Journal
3 BIOTECH
Volume 10, Issue 10, Pages -Publisher
SPRINGER HEIDELBERG
DOI: 10.1007/s13205-020-02415-x
Keywords
Family GH126; In silico analysis; Bacterial members out-of-firmicutes; Sequence-structural features; Thioredoxin-like fold; Leucine-rich repeat motif
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Funding
- Slovak Grant Agency VEGA [2/0146/17]
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The family GH126 is a family of glycoside hydrolases established in 2011. Officially, in the CAZy database, it counts similar to 1000 sequences originating solely from bacterial phylum Firmicutes. Two members, the proteins CPF_2247 fromClostridium perfringensand PssZ fromListeria monocytogeneshave been characterized as a probable alpha-amylase and an exopolysaccharide-specific glycosidase, respectively; their three-dimensional structures being also solved as possessing catalytic (alpha/alpha)(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 (alpha/alpha)(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.
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