Structural and functional insights into the glycoside hydrolase family 30 xylanase of the rumen bacterium Ruminococcus flavefaciens.

• Rf GH30 showed (β/α) 8 TIM barrel fold and an associated 'side-β structure'. • Circular dichroism displayed 28.09% α-helices and 21.02% β-strands in Rf GH30. • Molecular docking of Rf GH30 showed maximum binding affinity with xylobiose. • MD simulation of Rf GH30 xylobiose confirmed the structural specificity and stability. • Rf GH30 showed monomeric and monodispersed state at the lower concentration. The family 30 glycoside hydrolase (Rf GH30) from Ruminococcus flavefaciens expressing xylanase activity was homology modeled. The structure revealed a (β/α) 8 TIM barrel topology along with an associated 'side β-structure'. Secondary structure analysis by circular dichroism displayed 28.09% α-helices and 21.02% β-strands, which corroborated with the prediction results. Multiple Sequence Alignment and structure superposition of Rf GH30 with its homologue indicate that Glu200 and Glu302 are the catalytic residues displaying a retaining-type of catalysis. Molecular Dynamics (MD) simulation of Rf GH30 confirmed the structural compactness and steadiness of modeled structure. Molecular docking studies showed maximum binding affinity with xylobiose that was corroborated by the total binding Gibbs free energy of -160.5 kJ/mol calculated by g_mmpbsa tool. MD simulation of Rf GH30-xylobiose confirmed the structural specificity of catalytic residues and its increased stability in presence of ligand. Small angle X-ray scattering (SAXS) analysis of Rf GH30 confirmed its monodispersed, fully folded and elongated structure in solution form. Dummy atom model revealed monomeric form of Rf GH30 at 2.8 mg/ml, while at 4 mg/ml as dimer. Dynamic light scattering analysis of Rf GH30 showed monodispersity and increase in hydrodynamic radius (R h) from 2.0 to 4.0 mg/mL, displaying possible dimerization of Rf GH30 at 4.0 mg/mL as corroborated by SAXS analysis. The lowered zeta potential of Rf GH30 at 4 mg/mL also indicated the formation of a dimer. [Display omitted] [ABSTRACT FROM AUTHOR]