How many α-amylase GH families are there in the CAZy database?

Štefan Janeček,Birte Svensson

doi:10.1515/amylase-2022-0001

Abstract

Abstract The CAZy database is a web-server for sequence-based classification of carbohydrate-active enzymes that has become the worldwide and indispensable tool for scientists engaged in this research field. It was originally created in 1991 as a classification of glycoside hydrolases (GH) and currently, this section of CAZy represents its largest part counting 172 GH families. The present Opinion paper is devoted to the specificity of α-amylase (EC 3.2.1.1) and its occurrence in the CAZy database. Among the 172 defined GH families, four, i.e. GH13, GH57, GH119 and GH126, may be considered as the α-amylase GH families. This view reflects a historical background and traditions widely accepted during the previous decades with respect to the chronology of creating the individual GH families. It obeys the phenomenon that some amylolytic enzymes, which were used to create the individual GH families and were originally known as α-amylases, according to current knowledge from later, more detailed characterization, need not necessarily represent genuine α-amylases. Our Opinion paper was therefore written in an effort to invite the scientific community to think about that with a mind open to changes and to consider the seemingly unambiguous question in the title as one that may not have a simple answer.

Highlights

The current CAZy database that primarily catalogues structurally related catalytic domains of Carbohydrate-Active enZymes (CAZymes) [1] has its origin in the brilliant idea of Bernard Henrissat, who in 1991 classified glycoside hydrolases (GH) into families based on amino acid sequence similarities [2]
The overall classification concept most probably originated from classifying cellulases into families revealed by hydrophobic cluster analysis of their sequences [3]; an approach that has been applied to α-amylases [4]
(November 2021), there are 172 GH families and the entire CAZy database, in addition to GH classification, covers sections devoted to glycosyltransferases (GT; 114 families), polysaccharide lyases (PL; 42 families), carbohydrate esterases (CE; 19 families) and auxiliary activities (AA; 17 families); a section devoted to fully sequenced and annotated genomes is a part of the database [2,5,6,7,8,9,10]

Summary

Introduction

The current CAZy database (http://www.cazy.org/) that primarily catalogues structurally related catalytic domains of Carbohydrate-Active enZymes (CAZymes) [1] has its origin in the brilliant idea of Bernard Henrissat, who in 1991 classified glycoside hydrolases (GH) into families based on amino acid sequence similarities [2]. The unmatched scope and impact of the CAZy database motivated a Wikipedia-like project entitled “CAZypedia” (http://www.cazypedia.org/), which was initiated over a decade ago [14] as an original source for documentary presentation of key information on individual families that is truly complementary to CAZy. α-Amylase (EC 3.2.1.1) is one of the enzymes attracting profound research interests, especially from the beginning of the 1990s at which time ideas to define a family around the α-amylase became evident. It is not the intention to comprehensively cover all relevant details as would be the case of a typical Review; and only selected key references are included

The main α-amylase family GH13

The second α-amylase family – GH57

The family GH119

The family GH126

Conclusions