The intracellular protease from Pyrococcus horikoshii (PhpI) is a member of the DJ-1/ThiJ/PfpI superfamily, which is suggested to be involved in cellular protection against environmental stresses. In this study, flexible docking approach was employed to dock the ligand into the active site of PhpI. By analyzing the results, active site architecture and certain key residues responsible for substrate specificity were identified on the enzyme. Our docking result indicates that Glu12 plays an important role in substrate binding. The kinetic experiment conducted by Zhan shows that the E12T mutant is more stable than that of the wild-type. We also predict that Glu15, Lys43, and Tyr46 may be important in the catalytic efficiency and thermostability of enzyme. The new structural and mechanistic insights obtained from computational study should be valuable for detailed structures and mechanisms of the member of the DJ-1 superfamily.