Homology modeling and molecular docking of xylitol dehydrogenase from Aspergillus Oryzae

Abstract:

Abstract:［Objective］We investigated the structure model and function of xylitol dehydrogenase from Aspergillus oryzae．［Methods］ Xylitol dehydrogenase (XDH) gene from Aspergillus oryzae was cloned and sequenced．We constructed four tertiary structure models of XDH by homology modeling with Swiss-MODEL and Modeller and obtained the best quality model by evaluation of PROCHECK and Prosa2003. The dockings of NAD+，Zn2+ and xylitol with XDH were performed by Molsoft program． ［Results］ Structure analysis suggested that XDH was a member of medium-chain dehydrogenase/reductase (MDR) family．This was supported by the presence of the zinc-containing alcohol dehydrogenase signature and a typical alcohol dehydrogenase Rossmann fold pattern composed by NAD + binding domain present in MDR superfamily．The molecular docking indicated that amino acid residues Asp206，Arg211，Ser255，Ser301 and Arg303 in XDH binding domain had hydrogen bonding with NAD + ，His72 and Glu73 in catalytic domain had hydrogen bonding with Zn2 + ，Ile46，Ile349，Lys350 and Thr351 in catalytic domain had hydrogen bonding with xylitol． ［Conclusion］ These key amino acid residues might play a vital role in the XDH catalytic reaction and can instruct the further directed modification of XDH．