Capturing Covalent Catalytic Intermediates by Enzyme Mutants: Recent Advances in Methodologies and Applications

Covalent catalytic intermediates provide valuable information for revealing the catalytic mechanism, probing the enzyme activity and identifying substrate specificity. However, naturally formed covalent intermediates are too rapidly degraded for general biological studies. In order to capture transient covalent intermediates, a variety of chemical strategies have been developed over decades to extend the half-life of the enzyme-substrate intermediates (or close analogues) required for the downstream structural and functional studies. This review summarizes three general mechanism-based strategies for trapping covalent catalytic intermediates. In particular, enzyme mutant-based approaches, especially the introduction of genetically encoded 2,3-diaminopropionic acid to replace the catalytic cysteine/serine in proteases for acyl-enzyme intermediate trapping are described. In addition, the applications of trapped intermediates in structural, functional and protein labeling studies are presented, and the potential new directions of using enzyme substrate traps are discussed at the end of the review.