Thioesterases: a new perspective based on their primary and tertiary structures

Abstract

Thioesterases (TEs) are classified into EC 3.1.2.1 through EC 3.1.2.27 based on their activities on different substrates, with many remaining unclassified (EC 3.1.2.-). Analysis of primary and tertiary structures of known TEs casts a new light on this enzyme group. We used strong primary sequence conservation based on experimentally proved proteins as the main criterion, followed by verification with tertiary structure superpositions, mechanisms, and catalytic residue positions, to accurately define TE families. At present, TEs fall into 23 families almost completely unrelated to each other by primary structure. It is assumed that all members of the same family have essentially the same tertiary structure; however, TEs in different families can have markedly different folds and mechanisms. Conversely, the latter sometimes have very similar tertiary structures and catalytic mechanisms despite being only slightly or not at all related by primary structure, indicating that they have common distant ancestors and can be grouped into clans. At present, four clans encompass 12 TE families. The new constantly updated ThYme (Thioester-active enzYmes) database contains TE primary and tertiary structures, classified into families and clans that are different from those currently found in the literature or in other databases. We review all types of TEs, including those cleaving CoA, ACP, glutathione, and other protein molecules, and we discuss their structures, functions, and mechanisms.

Figure 1

Superimposed tertiary structures of single representatives of each TE family in a clan: TE-A acyl-CoA hydrolases from Escherichia coli (TE5) (green), Helicobacter pylori (TE9) (red), Pseudomonas sp. (TE10) (yellow), and Prochlorococcus marinus (TE12) (blue).

Figure 2

Superimposed tertiary structures of single representatives of each TE family in a clan: TE-B acyl-CoA hydrolases from Homo sapiens (TE8) (blue), Arthrobacter sp. (TE11) (red), and E. coli (TE13) (yellow).

Figure 3

Superimposed tertiary structures of single representatives of each TE family in a clan: TE-C acyl-ACP hydrolases from Homo sapiens (TE16) (blue), Saccharopolyspora erythraea (TE17) (red), and Amycolatopsis mediterranei (TE18) (yellow).

Figure 4

Superimposed tertiary structures of single representatives of each TE family in a clan: TE-D protein-acyl hydrolases from Bos taurus (TE20) (blue) and Homo sapiens (TE21) (yellow).