title: Characterization of temperature dependent and substrate-binding cleft movements in Bacillus circulans family 11 xylanase: a molecular dynamics investigation.
abstract: BACKGROUND
  Xylanases (EC 3.2.1.8) hydrolyze xylan, one of the most abundant plant polysaccharides found in nature, and have many potential applications in biotechnology.
  
  
  METHODS
  Molecular dynamics simulations were used to investigate the effects of temperature between 298 to 338 K and xylobiose binding on residues located in the substrate-binding cleft of the family 11 xylanase from Bacillus circulans (BcX).
  
  
  RESULTS
  In the absence of xylobiose the BcX exhibits temperature dependent movement of the thumb region which adopts an open conformation exposing the active site at the optimum catalytic temperature (328 K). In the presence of substrate, the thumb region restricts access to the active site at all temperatures, and this conformation is maintained by substrate/protein hydrogen bonds involving active site residues, including hydrogen bonds between Tyr69 and the 2' hydroxyl group of the substrate. Substrate access to the active site is regulated by temperature dependent motions that are restricted to the thumb region, and the BcX/substrate complex is stabilized by extensive intermolecular hydrogen bonding with residues in the active site.
  
  
  CONCLUSIONS
  These results call for a revision of both the "hinge-bending" model for the activity of group 11 xylanases, and the role of Tyr69 in the catalytic mechanism.
authors.affiliation: Departamento de Química, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto--Universidade de São Paulo Ribeirão Preto, SP, Brazil. davisv@usp.br
authors.forename: Davi Serradella
authors.initials: DS
authors.lastname: Vieira
authors.forename: Léo
authors.initials: L
authors.lastname: Degrève
authors.forename: Richard John
authors.initials: RJ
authors.lastname: Ward
mesh_terms: D001407:Bacillus / Q000201:enzymology*; D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism; D001665:Binding Sites; D002384:Catalysis; D003198:Computer Simulation; D030562:Databases, Protein; D043364:Endo-1,4-beta Xylanases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D007700:Kinetics; D008958:Models, Molecular; D009154:Mutation; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D013379:Substrate Specificity; D013696:Temperature
chemical_list: D001426:Bacterial Proteins; D043364:Endo-1,4-beta Xylanases