Although the a-chymases of primates and dogs are known as chymotrypsin-like proteases, the enzymatic properties of rodent a-chymases (rat mast cell protease 5/rMCP-5 and mouse mast cell protease 5/mMCP-5) have not been fully understood. We report that recombinant rMCP-5 and mMCP-5 are elastase-like proteases, not chymotrypsin-like proteases. An enzyme assay using chromogenic peptidyl substrates showed that mast cell protease-5s (MCP-5s) have a clear preference for small aliphatic amino acids (e.g. alanine, isoleucine, valine) in the P1 site of substrates. We used site-directed mutagenesis and computer modeling approaches to define the determinant residue for the substrate specificity of mMCP-5, and found that the mutant possessing a Gly substitution of the Val at position 216 (V216G) lost elastase-like activity but acquired chymase activity, suggesting that the Val216 dominantly restricts the substrate specificity of mMCP-5. Structural models of mMCP-5 and the V216G mutant based on the crystal structures of serine proteases (rMCP-2, human cathepsin G, and human chymase) revealed the active site differences that can account for the marked differences in substrate specificity of the two enzymes between elastase and chymase. These findings suggest that rodent a-chymases have unique biological activity different from the chymases of other species.Keywords: mast cell protease(s); chymase; elastase; chymotrypsin; substrate specificity; site-directed mutagenesis; homology modeling.Chymase is a chymotrypsin-like serine protease expressed exclusively in mast cells (MCs), where the protease is stored within the secretary granules and released along with tryptase, heparin, and histamine in response to allergen challenge or other stimuli [1]. Although the physiological function of this protease is still unclear, it is probably involved in various allergic inflammatory reactions, cardiovascular diseases, and chronic inflammatory diseases [2]. For example, the proposed actions of chymase include induction of microvascular leakage [3], inflammatory cell accumulation [4], neutrophil and lymphocyte chemotaxis [5], stimulation of bronchial gland secretion [6], mast cell degranulation [7], extracellular matrix degradation [8][9][10][11][12][13], and cytokine metabolism [14][15][16][17].Based on phylogenetic analyses of a large set of cDNAderived sequences and comparison of the substrate preferences of a smaller set of purified enzymes, mammalian chymases have been divided into two families, the a-and b-chymase families [18,19]. Mice and rats have a number of chymase isozymes that belong to the a-chymase family (mouse mast cell protease-5/mMCP-5 and rat mast cell protease-5/rMCP-5) and the b-chymase family (mMCP-1, 2, 4, rMCP-1, 2, 4) [20,21]. Primates and dogs, on the other hand, are generally thought to have just a single a-chymase [22][23][24]. Across mammalian species, the primary structures of a-chymases are much more similar to each other than to those of the b-chymases. For example, the amino acid sequences for human chymase...