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

The family 30 glycoside hydrolase (RfGH30) from Ruminococcus flavefaciens expressing xylanase activ-ity was homology modeled. The structure revealed a (,B/a)8 TIM barrel topology along with an asso-ciated 'side ,B-structure'. Secondary structure analysis by circular dichroism displayed 28.09% a-helices and 21.02% ,B-strands, which corroborated with the prediction results. Multiple Sequence Alignment and structure superposition of RfGH30 with its homologue indicate that Glu200 and Glu302 are the cat-alytic residues displaying a retaining-type of catalysis. Molecular Dynamics (MD) simulation of RfGH30 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 RfGH30-xylobiose confirmed the structural specificity of catalytic residues and its increased stability in presence of ligand. Small angle X-ray scattering (SAXS) analysis of RfGH30 confirmed its monodispersed, fully folded and elon-gated structure in solution form. Dummy atom model revealed monomeric form of RfGH30 at 2.8 mg/ml, while at 4 mg/ml as dimer. Dynamic light scattering analysis of RfGH30 showed monodispersity and in-crease in hydrodynamic radius (Rh) from 2.0 to 4.0 mg/mL, displaying possible dimerization of RfGH30 at 4.0 mg/mL as corroborated by SAXS analysis. The lowered zeta potential of RfGH30 at 4 mg/mL also indicated the formation of a dimer. (c) 2022 Elsevier B.V. All rights reserved.

Automated summary

This study investigated the structure and function of family 30 glycoside hydrolase from Ruminococcus flavefaciens. The results revealed the catalytic residues and ligand binding characteristics of the enzyme. Experimental techniques were used to validate the structural features and stability of the enzyme, providing various conformational information in solution.