The primary specificity of papain-like proteinases is largely determined by S2-P2 site interactions. According to the three-dimensional structure of a papain-inhibitor complex, the S2 subsite is defined by residues 67, 68, 133, 157, 160, and 205, with residues 133, 157, and 205 integrated into the wall and bottom of the side chain binding cavity. The S2 binding site specificity of this enzyme has been altered to mimic that of cathepsin B or L by the application of site-directed mutagenesis at these latter three positions in the cathepsin S sequence. The replacement of Gly-133 in cathepsin S by an alanine residue that is normally found at this position in both cathepsin B and L results in a pattern of specificity toward hydrophobic residues in P2 that is very similar to that of cathepsin B and L. The replacement of other cathepsin S S2 subsite residues with their cathepsin L equivalents (mutants Val-157-->Leu, Phe-205-->Ala) does not significantly change the specificity of cathepsin S. Cathepsin B is distinguished from both cathepsin L and S by its ability to efficiently hydrolyze substrates containing a basic P2 residue. A single mutation in position 205 of cathepsin S (Phe-205-->Glu) results in a change of specificity toward that of cathepsin B, i.e. the second-order rate constant for the hydrolysis of the cathepsin B-specific substrate benzyloxycarbonyl-Arg-Arg-4-methyl-7-coumaryl-amide is increased 77-fold for this mutant compared with the wild-type enzyme. A cathepsin S double mutant Gly-133-->Ala/Phe-205-->Glu is characterized by somewhat improved kinetic parameters compared with the Phe-205-->Glu single mutant. The hydrolysis rate of the benzyloxy-carbonyl-Arg-Arg-4-methyl-7-coumarylamide substrate by this double mutant is 130-fold higher than that of the wild-type enzyme. As with cathepsin B, the activities of the Phe-205-->Glu single and the Gly-133-->Ala/Phen-205-->Glu double mutants of cathepsin S toward the dibasic substrate is modulated by an additional ionizable group with a pKa of 5.7.