A strategy for rational enzyme design is reported and illustrated by the engineering of a protein catalyst for thiol-ester hydrolysis. Five mutants of human glutathione (GSH; ␥-Glu-Cys-Gly) transferase A1-1 were designed in the search for a catalyst and to provide a set of proteins from which the reaction mechanism could be elucidated. The single mutant A216H catalyzed the hydrolysis of the S-benzoyl ester of GSH under turnover conditions with a kcat͞KM of 156 M ؊1 ⅐min ؊1 , and a catalytic proficiency of >10 7 M ؊1 when compared with the first-order rate constant of the uncatalyzed reaction. The wild-type enzyme did not hydrolyze the substrate, and thus, the introduction of a single histidine residue transformed the wild-type enzyme into a turnover system for thiol-ester hydrolysis. By kinetic analysis of single, double, and triple mutants, as well as from studies of reaction products, it was established that the enzyme A216H catalyzes the hydrolysis of the thiol-ester substrate by a mechanism that includes an acyl intermediate at the side chain of Y9. Kinetic measurements and the crystal structure of the A216H GSH complex provided compelling evidence that H216 acts as a general-base catalyst. The introduction of a single His residue into human GSH transferase A1-1 created an unprecedented enzymatic function, suggesting a strategy that may be of broad applicability in the design of new enzymes. The protein catalyst has the hallmarks of a native enzyme and is expected to catalyze various hydrolytic, as well as transesterification, reactions.T he quest for new enzymes extends the boundaries of our understanding of catalysis and protein structure and is expected, when successful, to generate new biocatalysts for reactions that are not catalyzed by nature (1-3). It allows for unprecedented opportunities in chemistry, but the implementation of nonnative catalytic functions in protein scaffolds remains a challenge. The redesign of protein macromolecules provides a powerful strategy for engineering nonnatural reactive sites and determining structure-function relationships. For example, the functional swapping between native enzymes has been instructive (4-8), and new catalytic activities have been introduced by chemical modification of amino acid side chains (9). In addition, the incorporation of amino acid residues in the active sites of native enzymes has been used to alter the fate of the natural substrates or inhibitors (10-14). However, although it is possible in principle to modify the active site of any native enzyme to generate nonnatural activity, this approach has met with only limited success because of the difficulties involved in predicting the effect of sequence modifications on structure and function. Catalytic antibodies based on the properties of the immune system in generating binding sites that are complementary to transition-state analogues have been shown to be efficient catalysts for numerous chemical reactions (15)(16). Their catalytic efficiencies, based mainly on transition-state stabilization...