Takeda Kosei, Yoshida Hiromi, Izumori Ken, Kamitori Shigehiro
Life Science Research Center and Faculty of Medicine, Kagawa University, Miki-cho, Kita-gun, Kagawa 761-0793, Japan.
Biochim Biophys Acta. 2010 Jun;1804(6):1359-68. doi: 10.1016/j.bbapap.2010.01.018. Epub 2010 Feb 1.
d-Arabinose isomerase (d-AI), also known as l-fucose isomerase (l-FI), catalyzes the aldose-ketose isomerization of d-arabinose to d-ribulose, and l-fucose to l-fuculose. Bacillus pallidus (B. pallidus) d-AI can catalyze isomerization of d-altrose to d-psicose, as well as d-arabinose and l-fucose. Three X-ray structures of B. pallidus d-AI in complexes with 2-methyl-2,4-pentadiol, glycerol and an inhibitor, l-fucitol, were determined at resolutions of 1.77, 1.60 and 2.60 A, respectively. B. pallidus d-AI forms a homo-hexamer, and one subunit has three domains of almost equal size; two Rossmann fold domains and a mimic of the (beta/alpha) barrel fold domain. A catalytic metal ion (Mn(2+)) was found in the active site coordinated by Glu342, Asp366 and His532, and an additional metal ion was found at the channel for the passage of a substrate coordinated by Asp453. The X-ray structures basically supported the ene-diol mechanism for the aldose-ketose isomerization by B. pallidus d-AI, as well as Escherichia coli (E. coli) l-FI, in which Glu342 and Asp366 facing each other at the catalytic metal ion transfer a proton from C2 to C1 and O1 to O2, acting as acid/base catalysts, respectively. However, considering the ionized state of Asp366, the catalytic reaction also possibly occurs through the negatively charged ene-diolate intermediate stabilized by the catalytic metal ion. A structural comparison with E. colil-FI showed that B. pallidus d-AI possibly interconverts between "open" and "closed" forms, and that the additional metal ion found in B. pallidus d-AI may help to stabilize the channel region.
D-阿拉伯糖异构酶（d-AI），也被称为L-岩藻糖异构酶（l-FI），催化D-阿拉伯糖向D-核糖ulose以及L-岩藻糖向L-岩藻酮糖的醛糖-酮糖异构化反应。苍白芽孢杆菌（B. pallidus）的d-AI能够催化D-阿洛酮糖向D-阿洛酮糖的异构化反应，以及D-阿拉伯糖和L-岩藻糖的异构化反应。分别以1.77、1.60和2.60埃的分辨率测定了苍白芽孢杆菌d-AI与2-甲基-2,4-戊二醇、甘油和抑制剂L-岩藻糖醇形成的复合物的三种X射线结构。苍白芽孢杆菌d-AI形成同型六聚体，一个亚基有三个大小几乎相等的结构域；两个罗斯曼折叠结构域和一个模拟（β/α）桶状折叠结构域。在由Glu342、Asp366和His532配位的活性位点发现了一个催化金属离子（Mn(2+)），在由Asp453配位的底物通道处发现了另一个金属离子。X射线结构基本支持了苍白芽孢杆菌d-AI以及大肠杆菌（E. coli）l-FI进行醛糖-酮糖异构化反应的烯二醇机制，其中在催化金属离子处相对的Glu342和Asp366分别作为酸/碱催化剂，将质子从C2转移到C1以及从O1转移到O2。然而，考虑到Asp366的离子化状态，催化反应也可能通过由催化金属离子稳定的带负电荷的烯二醇盐中间体发生。与大肠杆菌l-FI的结构比较表明，苍白芽孢杆菌d-AI可能在“开放”和 “封闭” 形式之间相互转换，并且在苍白芽孢杆菌d-AI中发现的额外金属离子可能有助于稳定通道区域。
