A study of carboxylic ester hydrolases: structural classification, properties, and database

Abstract

The carboxylic ester hydrolases (CEHs) are enzymes that hydrolyze an ester bond to form a carboxylic acid and an alcohol. They are one of the enzyme groups that are most explored industrially for their applications in the food, flavor, pharmaceutical, organic synthesis, and detergent industries. We classified CEHs into families and clans according to their amino acid sequences (primary structures) and three-dimensional structures (tertiary structures). Our work has established the systematic structural classification of the CEHs. Primary structures of family members are similar to each other, and their active sites and reaction mechanisms are conserved. The tertiary structures of members of each clan, which is composed of different families, remain very similar, although amino acid sequences of members of different families are not similar. CEHs were divided into 127 families by use of BLAST, with 67 families being grouped into seven clans. Multiple sequence alignment and tertiary structures superposition were used, and active sites and reaction mechanisms were analyzed. Python and Shell scripts were implemented to automate the process of comparing CEH primary and tertiary structures. A comprehensive database, CASTLE (CArboxylic eSTer hydroLasEs), may be constructed to provide the primary and tertiary structures of CEHs. This database would be available at www.castle.enzyme.iastate.edu and will be accessible to the entire biology community.