A cavity with an appropriate size is the basis of the PPIase activity

Peptidyl-prolyl isomerases (PPIases) are biologically very important enzymes but their catalytic mechanism is not fully understood. Recently, our comprehensive mutational study on a PPIase, human FK506-binding protein 12 (FKBP12), suggested that only presence of a cavity was required for the catalysis. This study, however, could not determine what properties of the cavity were essential for the catalysis. In the present study, we focused on the size of the cavity and examined if an artificial PPIase activity could be achieved by a protein with a cavity of a size similar to that of FKBP12. We designed such a cavity on barnase, a bacterial nuclease without the PPIase-like activity, by a quadruple mutation F56G/R59G/H102Y/Y103G. The mutant barnase successfully exhibited weak yet significant PPIase activity. Furthermore, we searched the Protein Data Bank for proteins natively possessing such a cavity. Two of the identified non-PPIase proteins, alpha-amylase and prolyl endopeptidase, were tested for the PPIase activity and indeed catalyzed the isomerization of peptide bonds. These results suggest that a cavity with an appropriate size is the basis of the PPIase activity.