Proteases act in important homeostatic pathways and are tightly regulated. Here, we report an unusual structural mechanism of regulation observed by the 2.5-Å X-ray crystal structure of the serine protease, granzyme C. Although the active-site triad residues adopt canonical conformations, the oxyanion hole is improperly formed, and access to the primary specificity (S1) pocket is blocked through a reversible rearrangement involving Phe-191. Specifically, a register shift in the 190-strand preceding the activesite serine leads to Phe-191 filling the S1 pocket. Mutation of a unique Glu-Glu motif at positions 192-193 unlocks the enzyme, which displays chymase activity, and proteomic analysis confirms that activity of the wild-type protease can be released through interactions with an appropriate substrate. The 2.5-Å structure of the unlocked enzyme reveals unprecedented flexibility in the 190-strand preceding the active-site serine that results in Phe-191 vacating the S1 pocket. Overall, these observations describe a broadly applicable mechanism of protease regulation that cannot be predicted by template-based modeling or bioinformatic approaches alone.protease regulation ͉ register shift ͉ allostery P roteolysis plays an essential role in many biological pathways, an importance that is emphasized by the wide range and diversity of proteases that account for Ϸ2-3% of the human proteome (1). Of these, the largest group is the primary specificity (S1) family of serine proteases whose active sites contain three distinct features. The first is the catalytic triad (H57, D102, and S195 in chymotrypsin numbering) that creates a nucleophile to attack the substrate peptide bond. Mutation of any of these residues abolishes activity. Second is the ''oxyanion hole'' created by the main chain amide groups of S195 and G193. The positive charge in this region neutralizes a negatively charged oxygen atom in the substrate that is transiently formed during catalysis. Last, a conserved salt bridge is formed between the N-terminal amine group and the side chain of D194. This interaction introduces constraints on the active-site architecture that aid in cleavage efficiency.Given the diversity of irreversible effects that serine proteases can have on a variety of biological pathways, their actions are tightly regulated. During biosynthesis, most serine proteases follow a one-step activation pathway involving precursor processing. They are initially synthesized as inactive precursors (zymogens) in which the active site is unformed. Limited proteolysis at the N terminus removes the inactivating propeptide, thus allowing the protease to fold into a mature, active state. Once activated, serine proteases are controlled by a variety of inhibitors that may be either specific (for example, inhibitors of the serpin family) or nonspecific (such as ␣ 2 -macroglobulin) to ensure that they exert their effects only within the correct context. (3) or other proteins (4). This results in a two-step active-site assembly pathway for activation, from the ...