Abstract
Carboxylic ester hydrolases (CEHs), which catalyze the hydrolysis of carboxylic esters to produce alcohol and acid, are identified in three domains of life. In the Protein Data Bank (PDB), 136 crystal structures of bacterial CEHs (424 PDB codes) from 52 genera and metagenome have been reported. In this review, we categorize these structures based on catalytic machinery, structure and substrate specificity to provide a comprehensive understanding of the bacterial CEHs. CEHs use Ser, Asp or water as a nucleophile to drive diverse catalytic machinery. The α/β/α sandwich architecture is most frequently found in CEHs, but 3-solenoid, β-barrel, up-down bundle, α/β/β/α 4-layer sandwich, 6 or 7 propeller and α/β barrel architectures are also found in these CEHs. Most are substrate-specific to various esters with types of head group and lengths of the acyl chain, but some CEHs exhibit peptidase or lactamase activities. CEHs are widely used in industrial applications, and are the objects of research in structure- or mutation-based protein engineering. Structural studies of CEHs are still necessary for understanding their biological roles, identifying their structure-based functions and structure-based engineering and their potential industrial applications.
Highlights
Carboxylic ester hydrolases (CEHs, Enzyme Commission (EC) 3.1.1.-) are catalysts that hydrolyze linear and cyclic carboxylic ester bonds to produce carboxyl groups (–COOH) and alcohol groups (–OH) at termini.CEHs are found in all living organisms, including vertebrates, insects, fungi, plants, archaea and bacteria
The structures of 525 bacterial enzymes belonging to the EC 3.1.1.- group were released in the Protein Data Bank (PDB) database until 2019 July
424 structures of 136 CEHs from 52 genera and metagenomic samples were selected for the analysis, and 136 CEHs were classified based on EC numbers (Table 1)
Summary
Carboxylic ester hydrolases (CEHs, EC 3.1.1.-) are catalysts that hydrolyze linear and cyclic carboxylic ester bonds to produce carboxyl groups (–COOH) and alcohol groups (–OH) at termini. CEHs are found in all living organisms, including vertebrates, insects, fungi, plants, archaea and bacteria. The functional diversity of CEHs is mediated by substrate specificities on various biomolecules, such as carbohydrates [11], lipids [12], polypeptides [13,14], nucleic acids [15] and other small molecules [16]. Their catalytic reaction is followed by the cooperation of catalytic residues including a classical Ser-His-Asp triad and substrate-binding residues.
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