In silico investigation of endoglucanase produced by Bacillus inaquosorum KCTC 13429 for valorisation of lignocellulosic biomass

Endoglucanases (EGs) have a crucial catalytic role in the bioconversion of lignocellulosic biomass that leads to the production of various value-added products including biofuels, lactic acid, succinic acid, furan resins, vanillin, catechol, and adipic acid. However, high cost and low titer of endoglucanases are major limiting factors which affect the scale-up of lignocellulosic biomass valorization. There still exists potential in bioprospecting to identify novel strain for high production of endoglucanase. The cumbersome process of experimental identification can be moderated with in silico approach. Therefore, in this study, a strain of Bacillus inaquosorum KCTC 13429 has been screened using computational techniques which can be a potential source of high EG titer. An in-depth analysis of EG from this strain was carried out to get an insight into its structural dynamics and reaction mechanism. On the basis of phylogenetic tree analysis, it was found that the EG from B. inaquosorum KCTC 13429 belongs to glycoside hydrolase family 5 (GH5) subfamily 2. The predicted 3-D structure was validated using Ramachandran's plot which showed that 85.9% and 13.7% amino acid residues were present in the favored and additionally allowed regions respectively, suggesting that the shown predicted structure is highly reliable. As a member of the GH5 family, the predicted structure of the B. inaquosorum KCTC 13429 also had (beta/alpha)(8) folds which form the barrel-shaped structure. Active site prediction was carried out using multiple sequence alignment (MSA) and structural comparison studies. Molecular docking with three substrates showed that cellotetraose binding at the predicted active site had highest negative binding energy as - 7.5 kcal/mol. It was found that 13 residues at the predicted active site were involved in the binding with the substrate. Furthermore, based on docking results, molecular dynamic simulation of EG-cellotetraose complex was performed which confirmed that E169 acts as a proton donor and E257 acts as a nucleophile. It was discovered that EG from B. inaquosorum KCTC 13429 follows the double displacement mechanism which proceeds by the retention of anomeric carbon. This is the first report of in silico evaluation on endoglucanases from that B. inaquosorum KCTC 13429. The study indicated that B. inaquosorum KCTC 13429 can be developed as a commercial high EG yielding strain for degradation of cellulose-rich biomass. However, further experimental studies are required to confirm its applicability and potential utilization in biotechnology industries.

Automated summary

Endoglucanases (EGs) play a crucial role in the bioconversion of lignocellulosic biomass, but high cost and low titer are major limiting factors. Computational techniques were used to identify a potential high EG-producing strain, Bacillus inaquosorum KCTC 13429. Structural analysis revealed that the EG from this strain belongs to glycoside hydrolase family 5 (GH5) subfamily 2, with a predicted reliable 3-D structure and active site analysis showing promising potential for cellulose degradation.