Structural characterization and molecular dynamics simulations studies of family-10 xylanase from Bacillus firmus K-1 complex with xylopentaose: a novel feature of the xylanase catalytic mechanism

Surapong Pinitglang, Pattraporn Jommuengbout, Krongsakda Phakthanakanok, Khanok Ratanakhanokchai, Khin Lay Kyu

Abstract


Xylanases hydrolyze the β-1,4-linked xylose backbone of xylans, the majorhemicellulosic components of plant cell walls. They are especially useful in paper industrybecause they decrease the demand for chlorine-based chemicals in the wood pulpdelignification process. In this study, 3D structure of Xyn10A, a family 10 xylanase fromBacillus firmus K-1 was generated by homology modeling using X-ray structure of xylanasefrom Bacillus sp. strain NG-27 as a template. The root mean square deviation (RMSD) ofbackbone atoms between the X-ray and homology modeled structures was 0.8 Å. Binding ofxylopentaose (X5) to the Xyn10A was investigated using molecular dynamics simulations viacomparison the total energy, RMSD of Cα atom and root mean square fluctuation (RMSF) offree and complex forms of Xyn10A. In the reactive Xyn10A-X5 conformation, in which thetwo catalytic sites, E149 and E255 are precisely positioned for the catalytic reaction, the -1sugar moiety of the X5 adopted a 1C4 chair conformation for the Xyn10A. According to theRMSF, 13 amino acid residues in active site of complex form showed more flexibility thanthose of free form. The result suggested that they may implicate in binding to X5 at subsites -3 to +2 of substrate-binding site through hydrogen bonding and stacking interactions.Furthermore, the RMSF of X5 revealed that the substrate binding site of Xyn10A was morespecific to three middle xylose moieties than two terminal xylose moieties. The role of sugarmoiety interaction with Xyn10A in catalytic mechanism is discussed.

Keywords: Bacillus firmus, 3D structure, family 10 xylanase, homology modeling, moleculardynamics simulations


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