Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, SK-84551, Bratislava, Slovakia.
Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, SK-84551, Bratislava, Slovakia; Department of Biology, Faculty of Natural Sciences, University of SS. Cyril and Methodius, SK-91701, Trnava, Slovakia.
Carbohydr Res. 2020 Aug;494:108082. doi: 10.1016/j.carres.2020.108082. Epub 2020 Jun 23.
The glycoside hydrolase (GH) family 126 was established based on the X-ray structure determination of the amylolytic enzyme CPF_2247 from Clostridium perfringens genome. Its original identification as a putative carbohydrate-active enzyme was based on its low, yet significant sequence identity to members of the family GH8, which are inverting endo-β-1,4-glucanases. As the family GH8 forms the clan GH-M with GH48, the CPF_2247 protein also exhibits similarities with members of the family GH48. The original screening of the CPF_2247 on carbohydrate substrates demonstrated its activity on glycogen and amylose, thus classifying this protein as an "α-amylase". It should be pointed out, however, there are apparent inconsistencies concerning the exact enzyme specificity of the "amylase" CPF_2247, since it exhibits both the endo- and exo-fashion of action. The family GH126 currently counts ~1000 amino acid sequences solely from Bacteria; all belonging to the phylum Firmicutes. The present study delivers the first detailed bioinformatics study of 117 selected amino acid sequences from the family GH126, featuring the insightful sequence-structure comparison with the aim to define seven conserved sequence regions and elucidate the evolutionary relationships within the family. In addition, a comparative structural analysis of the GH126 members with representatives of other GH families adopting the same (α/α)-barrel catalytic domain fold indicates the possible sharing a catalytic residue between the families GH126 and GH76.
糖苷水解酶（GH）家族 126 是基于梭菌内切葡聚糖酶 CPF_2247 的 X 射线结构测定而建立的。最初将其鉴定为潜在的碳水化合物活性酶是基于其与家族 GH8 的成员（反转内-β-1,4-葡聚糖酶）具有低但显著的序列同一性。由于家族 GH8 与 GH48 形成 GH-M 族，CPF_2247 蛋白也与家族 GH48 的成员具有相似性。最初对 CPF_2247 在碳水化合物底物上的筛选表明其对糖原和直链淀粉具有活性，因此将该蛋白归类为“α-淀粉酶”。然而，应该指出的是，关于“淀粉酶”CPF_2247 的确切酶特异性存在明显的不一致，因为它表现出内切和外切作用方式。家族 GH126 目前仅从细菌中计数了约 1000 个氨基酸序列；全部属于厚壁菌门。本研究首次对家族 GH126 的 117 个选定氨基酸序列进行了详细的生物信息学研究，通过深入的序列-结构比较，旨在定义七个保守序列区域，并阐明家族内的进化关系。此外，对采用相同（α/α）-桶催化结构域折叠的 GH126 成员与其他 GH 家族代表成员的结构比较分析表明，GH126 家族和 GH76 家族之间可能存在催化残基的共享。
