title: Insights from modeling the 3D structure of NAD(P)H-dependent D-xylose reductase of Pichia stipitis and its binding interactions with NAD and NADP.
abstract: NAD(P)H-dependent d-xylose reductase is a homodimeric oxidoreductase that belongs to the aldo-keto reductase superfamily. The enzyme has the special function to catalyze the first step in the assimilation of xylose into yeast metabolic pathways. Performing this function via reducing the open chain xylose to xylitol, the xylose reductase of Pichia stipitis is one of the most important enzymes that can be used to construct recombinant Saccharomyces cerevisiae strain for utilizing xylose and producing alcohol. To investigate into the interaction mechanism of the enzyme with its ligand NAD and NADP, the 3D structure was developed for the NAD(P)H-dependent d-xylose reductase from P. stipitis. With the 3D structure, the molecular docking operations were conducted to find the most stable bindings of the enzyme with NAD and NADP, respectively. Based on these results, the binding pockets of the enzyme for NAD and NADP have been explicitly defined. It has been found that the residues in forming the binding pockets for both NAD and NADP are almost the same and mainly hydrophilic. These findings may be used to guide mutagenesis studies, providing useful clues to modify the enzyme to improve the utilization of xylose for producing alcohol. Also, because human aldose reductases have the function to reduce the open chain form of glucose to sorbitol, a process physiologically significant for diabetic patients at the time that their blood glucose levels are elevated, the information gained through this study may also stimulate the development of new strategies for therapeutic treatment of diabetes.
authors.affiliation: Bioinformatics Center, Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Graduate School of the Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
authors.forename: Jing-Fang
authors.initials: JF
authors.lastname: Wang
authors.forename: Dong-Qing
authors.initials: DQ
authors.lastname: Wei
authors.forename: Ying
authors.initials: Y
authors.lastname: Lin
authors.forename: Yong-Hua
authors.initials: YH
authors.lastname: Wang
authors.forename: Hong-Li
authors.initials: HL
authors.lastname: Du
authors.forename: Yi-Xve
authors.initials: YX
authors.lastname: Li
authors.forename: Kuo-Chen
authors.initials: KC
authors.lastname: Chou
mesh_terms: D000438:Alcohols; D000449:Aldehyde Reductase / Q000737:chemistry*; D000595:Amino Acid Sequence; D006860:Hydrogen Bonding; D008024:Ligands; D008958:Models, Molecular; D008968:Molecular Conformation; D008969:Molecular Sequence Data; D009243:NAD / Q000737:chemistry*; D009249:NADP / Q000737:chemistry*; D010843:Pichia / Q000201:enzymology*; D011485:Protein Binding; D011522:Protons; D017386:Sequence Homology, Amino Acid
chemical_list: D000438:Alcohols; D008024:Ligands; D011522:Protons; D009243:NAD; D009249:NADP; D000449:Aldehyde Reductase