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

TLDR

Enzymes in a family can catalyze diverse reactions—from hydrolysis of C–O, C–N, and C–C bonds to oxidoreductase, acyl‑transferase, lyase, and isomerase activities—even when they share identical catalytic machinery. The review investigates α/β‑hydrolase fold enzymes that contain a serine‑histidine‑aspartate catalytic triad. These enzymes use a canonical esterase mechanism with eight variations, eight lyase‑type elimination reactions lacking an acyl intermediate (and sometimes the catalytic serine), and overall diversity arises from substrate‑binding differences, distinct chemical step requirements, and occasionally additional active‑site residues. Despite sharing the same fold and catalytic triad, the enzymes perform seventeen distinct reaction mechanisms, demonstrating that substrate binding differences and non‑catalytic residues generate new mechanisms essential for enzyme design.

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.