Homology modeling and molecular docking of xylitol dehydrogenase from Aspergillus Oryzae
- 化学化工－已发表论文 
【目的】研究米曲霉木糖醇脱氢酶基因的结构与功能。【方法】克隆测序来源于米曲霉的木糖醇脱氢酶(XdH)基因,利用SWISS-MOdEl和MOdEllEr对XdH进行三级结构模建,通过PrOCHECk和PrOSA2003对得到的4个目标模型进行评价,从中得到一个最佳模型。在同源建模的基础上,通过分子对接软件MOlSOfTICM-PrO,对辅因子进行对接,预测了XdH与nAd+、zn2+作用的相关残基。寻找底物木糖醇与XdH结合的可能活性口袋,用MOlSOfT模拟XdH与木糖醇的对接,预测了酶与底物作用的关键氨基酸残基。【结果】结构分析显示,米曲霉XdH含有醇脱氢酶家族锌指纹结构和典型醇脱氢酶rOSSMAnn折叠的辅酶结合域,属于MEdIuM-CHAIn脱氢酶(Mdr)家族。通过对接研究,预测了XdH与nAd+之间形成氢键的氨基酸有ASP206、Arg211、SEr255、SEr301和Arg303,这些氨基酸位于结合域,与zn2+形成氢键的氨基酸有HIS72和glu73,位于催化域,与天然底物木糖醇形成氢键的氨基酸有IlE46、IlE349、lyS350和THr351,位于催化域。【结论】所得信息对XdH分子定向改造、拓展米曲霉工业应用范围有重要意义。[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.