How the Same Core Catalytic Machinery Catalyzes 17 Different Reactions: the Serine-Histidine-Aspartate Catalytic Triad of α/β-Hydrolase Fold Enzymes

Abstract

Enzymes within a family often catalyze different reactions. In some cases, this variety stems from different catalytic machinery, but in other cases the machinery is identical; nevertheless, the enzymes catalyze different reactions. In this review, we examine the subset of α/β-hydrolase fold enzymes that contain the serine-histidine-aspartate catalytic triad. In spite of having the same protein fold and the same core catalytic machinery, these enzymes catalyze seventeen different reaction mechanisms. The most common reactions are hydrolysis of C–O, C–N and C–C bonds (Enzyme Classification (EC) group 3), but other enzymes are oxidoreductases (EC group 1), acyl transferases (EC group 2), lyases (EC group 4) or isomerases (EC group 5). Hydrolysis reactions often follow the canonical esterase mechanism, but eight variations occur where either the formation or cleavage of the acyl enzyme intermediate differs. The remaining eight mechanisms are lyase-type elimination reactions, which do not have an acyl enzyme intermediate and, in four cases, do not even require the catalytic serine. This diversity of mechanisms from the same catalytic triad stems from the ability of the enzymes to bind different substrates, from the requirements for different chemical steps imposed by these new substrates and, only in about half of the cases, from additional hydrogen bond partners or additional general acids/bases in the active site. This detailed analysis shows that binding differences and non-catalytic residues create new mechanisms and are essential for understanding and designing efficient enzymes.

Facilitating the Evolution of Esterase Activity from a Promiscuous Enzyme (Mhg) with Catalytic Functions of Amide Hydrolysis and Carboxylic Acid Perhydrolysis by Engineering the Substrate Entrance Tunnel

“…2A), pNPB forms two hydrogen bonds with NH of Met99 and Tyr32, and its carbonyl carbon is in close proximity to HO of Ser98. The catalytic mechanism of an esterase was reported to be similar to that of an amidase (25). In an amidase, the carbonyl oxygen atom of the substrate initially binds to the active site through the oxyanion hole, which is formed by nitrogen atoms of Tyr32 and Met99.…”

“…ited the highest activity, which may result from the synergistic effects of the two sites (9). Esterase is predicted to be the ancestor of a number of different types of enzymes (25). In the research of evolutionary analysis, Devamani and his coworkers found that the predicted ancestral enzymes of hydroxyl nitrile lyases shared the Ser-His-Asp catalytic triad and that they had a conserved function of hydrolysis of esters (29).…”

An α/β-hydrolase fold protein in the biosynthesis of thiostrepton exhibits a dual activity for endopeptidyl hydrolysis and epoxide ring opening/macrocyclization

“…3A). The conversion of 2′ to 1′ relies on the nucleophillic attack of the amino group of Ile1 onto the C7′ position of QA in a regio-and stereo-selective manner, mechanistically similar to the reactions catalyzed by various epoxide hydrolases that belong to the α/β-hydrolase superfamily (25,26). These epoxide hydrolases usually share a Ser-His-Asp triad and catalyze epoxide ring opening by using H 2 O as the nucleophillic agent.…”

Mechanism-Guided Discovery of an Esterase Scaffold with Promiscuous Amidase Activity

“…This phenomenon, collectively known as "promiscuity" [18], presumably allows for an increased fitness of the organism through the evolution of novel catalytic functions. Some prominent examples include the α,β-hydrolase fold [19] that is capable of harnessing 17 different reaction mechanisms [20], P450 monooxygenase-catalyzed cyclization [21], cyclopropanation [14], and γ-humulene synthase that generates 52 different natural products starting from the same polyisoprene substrate [22]. As accelerating promiscuous activities through enzyme engineering constitutes a cornerstone for expanding the catalytic scope of enzymes [15], an enhanced fundamental understanding of the molecular mechanisms underpinning the evolution of the catalytic function is desired.…”