Janeček Štefan, Majzlová Katarína, Svensson Birte, MacGregor E Ann
Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia.
Department of Biology, Faculty of Natural Sciences, University of SS. Cyril and Methodius, Trnava, Slovakia.
Proteins. 2017 Aug;85(8):1480-1492. doi: 10.1002/prot.25309. Epub 2017 May 11.
Within the CAZy database, there are 81 carbohydrate-binding module (CBM) families. A CBM represents a non-catalytic domain in a modular arrangement of glycoside hydrolases (GHs). The present in silico study has been focused on starch-binding domains from the family CBM41 that are usually part of pullulanases from the α-amylase family GH13. Currently there are more than 1,600 sequences classified in the family CBM41, almost exclusively from Bacteria, and so a study was undertaken in an effort to divide the members into relevant groups (subfamilies) and also to contribute to the evolutionary picture of family CBM41. The CBM41 members adopt a β-sandwich fold (∼100 residues) with one carbohydrate-binding site formed by the side-chains of three aromatic residues that interact with carbohydrate. The family CBM41 can be divided into two basic subdivisions, distinguished from each other by a characteristic sequence pattern or motif of the three essential aromatics as follows: (i) "W-W-∼10aa-W" (the so-called Streptococcus/Klebsiella-type); and (ii) "W-W-∼30aa-W" (Thermotoga-type). Based on our bioinformatics analysis it is clear that the first and second positions of the motif can be occupied by aromatic residues (Phe, Tyr, His) other than tryptophan, resulting in the existence of six different carbohydrate-binding CBM41 groups, that reflect mostly differences in taxonomy, but which should retain the ability to bind an α-glucan. In addition, three more groups have been proposed that, although lacking the crucial aromatic motif, could possibly employ other residues from remaining parts of their sequence for binding carbohydrate. Proteins 2017; 85:1480-1492. © 2017 Wiley Periodicals, Inc.
在CAZy数据库中，有81个碳水化合物结合模块（CBM）家族。CBM代表糖苷水解酶（GH）模块化排列中的一个非催化结构域。目前的计算机模拟研究聚焦于CBM41家族的淀粉结合结构域，这些结构域通常是α-淀粉酶家族GH13中支链淀粉酶的一部分。目前，CBM41家族中有1600多个序列被分类，几乎全部来自细菌，因此开展了一项研究，试图将这些成员划分为相关的组（亚家族），并为CBM41家族的进化图谱做出贡献。CBM41家族成员采用β-三明治折叠结构（约100个残基），有一个由三个与碳水化合物相互作用的芳香族残基的侧链形成的碳水化合物结合位点。CBM41家族可分为两个基本亚类，它们通过三个必需芳香族残基的特征序列模式或基序相互区分，如下：（i）“W-W-约10个氨基酸-W”（所谓的链球菌/克雷伯菌型）；（ii）“W-W-约30个氨基酸-W”（嗜热栖热菌型）。基于我们的生物信息学分析，很明显该基序的第一和第二个位置可以被色氨酸以外的芳香族残基（苯丙氨酸、酪氨酸、组氨酸）占据，从而产生六个不同的碳水化合物结合CBM41组，这些组主要反映了分类学上的差异，但应保留结合α-葡聚糖的能力。此外，还提出了另外三个组，尽管它们缺乏关键的芳香基序，但可能利用其序列其余部分的其他残基结合碳水化合物。《蛋白质》2017年；85：1480 - 1492。©2017威利期刊公司。
