of researchers working with the xylanases.
真菌内切-1,4-β-木聚糖酶（EC3.2.1.8）因其广泛的工业应用，已成为近年来研究最多的工业酶之一。尽管其具有重要意义，但真菌来源的这些酶中保守水分子在催化活性和结构稳定性方面的作用尚未得到深入研究。我们的计算结构生物信息学和分子动力学模拟研究已确定存在七个不变水分子（IW1 - IW7），并揭示了来自八种不同真菌的G-木聚糖酶中这些保守水分子的立体化学和电子效应。埋藏的水分子IW1和IW2可能在催化中起决定性作用，也可能与酶的配体结合过程有关，而IW3、IW4、IW5、IW6和IW7可能通过氢键参与稳定重要的（H144/R145）残基。它们可能还参与二级结构的稳定并起到锚定作用以维持其立体化学结构。此外，在酶表面观察到的扭曲的“W”形特征几何结构可用于在G族木聚糖酶其他未知成员的电子密度图中识别亲水性中心。这项计算研究的结果可能会引起大量研究木聚糖酶的研究人员的兴趣。
