Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 84551, Bratislava, Slovakia.
Department of Biology, Faculty of Natural Sciences, University of SS. Cyril and Methodius, Nám. J. Herdu 2, 91701, Trnava, Slovakia.
Extremophiles. 2020 Mar;24(2):207-217. doi: 10.1007/s00792-019-01147-y. Epub 2019 Nov 16.
α-Amylase catalyzes the endohydrolysis of α-1,4-glucosidic linkages in starch and related α-glucans. In the CAZy database, most α-amylases have been classified into the family GH13 counting at present more than 80,000 sequences and ~ 30 different enzyme specificities. The family has already been divided into 42 subfamilies, but additional subfamilies are still emerging. The present bioinformatics study was undertaken in an effort to propose a novel GH13 subfamily around the experimentally characterized α-amylase from the halophilic archaeon Haloarcula hispanica, which until now has not been assigned to any GH13 subfamily. The in silico analysis resulted in collecting a convincing group of putative haloarchaeal α-amylase homologues sharing sequence similarities mainly in their conserved sequence regions (CSRs) and forming a cluster in the evolutionary tree, which is well separated from representatives of established GH13 subfamilies. One of the most exclusive sequence features of the novel GH13 subfamily is the tyrosine (Tyr79 in H. hispanica α-amylase numbering) succeeding the glycine at the beginning of the CSR-VI at the β2 strand of the catalytic TIM-barrel. Evolutionarily, the novel GH13 α-amylase subfamily was most closely related to two clusters of GH13 subfamilies with the specificity of α-amylase, i.e. subfamilies GH13_5, 6 and 7 as well as GH13_15, 24, 27 and 28.
α-淀粉酶催化淀粉和相关α-葡聚糖中α-1,4-糖苷键的内水解。在 CAZy 数据库中，大多数α-淀粉酶已被归类为 GH13 家族，目前已有超过 80,000 个序列和~30 种不同的酶特异性。该家族已经分为 42 个亚家族，但仍在不断出现新的亚家族。本生物信息学研究旨在提出一种新的 GH13 亚家族，该亚家族围绕嗜盐古菌 Haloarcula hispanica 中经实验表征的α-淀粉酶展开，该酶迄今尚未被分配到任何 GH13 亚家族。计算机分析结果收集了一组令人信服的假定嗜盐古菌α-淀粉酶同源物，它们主要在其保守序列区（CSRs）中具有序列相似性，并在进化树中形成一个聚类，与已建立的 GH13 亚家族的代表明显分开。新 GH13 亚家族的一个最独特的序列特征是 CSR-VI 的β2 链上甘氨酸之后紧接着酪氨酸（H. hispanica α-淀粉酶编号为 Tyr79）。从进化的角度来看，新型 GH13 α-淀粉酶亚家族与两个具有α-淀粉酶特异性的 GH13 亚家族簇最为密切相关，即亚家族 GH13_5、6 和 7 以及 GH13_15、24、27 和 28。
