In silico analysis of xylanase in Bacillus coagulans ST-6

Abstract

Bacillus coagulans ST-6 is a thermophile isolated from a local hot spring in Malaysia. It expresses xylanase activity and has potential industrial applications. In silico structure prediction and modeling of a 210 amino acid sequence (XYNBC) translated from 872 bp Bacillus coagulans ST-6 xylanase gene was performed. The predicted molecular weight of the translated amino acid sequence is 20 kDa with theoretical isoelectric point value at 9.10 predicting that the xylanase belongs to the GH11 xylanase family. The protein is predicted to be hydrophilic with Grand average of hydropathicity (GRAVY) value of -0.6555 and possibly has better interaction with water. Predicted motif for XYNBC was revealed to be from Glycosyl hydrolases family 11(IPR00137) with signature motif 1 and 2 and only one known activity, xylanase. A three-dimensional (3D) model was constructed using PDB ID 2DCZ|A (http://www.rcsb. org) as the template as it has the highest similarity with XYNBC protein sequence. The 2DCZ|A xylanase sequence is from Bacillus Subtilis family-11 and is 185 amino acid long. The predicted 3D model consists of eleven beta sheets and one alpha helix. The stereochemical quality of protein structure revealed by Ramachandran Plot showed acceptable model with 99.4% residues fall in the most favored regions. Ten residues were predicted to be involved in active sites where residues Tyr7, Val15 and Asn16 are located at beta sheet while Asp118, Gly119, Thr120 are located at the loop. The catalytic residues E78 and E172 common to other G1H1 xylanases were also revealed.