Vieira Davi Serradella, Degrève Léo, Ward Richard John
Departamento de Química, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto--Universidade de São Paulo Ribeirão Preto, SP, Brazil.
Biochim Biophys Acta. 2009 Oct;1790(10):1301-6. doi: 10.1016/j.bbagen.2009.04.017. Epub 2009 May 4.
Xylanases (EC 3.2.1.8) hydrolyze xylan, one of the most abundant plant polysaccharides found in nature, and have many potential applications in biotechnology.
Molecular dynamics simulations were used to investigate the effects of temperature between 298 to 338 K and xylobiose binding on residues located in the substrate-binding cleft of the family 11 xylanase from Bacillus circulans (BcX).
In the absence of xylobiose the BcX exhibits temperature dependent movement of the thumb region which adopts an open conformation exposing the active site at the optimum catalytic temperature (328 K). In the presence of substrate, the thumb region restricts access to the active site at all temperatures, and this conformation is maintained by substrate/protein hydrogen bonds involving active site residues, including hydrogen bonds between Tyr69 and the 2' hydroxyl group of the substrate. Substrate access to the active site is regulated by temperature dependent motions that are restricted to the thumb region, and the BcX/substrate complex is stabilized by extensive intermolecular hydrogen bonding with residues in the active site.
These results call for a revision of both the "hinge-bending" model for the activity of group 11 xylanases, and the role of Tyr69 in the catalytic mechanism.
木聚糖酶（EC 3.2.1.8）可水解木聚糖，木聚糖是自然界中含量最为丰富的植物多糖之一，在生物技术领域具有诸多潜在应用。
运用分子动力学模拟研究了298至338 K温度范围以及木二糖结合对来自环状芽孢杆菌的11家族木聚糖酶（BcX）底物结合裂隙中残基的影响。
在不存在木二糖的情况下，BcX的拇指区域呈现出温度依赖性运动，在最佳催化温度（328 K）时采用开放构象，暴露活性位点。在有底物存在时，拇指区域在所有温度下都会限制对活性位点的 access，并且这种构象通过涉及活性位点残基的底物/蛋白质氢键得以维持，包括Tyr69与底物2'羟基之间的氢键。底物对活性位点的 access 受限于仅在拇指区域发生的温度依赖性运动的调节，并且BcX/底物复合物通过与活性位点残基广泛的分子间氢键而得以稳定。
这些结果要求对11家族木聚糖酶活性的“铰链弯曲”模型以及Tyr69在催化机制中的作用进行修订。
