TY - JOUR
T1 - A cavity with an appropriate size is the basis of the PPIase activity
AU - Ikura, Teikichi
AU - Kinoshita, Kengo
AU - Ito, Nobutoshi
N1 - Funding Information:
This work was supported by Grants-in-Aid for Scientific Research (Nos 16041210 and 18031009) from the Ministry of Education, Culture, Sports, Science and Technology of Japan. K.K. was supported by a Grant-in-Aid for Scientific Research on Priority Areas from the Ministry of Education, Culture, Sports, Science and Technology of Japan.
PY - 2008/2
Y1 - 2008/2
N2 - 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, α-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.
AB - 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, α-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.
KW - Barnase
KW - Cavity-creating mutation
KW - Design of protein function
KW - Peptidyl-prolyl isomerase activity
KW - Stochastic binding and releasing model
UR - http://www.scopus.com/inward/record.url?scp=39749083945&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=39749083945&partnerID=8YFLogxK
U2 - 10.1093/protein/gzm087
DO - 10.1093/protein/gzm087
M3 - Article
C2 - 18175776
AN - SCOPUS:39749083945
SN - 1741-0126
VL - 21
SP - 83
EP - 89
JO - Protein Engineering, Design and Selection
JF - Protein Engineering, Design and Selection
IS - 2
ER -