Crystal structure of glycoside hydrolase family 127 β-L-arabinofuranosidase from Bifidobacterium longum
Crystal structure of glycoside hydrolase family 127 β-L-arabinofuranosidase from Bifidobacterium longum
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DOI：
10.1016/j.bbrc.2014.03.096
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发表时间：
2014-04-25
影响因子：
3.1
通讯作者：
Fushinobu, Shinya
中科院分区：
文献类型：
--
作者：
Ito, Tasuku;Saikawa, Kyo;Fushinobu, Shinya
尽管β-L-阿拉伯呋喃低聚糖在植物细胞中广泛分布，但作用于β-连接的阿拉伯呋喃糖苷的酶直到最近才为人所知。最近，在长双歧杆菌中新发现的羟脯氨酸连接的β-L-阿拉伯低聚糖降解体系中发现了糖苷水解酶家族中的一个β-L-阿拉伯尿苷酶(HypBA1)。在这里，我们报道了无配体和β-L-阿拉伯呋喃糖络合物形式的HypBA1的晶体结构。HypBA1的结构由一个催化桶结构域和两个额外的β-三明治结构域组成，其中一个β-三明治结构域参与二聚体的形成。有趣的是，在活性部位有一个前所未有的与锌离子结合的基序，与谷氨酸和三个半胱氨酸配位。谷氨酸残基远离β-L-阿拉伯呋喃葡萄糖配体的无规碳，但有一个半胱氨酸残基适合于糖苷键断裂的亲核攻击。活性中心周围的残基在GH127成员中高度保守。基于生化实验和量子力学计算，提出了以半胱氨酸为亲核剂的可能反应机理。(C)2014 Elsevier Inc.保留所有权利。
Enzymes acting on beta-linked arabinofuranosides have been unknown until recently, in spite of wide distribution of beta-L-arabinofuranosyl oligosaccharides in plant cells. Recently, a beta-L-arabinofuranosidase from the glycoside hydrolase family 127 (HypBA1) was discovered in the newly characterized degradation system of hydroxyproline-linked beta-L-arabinooligosaccharides in the bacterium Bifidobacterium longum. Here, we report the crystal structure of HypBA1 in the ligand-free and beta-L-arabinofuranose complex forms. The structure of HypBA1 consists of a catalytic barrel domain and two additional beta-sandwich domains, with one beta-sandwich domain involved in the formation of a dimer. Interestingly, there is an unprecedented metal-binding motif with Zn2+ coordinated by glutamate and three cysteines in the active site. The glutamate residue is located far from the anomeric carbon of the beta-L-arabinofuranose ligand, but one cysteine residue is appropriately located for nucleophilic attack for glycosidic bond cleavage. The residues around the active site are highly conserved among GH127 members. Based on biochemical experiments and quantum mechanical calculations, a possible reaction mechanism involving cysteine as the nucleophile is proposed. (C) 2014 Elsevier Inc. All rights reserved.