Unveiling the calcium role on GH43 beta-xylosidases / alpha-L-arabinofuranosidases catalysis by QM/MM molecular dynamics methods

Abstract

Glycoside hydrolases from family 43 (GH43) act on the degradation of key polysaccharides that constitute the hemicellulose such as xylan and arabinans. However, despite this family having a strong correlation with plant cell wall deconstruction and being ubiquitous in plant biomass maceration specialized organisms, it is still poorly explored. GH43 is a very polyspecific family, divided into 37 subfamilies and there are many mechanistic details that remain unknown, such as the role of the calcium ion and how it influences the catalysis in some GH43 members. In Xanthomonas citri pv citri (Xac), the causative agent of citrus canker, it was identified multiple GH43 genes suggesting the existence of functional divergence and distinct biological roles. During Post-Doctorate to which this project is linked, we solved different crystal structures of Xac GH43 enzymes and one of them is strongly influenced by a calcium ion. In order to access the mechanistic basis of the importance of metal binding in enzymes, computational methods have shown to be a valuable tool, specially using the quantum mechanical/molecular mechanics (QM/MM) approach. This state-of-art methodology has the ability to describe and predict chemical processes in complex environments such as catalytic processes in enzyme active sites. In this project, our aim is to use such methods to understand the role the calcium ion and the second interaction shell in GH43 catalysis. It is important to highlight the successful application of QM/MM simulations in order to unveil mechanistic details of carbohydrate-active enzymes (CAZymes) by Prof. Carme Rovira group, who has published high impact papers in collaboration with other renowned researchers, being a global reference in this field. Therefore, this BEPE Fellowship will allow the gain of knowledge in a valuable tool for studying glycoside hydrolases and will contribute for both the Post-Doctorate development and the Thematic Project to which this Fellowship request is linked.