Department of Chemical Engineering, Konkuk University, Seoul 143-701, Republic of Korea.
J Mol Graph Model. 2010 Jun;28(8):707-13. doi: 10.1016/j.jmgm.2010.01.004. Epub 2010 Jan 18.
L-arabinitol 4-dehydrogenase (LAD1; EC 1.1.1.12) is an enzyme in the L-arabinose catabolic pathway of fungi that catalyzes the conversion of L-arabinitol into L-xylulose. The primary objective of this work is to identify the catalytic and coenzyme binding domains of LAD1 from Hypocrea jecorina in order to provide better insight into the possible catalytic events in these domains. The 3D structure of NAD(+)-dependent LAD1 was developed based on the crystal structure of human sorbitol dehydrogenase as a template. A series of molecular mechanics and dynamics operations were performed to find the most stable binding interaction for the enzyme and its ligands. Using the verified model, a docking study was performed with the substrate L-arabinitol, Zn(2+) and NAD(+). This study found a catalytic Zn(2+) binding domain (Cys66, His91, Glu92 and Glu176) and a cofactor NAD(+) binding domain (Gly202, ILeu204, Gly205, Cys273, Arg229 and Val298) with strong hydrogen bonding contacts with the substrate and cofactor. The binding pockets of the enzyme for l-arabinitol, NAD(+), and Zn(2+) have been explicitly defined. The results from this study should guide future mutagenesis studies and provide useful clues for engineering enzymes to improve the utilization of polyols for rare sugar production.
L-阿拉伯糖醇 4-脱氢酶（LAD1；EC 1.1.1.12）是一种真菌 L-阿拉伯糖分解代谢途径中的酶，可催化 L-阿拉伯糖醇转化为 L-木酮糖。这项工作的主要目的是鉴定粗糙脉孢菌 LAD1 的催化和辅酶结合结构域，以便更好地了解这些结构域中可能的催化事件。以人山梨醇脱氢酶的晶体结构为模板，构建了 NAD(+)-依赖性 LAD1 的三维结构。进行了一系列分子力学和动力学操作，以找到酶及其配体最稳定的结合相互作用。使用验证后的模型，对底物 L-阿拉伯糖醇、Zn(2+)和 NAD(+)进行了对接研究。这项研究发现了一个催化 Zn(2+)结合结构域（Cys66、His91、Glu92 和 Glu176）和一个辅酶 NAD(+)结合结构域（Gly202、ILeu204、Gly205、Cys273、Arg229 和 Val298），它们与底物和辅酶具有很强的氢键相互作用。明确定义了酶对 L-阿拉伯糖醇、NAD(+)和 Zn(2+)的结合口袋。这项研究的结果应该为未来的突变研究提供指导，并为工程酶以提高多元醇在稀有糖生产中的利用提供有用的线索。
