Tryptases I and II were heterologously expressed and purified in yeast to functionally characterize the substrate specificity of each enzyme. Three positional scanning combinatorial tetrapeptide substrate libraries were used to determine the primary and extended substrate specificity of the proteases. Both enzymes have a strict primary preference for cleavage after the basic amino acids, lysine and arginine, with only a slight preference for lysine over arginine. I and II tryptase share similar extended substrate specificity, with preference for proline at P4, preference for arginine or lysine at P3, and P2 showing a slight preference for asparagine. Measurement of kinetic constants with multiple substrates designed for -tryptases reveal that selectivity is highly dependent on ground state substrate binding. Coupled with the functional determinants, structural determinants of tryptase substrate specificity were identified. Molecular docking of the preferred substrate sequence to the three-dimensional tetrameric tryptase structure reveals a novel extended substrate binding mode that involves interactions from two adjacent protomers, including P4 Thr-96, P3 Asp-60B and Glu-217, and P1 Asp-189. Based on the determined substrate information, a mechanism-based tetrapeptide-chloromethylketone inhibitor was designed and shown to be a potent tryptase inhibitor. Finally, the cleavage sites of several physiologically relevant substrates of -tryptases show consistency with the specificity data presented here.Mast cells, mediators of inflammatory and allergic response, are found throughout the body concentrated near blood vessels in connective tissue and the mucous membranes of the respiratory and gastrointestinal tract. They play an important role in innate and acquired immune responses through the release of dense granules upon activation. Mast cell activation has also been implicated as a mediator of asthma and other inflammatory diseases. The major components of mast cell secretory granules are the tryptase serine proteases (1). Tryptases are secreted as catalytically active tetramers that are resistant to inactivation by plasma inhibitors. The 3-Å crystal structure has been solved and reveals a ringlike structure with the four active sites facing a central cavity (2). Several in vitro studies have identified multiple substrates for tryptase, including neuropeptides, fibrinogen, stromelysin, prourokinase, prothrombin, and protease-activated receptor-2 (3-6). Human chromosome 16 encodes several homologous tryptase genes, designated tryptase ␣, , and ␥ (7, 8). The -tryptases share greater than 99% sequence identity, with tryptase I and II differing by a single N-glycosylation site. It is unclear why so many highly similar tryptases are expressed by mast cells. One possibility is that they each perform different proteolytic functions that may be reflected in their substrate specificity preferences. Indeed, it has recently been shown that a single amino acid substitution between tryptase ␣ and tryptase II account...