The primary specificity of papain-like cysteine proteases (family C1, clan CA) is determined by S2-P2 interactions. Despite the high amino acid sequence identities and structural similarities between cathepsins K and L, only cathepsin K is capable of cleaving interstitial collagens in their triple helical domains. To investigate this specificity, we have engineered the S2 pocket of human cathepsin K into a cathepsin L-like subsite. Using combinatorial fluorogenic substrate libraries, the P1-P4 substrate specificity of the cathepsin K variant, Tyr67Leu/Leu205Ala, was determined and compared with those of cathepsins K and L. The introduction of the double mutation into the S2 subsite of cathepsin K rendered the unique S2 binding preference of the protease for proline and leucine residues into a cathepsin L-like preference for bulky aromatic residues. Homology modeling and docking calculations supported the experimental findings. The cathepsin L-like S2 specificity of the mutant protein and the integrity of its catalytic site were confirmed by kinetic analysis of synthetic di-and tripeptide substrates as well as pH stability and pH activity profile studies. The loss of the ability to accept proline in the S2 binding pocket by the mutant protease completely abolished the collagenolytic activity of cathepsin K whereas its overall gelatinolytic activity remained unaffected. These results indicate that Tyr67 and Leu205 play a key role in the binding of proline residues in the S2 pocket of cathepsin K and are required for its unique collagenase activity.Type I collagen is the major component of the organic bone matrix which is continually degraded and resynthesized during the bone remodeling process (1). It consists of covalently cross-linked triple helices containing two R1(I) and one R2(I) chains. Large regions of the collagen chains are composed of repeating Gly-Pro-Xaa sequences, where Xaa is mainly proline and/or 4-trans-L-hydroxyproline (2). Degradation of the triple helical type I collagen is achieved by several members of the matrix metalloprotease family (MMPs) such as MMPs 1, 2, 8, and 13 (3) and the papainlike cysteine protease, cathepsin K (4). MMPs selectively cleave collagens through a single scission across all three chains and generate about three-fourth and one-fourth length collagen fragments (5) whereas cathepsin K, similar to bacterial collagenases, cleaves type I and II collagens at multiple sites within their triple helical domains (6, 7). In contrast, other cysteine proteases such as cathepsins L and B cleave collagens only in their nonhelical telopeptide regions (8).Cathepsin K is predominantly expressed in osteoclasts and has been implicated in bone resorption (9-11). The specific role of cathepsin K in bone resorption was demonstrated by the discovery that deficiency in cathepsin K activity causes an inherited autosomal recessive bone dysplasia, pycnodysostosis (12). Several cleavage sites of cathepsin K in the triple helical regions of type I and II collagens have been identified (6,...