Abstract

Glycoside hydrolases (GHs) have been classified in the CAZy database into 153 GH families. Currently, there might be four α-amylase families: the main family GH13, the family GH57 with related GH119 and, eventually, also GH126. The family GH57 was established in 1996 as the second and smaller α-amylase family. In addition to α-amylase, it contains 4-α-glucanotransferase, α-glucan branching enzyme, amylopullulanase, dual-specificity amylopullulanase–cyclomaltodextrinase, non-specified amylase, maltogenic amylase and α-galactosidase. The family GH57 enzymes employ the retaining reaction mechanism, share five typical conserved sequence regions and possess catalytic (β/α)7-barrel succeeded by a four-helix bundle with the catalytic machinery consisting of catalytic nucleophile and proton donor (glutamic acid and aspartic acid at strands β4 and β7, respectively). The present bioinformatics study delivers a detailed sequence comparison of 1602 family GH57 sequences with the aim to highlight the uniqueness of each enzyme’s specificity and all eventual protein groups. This was achieved by creating the evolutionary tree focused on both the enzyme specificities and taxonomical origin. The substantial increase of numbers of sequences from recent comparisons done more than 5 years ago has allowed to refine the details of the sequence logos for the individual enzyme specificities. The study identifies a new evolutionary distinct group of α-galactosidase-related enzymes with until-now-undefined enzyme specificity but positioned on the evolutionary tree on a branch adjacent to α-galactosidases. The specificity of α-galactosidase is, moreover, the only one of the entire family GH57 for which there is no structural support for the proposal of the proton donor based on sequence analysis. The analysis also suggests a few so-called “like” protein groups related to some family GH57 enzyme specificities but lacking one or both catalytic residues.

Highlights

  • Introduction αAmylase (EC 3.2.1.1) is a glycoside hydrolase (GH) catalyzing in an endo-fashion the hydrolysis of α-1,4-glucosidic linkages in starch and related polysaccharides and α-glucans

  • The really huge number of sequences that has still been rapidly increasing led to definition of subfamilies (Oslancova and Janecek 2002), which resulted in dividing the family into official GH13 subfamilies by Carbohydrate-Active enZymes database (CAZy) curators (Stam et al 2006), the subfamily members exhibiting a higher degree of sequence similarity to each other than to members of other GH13 subfamilies

  • The present study may represent the most complete and detailed bioinformatics analysis of the α-amylase family GH57 since it delivers a comparison of 1602 GH57 sequences (Table S1)

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Summary

Introduction

Introduction αAmylase (EC 3.2.1.1) is a glycoside hydrolase (GH) catalyzing in an endo-fashion the hydrolysis of α-1,4-glucosidic linkages in starch and related polysaccharides and α-glucans. Despite the fact that the catalytic action of any α-amylase should be, in principle, the same, different protein molecules may have evolved even within the same organisms to possess the same catalytic activity of the α-amylase (Janecek et al 2014). This means that in the Carbohydrate-Active enZymes database (CAZy; http://www.cazy.org/; Cantarel et al 2009), there have been created more α-amylase GH families reflecting especially unambiguous differences in amino acid sequences. The family GH13 constitutes the clan GH-H together with related families GH70 and GH77 (Cantarel et al 2009; Janecek and Gabrisko 2016)

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