Xylitol is a high-value low-calorie sweetener used as sugar substitute in food and pharmaceutical industry. Xylitol phosphate dehydrogenase (XPDH) catalyses the conversion of d-xylulose 5-phosphate (XU5P) and d-ribulose 5-phosphate (RU5P) to xylitol and ribitol respectively in the presence of nicotinamide adenine dinucleotide hydride (NADH). Although these enzymes have been shown to produce xylitol and ribitol, there is an incomplete understanding of the mechanism of the catalytic events of these reactions and the detailed mechanism has yet to be elucidated. The main goal of this work is to analyse the conformational changes of XPDH-bound ligands such as zinc^, NADH, XU5P, and RU5P to elucidate the key amino acids involved in the substrate binding. In silico modelling, comparative molecular dynamics simulations, interaction analysis and conformational study were carried out on three XPDH enzymes of the Medium-chain dehydrogenase (MDR) family in order to elucidate the atomistic details of conformational transition, especially on the open and closed state of XPDH. The analysis also revealed the possible mechanism of substrate specificity that are responsible in the catalyse hydride transfer are the residues His58 and Ser39 which would act as the proton donor for reduction of XU5P and RU5P respectively. The structural comparison and MD simulations displayed a significant difference in the conformational dynamics of the catalytic and coenzyme loops between Apo and XPDH-complexes and highlight the contribution of newly found triad residues. This study would assist future mutagenesis study and enzyme modification work to increase the catalysis efficiency of xylitol production in the industry.

木糖醇是一种高价值的低热量甜味剂，在食品和制药行业中用作糖的代用品。木糖醇磷酸脱氢酶（XPDH）催化的转化d -xylulose -5-磷酸（XU5P）和d -ribulose -5-磷酸（RU5P）为木糖醇和分别在烟酰胺腺嘌呤二核苷酸氢化物（NADH）存在核糖醇。尽管已显示这些酶可产生木糖醇和核糖醇，但对这些反应的催化作用机理尚不完全了解，其详细机理尚待阐明。这项工作的主要目的是分析XPDH结合的配体（如锌^， NADH，XU5P和RU5P）的构象变化，以阐明参与底物结合的关键氨基酸。电脑为了阐明构象转变的原子细节，特别是关于XPDH的开闭状态，对中链脱氢酶（MDR）家族的三种XPDH酶进行了建模，比较分子动力学模拟，相互作用分析和构象研究。分析还揭示了底物特异性的可能机制，其负责催化氢化物转移是残基His58和Ser39，它们分别充当质子供体，分别还原XU5P和RU5P。结构比较和MD模拟显示Apo和XPDH复合物之间的催化和辅酶环的构象动力学存在显着差异，并突出了新发现的三单元组残基的贡献。