In silico Structural Characterization and Molecular Docking Studies of First Glucuronoxylan-Xylanohydrolase (Xyn30A) from Family 30 Glycosyl Hydrolase (GH30) from Clostridium thermocellum

摘要

OXynGH30 is a carbohydrate active modular enzyme and component of cellulosome of Clostridium thermocellum. The full length CzXynGH30 contains an N-terminal catalytic module named as Xyn30A and a family 6 carbohydrate binding module (CBM6) at C-terminus. Xyn30A was modeled by computer prom-am Modeller9v8 taking crystal structure of XynC from B. subtilis as a template to generate the molecular model Model refinement was done using energy minimization by implementing steepest descent algorithm with GROMOS96 43al force field. Quality assessment by Ramachandran plot showed that 91 % amino acids lie in most favourable region and 9% in additional allowed region. Structural analysis depicted that Xyn30A has a (β/α)8 barrel fold. Additionally, it had a β-strand rich structure called side β-structure' attached with main catalytic core. Structural superimposition reflected that Glul36 act as a catalytic acid/base while Glu225 act as a catalytic nucleophile. Multiple sequence alignment showed that these catalytic residues are conserved within the family. The docking results showed that these residues display polar interaction with lin-ear and substituted xylo-oligosaccharides. The binding interaction of ligands depicted that aromatic amino acids Trp81, Tyrl39, Trpl43, Phel72, Hisl98, Tyr200, Tyr227, Trp264 and Tyr265 create binding site pocket around the active site. We report overall structural feature, conserved active site residues and enzyme-ligand docking of first glucuronoxylan-xylanohydrolase (Xyn30A) of family 30 glycosyl hydrolase (GH30) from Clostridium thermocellum.