Crystal structure of a family 54 α-L-arabinofuranosidase reveals a novel carbohydrate-binding module that can bind arabinose
Crystal structure of a family 54 α-L-arabinofuranosidase reveals a novel carbohydrate-binding module that can bind arabinose
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DOI：
10.1074/jbc.m405390200
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发表时间：
2004-10-22
影响因子：
4.8
通讯作者：
Fushinobu, S
中科院分区：
文献类型：
--
作者：
Miyanaga, A;Koseki, T;Fushinobu, S
作为糖苷水解酶家族54（GH54）酶的第一个已知结构，我们确定了白曲霉IFO 4308 α-L-阿拉伯呋喃糖苷酶（AkAbfB）的游离和阿拉伯糖复合物形式的晶体结构。AkAbfB包含两个结构域：催化结构域和阿拉伯糖结合结构域（ABD）。催化结构域具有类似于clan-B糖苷水解酶的β-夹心折叠。ABD具有与碳水化合物结合模块（CBM）家族13相似的β-三叶折叠。然而，ABD显示了许多不同于CBM家族13的特征，这表明它可以被归类为一个新的CBM家族。在阿拉伯糖复合物结构中，三个阿拉伯呋喃糖分子之一通过许多相互作用与催化结构域结合。有趣的是，在两个相邻的半胱氨酸残基之间形成的二硫键识别活性位点中的阿拉伯呋喃糖分子。根据该阿拉伯呋喃糖的位置和突变研究结果，确定亲核体和酸/碱残基分别为Glu（221）和Asp（297）。另外两个阿拉伯呋喃糖分子与ABD结合。在ABD处结合的两个阿拉伯呋喃糖分子的O-1原子都指向溶剂，表明这些位点都可以容纳与装饰的阿拉伯聚糖连接的阿拉伯呋喃糖侧链部分。
As the first known structures of a glycoside hydrolase family 54 (GH54) enzyme, we determined the crystal structures of free and arabinose-complex forms of Aspergillus kawachii IFO4308 alpha-L-arabinofuranosidase (AkAbfB). AkAbfB comprises two domains: a catalytic domain and an arabinose-binding domain (ABD). The catalytic domain has a beta-sandwich fold similar to those of clan-B glycoside hydrolases. ABD has a beta-trefoil fold similar to that of carbohydrate-binding module (CBM) family 13. However, ABD shows a number of characteristics distinctive from those of CBM family 13, suggesting that it could be classified into a new CBM family. In the arabinose-complex structure, one of three arabinofuranose molecules is bound to the catalytic domain through many interactions. Interestingly, a disulfide bond formed between two adjacent cysteine residues recognized the arabinofuranose molecule in the active site. From the location of this arabinofuranose and the results of a mutational study, the nucleophile and acid/ base residues were determined to be Glu(221) and Asp(297), respectively. The other two arabinofuranose molecules are bound to ABD. The O-1 atoms of the two arabinofuranose molecules bound at ABD are both pointed toward the solvent, indicating that these sites can both accommodate an arabinofuranose side-chain moiety linked to decorated arabinoxylans.