MODELLING AND LIGAND INTERACTION STUDIES OF ENDO-1,4-BETA-XYLANASE FROM BACILLUS SUBTILIS

Abstract

Xylanase is the name given to a class of enzymes which degrade the linear polysaccharide beta-1,4- xylan into xylose, thus breaking down hemicellulose, which is a major component of the cell wall of plants. The sequence of Xylanase from Bacillus subtilis was obtained from NCBI. The predicted domain was searched to find out the related protein structure to be used as a template by the Basic Local Alignment Search Tool (BLAST) program against Protein Databank (PDB). Sequence that showed maximum identity with high score and less e-value was aligned and used as a reference structure to build a 3D model for Xylanase. In order to understand the mechanisms of ligand binding and the interaction between the ligand and the Xylanase a three-dimensional (3D) model of the Xylanase is generated based on the crystal structure of the Template by using the Modeller. With the aid of the molecular mechanics and molecular dynamics methods, the final refined model is obtained and is further assessed by Profile-3D, which shows that the refined model is reliable. With this model, a flexible docking study is performed with the acetate ion as ligand. After the docking studies, important determined residues in binding are identified. The hydrogen bonds play an important role for the stability of the complex. These results may be helpful for further experimental investigations.