Classification of glycosyl hydrolases based on structural homology

Abstract

   Glycosyl hydrolases are a well-known group of enzymes, which hydrolyze the glycosidic bond between carbohydrates, or between a carbohydrate and different molecules. Glycosyl hydrolases play a vital role in the human body, and are widely used in industrial applications. Glycosyl hydrolases classification is based on substrate specificity and amino acid or nucleotide sequence similarity which reflects their evolutionary relationship.

   Our aim, in this study, was to carry out the classification of glycosyl hydrolases, based solely on structural similarity which was made possible by the several structures available in the databases and the availability of computing power to conduct such a computationally intensive task, in a reasonable time-frame. It was also aimed that the structural similarity based classification be compared to the present classification system.

   Based on an all-against-all comparison, we conducted a structural comparison of glycosyl hydrolases. The results are presented graphically. The graphical representation defined 24 structurally homologous classes. The classification was validated using C_α - C_α distance analysis and amino acid sequence cluster analysis.

   Advantages of this method are that – being an automated method – it is fast, simple and reproducible. Glycosyl hydrolases could be classified into 24 separate classes. N-glycosyl and O-glycosyl hydrolases (both forming binding and catalytic domain classes as well) were clearly different, the former consisting of 8 classes, and the latter consisting of 16 classes. Structural classes simplified the previous classification system. This classification represents the current glycosyl hydrolase family system, but also extends it especially concerning the clan system.