Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, SK-84551 Bratislava, Slovakia; Department of Biology, Faculty of Natural Sciences, University of SS. Cyril and Methodius, Nám. J. Herdu 2, SK-91701 Trnava, Slovakia.
Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, SK-84551 Bratislava, Slovakia; Department of Biology, Faculty of Natural Sciences, University of SS. Cyril and Methodius, Nám. J. Herdu 2, SK-91701 Trnava, Slovakia.
Biotechnol Adv. 2019 Dec;37(8):107451. doi: 10.1016/j.biotechadv.2019.107451. Epub 2019 Sep 16.
The term "starch-binding domain" (SBD) has been applied to a domain within an amylolytic enzyme that gave the enzyme the ability to bind onto raw, i.e. thermally untreated, granular starch. An SBD is a special case of a carbohydrate-binding domain, which in general, is a structurally and functionally independent protein module exhibiting no enzymatic activity but possessing potential to target the catalytic domain to the carbohydrate substrate to accommodate it and process it at the active site. As so-called families, SBDs together with other carbohydrate-binding modules (CBMs) have become an integral part of the CAZy database (http://www.cazy.org/). The first two well-described SBDs, i.e. the C-terminal Aspergillus-type and the N-terminal Rhizopus-type have been assigned the families CBM20 and CBM21, respectively. Currently, among the 85 established CBM families in CAZy, fifteen can be considered as families having SBD functional characteristics: CBM20, 21, 25, 26, 34, 41, 45, 48, 53, 58, 68, 69, 74, 82 and 83. All known SBDs, with the exception of the extra long CBM74, were recognized as a module consisting of approximately 100 residues, adopting a β-sandwich fold and possessing at least one carbohydrate-binding site. The present review aims to deliver and describe: (i) the SBD identification in different amylolytic and related enzymes (e.g., CAZy GH families) as well as in other relevant enzymes and proteins (e.g., laforin, the β-subunit of AMPK, and others); (ii) information on the position in the polypeptide chain and the number of SBD copies and their CBM family affiliation (if appropriate); (iii) structure/function studies of SBDs with a special focus on solved tertiary structures, in particular, as complexes with α-glucan ligands; and (iv) the evolutionary relationships of SBDs in a tree common to all SBD CBM families (except for the extra long CBM74). Finally, some special cases and novel potential SBDs are also introduced.
术语“淀粉结合域”（SBD）已应用于一种淀粉酶中的一个结构域，该结构域使酶具有结合生淀粉（即未经热处理的颗粒状淀粉）的能力。SBD 是碳水化合物结合域的特殊情况，一般来说，碳水化合物结合域是一个结构和功能上独立的蛋白质模块，没有酶活性，但具有将催化结构域靶向碳水化合物底物的潜力，以容纳它并在活性位点对其进行加工。作为所谓的家族，SBD 与其他碳水化合物结合模块（CBM）一起已成为 CAZy 数据库（http://www.cazy.org/）的一个组成部分。前两个描述良好的 SBD，即曲霉型 C 端和根霉型 N 端 SBD，分别被分配到 CBM20 和 CBM21 家族。目前，在 CAZy 中 85 个已建立的 CBM 家族中，有 15 个可以被认为是具有 SBD 功能特征的家族：CBM20、21、25、26、34、41、45、48、53、58、68、69、74、82 和 83。除了超长的 CBM74 外，所有已知的 SBD 都被认为是由大约 100 个残基组成的模块，采用β-三明治折叠，并具有至少一个碳水化合物结合位点。本综述旨在提供和描述：（i）在不同的淀粉水解酶和相关酶（例如 CAZy GH 家族）以及其他相关酶和蛋白质（例如 laforin、AMPK 的β亚基等）中 SBD 的鉴定；（ii）关于在多肽链中的位置和 SBD 拷贝的数量及其 CBM 家族归属（如果适用）的信息；（iii）SBD 的结构/功能研究，特别关注已解决的三级结构，特别是与α-葡聚糖配体的复合物；以及（iv）SBD 在所有 SBD CBM 家族（超长的 CBM74 除外）共有的树中的进化关系。最后，还介绍了一些特殊情况和新的潜在 SBD。
