title: [In silico structural characterization and molecular docking studies of first glucuronoxylan-xylanohydrolase (Xyn30a) from family-30 glycosyl hydrolase (GH30) from Clostridium thermocellum].
abstract: CtXynGH30 is a carbohydrate active modular enzyme and component of cellulosome of Clostridium thermocellum. The full length CtXynGH30 contains an N-terminal catalytic module named as Xyn30A and a family 6 carbohydrate binding module (CBM6) at C-terminuis. Xyn30A was modeled by computer program 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 (beta/alpha)8 barrel fold. Ad- ditionally, it had a beta-strand rich structure called 'side beta-structure' attached with main catalytic core. Structural superimposition reflected that Glu136 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 linear and substituted xylo-oligosaccharides. The binding interaction of ligands depicted that aromatic amino acids Trp81, Tyr139, Trp143, Phe172, His198, Tyr200, Tyr227, Trp264 and Tyr265 create binding site pocket around the active site. We report overall structural feature, conserved active site residues and enzymeligand docking of first glucuronoxylan-xylanohydrolase (Xyn30A) of family 30 glycosyl hydrolase (GH30) from Clostridium thermocellum.
authors: Anil Kumar
authors: AK
authors: Verma
authors: Arun
authors: A
authors: Goyal
mesh_terms: D000595:Amino Acid Sequence; D001412:Bacillus subtilis / Q000737:chemistry / Q000201:enzymology; D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism; D020134:Catalytic Domain; D048013:Acetivibrio thermocellus / Q000737:chemistry* / Q000201:enzymology; D017124:Conserved Sequence; D062105:Molecular Docking Simulation; D008969:Molecular Sequence Data; D011485:Protein Binding; D017433:Protein Structure, Secondary; D016415:Sequence Alignment; D040681:Structural Homology, Protein; D013379:Substrate Specificity; D014990:Xylans / Q000737:chemistry* / Q000378:metabolism; D014995:Xylosidases / Q000737:chemistry* / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; D014990:Xylans; D014995:Xylosidases; C068045:glucuronoxylan xylanohydrolase