Extension of the taxonomic coverage of the family GH126 outside Firmicutes and in silico characterization of its non-cat
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ORIGINAL ARTICLE
Extension of the taxonomic coverage of the family GH126 outside Firmicutes and in silico characterization of its non‑catalytic terminal domains Lenka Kerényiová1 · Štefan Janeček1,2 Received: 20 July 2020 / Accepted: 27 August 2020 © The Author(s) 2020
Abstract 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 Clostridium perfringens and PssZ from Listeria monocytogenes have been characterized as a probable α-amylase and an exopolysaccharidespecific glycosidase, respectively; their three-dimensional structures being also solved as possessing catalytic (α/α)6-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)6-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. Keywords Family GH126 · In silico analysis · Bacterial members out-of-firmicutes · Sequence-structural features · Thioredoxin-like fold · Leucine-rich repeat motif Abbreviations CAZy Carbohydrate-active enzymes CBM Carbohydrate-binding module CDD Conserved Domain Database CSR Conserved sequence region
GH Glycoside hydrolase LRR Leucine-rich repeat PDB Protein Data Bank SBD Starch-binding domain RMSD Root-mean square deviation
Electronic supplementary material The online version of this article (https://doi.org/10.1007/s13205-020-02415-x) contains supplementary material, which is available to authorized users.
Introduction
* Štefan Janeček [email protected] 1
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
2
In the sequence-based classification of glycoside hydrolases (GHs) of the
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