Molecular dynamics–based structural insights of the first putative endoglucanase, Ps GH5A of glycoside hydrolase family 5 from Pseudopedobacter saltans

Context The putative endoglucanase, Ps GH5A, from Pseudopedobacter saltans of family GH5 contains a catalytic module, Ps GH5 (β/α) 8 -TIM barrel), at N-terminal followed by a family 6 carbohydrate-binding module (CBM6, β-sandwich). Superposition of Ps GH5A with PDB homologs revealed Glu220 and Glu318 as evolutionarily conserved and catalytic residues performing the hydrolysis through retaining-type mechanism, a canonical property of GH5 family. Ps GH5A showed higher affinity for longer cellooligosaccharides, as long as cellodecaose with binding free energy (∆ G ) of − 13.72 kcal/mol upon the molecular docking, thereby indicating the endo-mode of hydrolysis. The radius of gyration, Rg (2.7 nm), and solvent accessible surface area, SASA (229.6 nm 2 ), of Ps GH5A-Cellotetraose complex were determined by MD simulation which was lower than that of Ps GH5A (Rg, 2.8 nm, SASA, 267 nm 2 ) demonstrating the compactness and affinity of Ps GH5A with the cellulosic ligands. Cellulose compatibility of Ps GH5A was further confirmed by MMPBSA and per-residue decomposition analysis, where notable ∆ G of − 54.38 kcal/mol for Ps GH5A-Cellotetraose complex was observed. Thus, Ps GH5A could be potentially an efficient endoglucanase as it accommodated larger cellooligosaccharides at its active-site. Ps GH5A is the first putative endoglucanase studied here from P. saltans which could be genome-mined for lignocellulosic biomass saccharification in the renewable energy sector. Methods The 3-D structure of Ps GH5A generated by AlphaFold2, RaptorX, SwissModel, Phyre2 and Robetta tool; YASARA was used for energy minimization of built models. UCLA SAVES-v6 was used for quality assessment of models. Molecular Docking was performed using SWISS-DOCK server and Chimera software. Molecular Dynamics simulations and MMPBSA analysis of Ps GH5A and Ps GH5A-Cellotetraose complex were performed on GROMACS 2019.6. Graphical abstract