Thioesterase enzyme families: Functions, structures, and mechanisms

Abstract

Thioesterases are enzymes that hydrolyze thioester bonds in numerous biochemical pathways, for example in fatty acid synthesis. This work reports known functions, structures, and mechanisms of updated thioesterase enzyme families, which are classified into 35 families based on sequence similarity.Each thioesterase family is based on at least one experimentally characterized enzyme, and most families have enzymes that have been crystallized and their tertiary structure resolved. Classifying thioesterases into families allows to predict tertiary structures and infer catalytic residues and mechanisms of all sequences in a family, which is particularly useful because the majority of known protein sequence have no experimental characterization. Phylogenetic analysis of experimentally characterized thioesterases that have structures with the two main structural folds reveal convergent and divergent evolution. Based on tertiary structure superimposition, catalytic residues are predicted.

Determinants of substrate specificity in a catalytically diverse family of acyl-ACP thioesterases from plants

“…1 B, File S 1 ). When models of the ALT active unit are superposed with that of Ec YbgC, Asn24 aligns structurally with a predicted catalytic His25 residue of YbgC [ 35 , 45 , 46 ] (Fig. 1 B, Fig.…”

“…However, little work has been done to understand the biochemical underpinnings of substrate specificity within this enzyme clade [ 35 ]. Despite plant ALTs being acyl-ACP thioesterases, not acyl-CoA thioesterases like other enzymes that share the same core catalytic domain structure, information regarding the determinants of ALT substrate specificity could still be extended to related bacterial single hot dog-fold thioesterases [ 35 ]. Amino acids that demonstrably modified substrate specificity in the chimeric ALTs and were predicted to be acyl binding cavity-forming residues in computational models, align consistently to cavity-forming residues in the crystal structure of E. coli YbgC (Fig.…”

“…The predicted homo-oligomeric unit for all modelled ALTs was a homotetramer with dihedral symmetry, similarly to other Type 9 single hot dog-fold bacterial thioesterases with solved crystal structures, including the E. coli acyl-ACP thioesterase YbgC (accession no. 5 T06 on the RCSB PDB) [ 35 , 45 ]. For each ALT, the structure with the lowest free energy score out of 50 homotetrameric structures generated by HSYMDOCK was used for further analysis.…”

“…According to the ThYme (thioester-active enzyme) database, ALT enzymes belong to the Type 9 subfamily of single hot dog-fold thioesterases, within a phylogenetic clade that includes bacterial enzymes such as the YbgC and YbaW medium-chain acyl-CoA thioesterases, and 4-hydroxybenzoyl-CoA thioesterases [ 35 ]. Little research has been done on how protein sequence relates to substrate specificity in this clade, and an iterative domain-swapping approach was an attractive starting point for investigating the determinants of substrate specificity in ALTs.…”

Molecular study on recombinant cold-adapted, detergent- and alkali stable esterase (EstRag) from Lysinibacillus sp.: a member of family VI

“…It is recognized, however, for human acyl-protein thioesterase I, which shares significant sequence and structural similarities with esterases from the family VI. The in vivo functionality of acyl protein thioesterases is S-palmitoylation of cysteine residues in G protein alpha subunits I (Pesaresi and Lamba 2005 ; Caswell et al 2022 ). EstRag's structural and sequence similarities to the PDB template entry 1AUO of P. fluorescens , a member of family VI, were determined using TM-align and SAS online programs.…”