Kerényiová Lenka, Janeček Štefan
Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, 84551 Bratislava, Slovakia.
Department of Biology, Faculty of Natural Sciences, University of SS. Cyril and Methodius, 91701 Trnava, Slovakia.
3 Biotech. 2020 Oct;10(10):420. doi: 10.1007/s13205-020-02415-x. Epub 2020 Sep 8.
The family GH126 is a family of glycoside hydrolases established in 2011. Officially, in the CAZy database, it counts ~ 1000 sequences originating solely from bacterial phylum Firmicutes. Two members, the proteins CPF_2247 from and PssZ from have been characterized as a probable α-amylase and an exopolysaccharide-specific glycosidase, respectively; their three-dimensional structures being also solved as possessing catalytic (α/α)-barrel fold. Previously, based on a detailed in silico analysis, the seven conserved sequence regions (CSRs) were identified for the family along with elucidating basic evolutionary relationships within the family members. The present study represents a continuation study focusing on two particular aims: (1) to find out whether the taxonomic coverage of the family GH126 might be extended outside the Firmicutes and, if positive, to deliver those out-of-Firmicutes proteins with putting them into the context of the family; and (2) to identify the family members containing the N- and/or C-terminal extensions of their polypeptide chain, additional to the catalytic (α/α)-barrel domain, and perform the bioinformatics characterization of the extra domains. The main results could be summarized as follows: (1) 17 bacterial proteins caught by BLAST searches outside Firmicutes (especially from phyla Proteobacteria, Actinobacteria and Bacteroidetes) have been found and convincingly suggested as new family GH126 members; and (2) a thioredoxin-like fold and various leucine-rich repeat motifs identified by Phyre2 structure homology modelling have been recognized as extra domains occurring most frequently in the N-terminal extensions of family GH126 members possessing a modular organization.
GH126家族是2011年建立的糖苷水解酶家族。在CAZy数据库中,正式记录了约1000个仅来自厚壁菌门细菌的序列。该家族的两个成员,来自[具体来源1]的CPF_2247蛋白和来自[具体来源2]的PssZ蛋白,分别被鉴定为可能的α-淀粉酶和胞外多糖特异性糖苷酶;它们的三维结构也已解析,具有催化性的(α/α)桶状折叠。此前,基于详细的计算机分析,确定了该家族的七个保守序列区域(CSR),并阐明了家族成员之间的基本进化关系。本研究是一项后续研究,重点关注两个特定目标:(1)确定GH126家族的分类学覆盖范围是否可以扩展到厚壁菌门之外,如果是,则将这些非厚壁菌门的蛋白质纳入该家族的背景中;(2)识别除催化性(α/α)桶状结构域外,其多肽链含有N端和/或C端延伸的家族成员,并对这些额外结构域进行生物信息学表征。主要结果可总结如下:(1)通过BLAST搜索在厚壁菌门之外(特别是来自变形菌门、放线菌门和拟杆菌门)发现了17种细菌蛋白,并令人信服地将其建议为新的GH126家族成员;(2)通过Phyre2结构同源建模鉴定的硫氧还蛋白样折叠和各种富含亮氨酸的重复基序,被认为是在具有模块化组织的GH126家族成员的N端延伸中最常出现的额外结构域。