Abstract

Cellulases are the enzymes with diverse range of industrial applications. Cellulases degrade cellulose into monomeric glucose units by hydrolysing β-1,4-glycosidic bonds. There are three components of cellulases: a) endoglucanase, b) exoglucanase and c) β-glucosidase which act synergistically in cellulose bioconversion. The cellulases are the third largest industrial enzymes with a great potential in bioethanol production. In this investigation, a β-glucosidase of a thermophilic fungus Myceliophthora thermophila (MtBgl3c) was analysed for its structural characterization using in silico approaches. The protein structure of MtBgl3c is unknown, therefore an attempt has been made to model 3D structure using Modeller 9.23 software. The MtBgl3c protein model generated was validated from Verify 3D and ERRAT scores of 89.37% and 71.25%, respectively derived from SAVES. Using RAMPAGE the Ramachandran plot was generated, which predicted the accuracy of the 3D model with 91.5% amino acid residues in the favored region. The ion binding and N-glycosylation sites were also predicted. The generated model was docked with cellobiose to predict the most favorable binding sites of MtBgl3c. The key amino acid residues involved in cellobiose bonding are Val88, Asp106, Asp287, Tyr255, Arg170, Glu514. The catalytic conserved amino residues of MtBgl3c were identified. The dock score of cellobiose with MtBgl3c is much lower (–6.46 kcal/mol) than that of glucose (–5.61 kcal/mol), suggesting its high affinity for cellobiose. The docking data of MtBgl3c with glucose illustrate its tolerance to glucose. The present study provides insight into structural characteristics of the MtBgl3c which can be further validated by experimental data.

• Highlights

• 3D structure of β-glucosidase (MtBgl3c) of Myceliophthora thermophila is being proposed based on computational analyses

• The amino acid residues Asp106, Asp287, Tyr255, Arg170 and Glu514 have been identified to play catalytically important role in substrate binding

• Docking and interaction of MtBgl3c with cellobiose and glucose has been confirmed

• Docking analysis of MtBgl3c with glucose suggested its glucose tolerance

• The data would be useful in engineering enzymes for attaining higher catalytic efficiency

Communicated by Ramaswamy H. Sarma

摘要

纤维素酶是具有广泛工业应用范围的酶。纤维素酶通过水解β-1,4-糖苷键将纤维素降解为单体葡萄糖单元。纤维素酶由三部分组成：a）内切葡聚糖酶，b）外切葡聚糖酶和c）β-葡萄糖苷酶，它们在纤维素生物转化中起协同作用。纤维素酶是第三大工业酶，在生物乙醇生产中具有巨大潜力。在这项研究中，使用计算机分析了嗜热真菌嗜热毁丝霉菌（MtBgl3c）的β-葡萄糖苷酶的结构特征方法。MtBgl3c的蛋白质结构未知，因此尝试使用Modeller 9.23软件对3D结构进行建模。生成的MtBgl3c蛋白模型通过分别来自SAVES的Verify 3D和ERRAT得分为89.37％和71.25％进行了验证。使用RAMPAGE生成Ramachandran图，该图预测了在偏爱区域中具有91.5％氨基酸残基的3D模型的准确性。还预测了离子结合和N-糖基化位点。生成的模型与纤维二糖对接，以预测MtBgl3c最有利的结合位点。纤维二糖键合中涉及的关键氨基酸残基是Val88，Asp106，Asp287，Tyr255，Arg170，Glu514。鉴定了MtBgl3c的催化保守氨基残基。纤维二糖与MtBgl3c的对接得分要低得多（–6。46 kcal / mol）比葡萄糖（–5.61 kcal / mol）高，表明其对纤维二糖的亲和力高。MtBgl3c与葡萄糖的对接数据说明了其对葡萄糖的耐受性。本研究提供了对MtBgl3c的结构特征的见解，可以通过实验数据进一步验证。

• 强调

• 基于计算分析，提出嗜热毁丝霉菌β-葡萄糖苷酶（MtBgl3c）的3D结构

• 已鉴定出氨基酸残基Asp106，Asp287，Tyr255，Arg170和Glu514在底物结合中起催化作用

• 已确认MtBgl3c与纤维二糖和葡萄糖的对接和相互作用

• 葡萄糖对MtBgl3c的对接分析表明其对葡萄糖的耐受性

• 该数据可用于工程酶以获得更高的催化效率

由Ramaswamy H.Sarma沟通