Some Evidence Suggesting the Existence of P2 and B3 Sites in the Active Site of Bovine Pancreatic Ribonuclease A1

Abstract

In order to clarify the subsite structure of ribonuclease A (RNase A), the interactions of pdTp, pAp, dTpdAp, and pdTpdAp with RNase A were investigated by means of kinetic studies and ³¹ P NMR spectroscopy. The pH profile of the ³¹ P NMR spectrum of RNase A-pdTp complex indicated the interaction of the 3'- and 5'-phosphates with RNase A. The signal of 3'-phosphate of pdTp in the presence of RNase A gave a characteristic titration curve indicating the participation of more than 2 ionic groups in the P ₁ subsite. A similar ³¹ P NMR titration was observed in the case of 5'-phosphate of pAp in the presence of RNase A. The results indicated that pAp interacted with RNase A at the P ₁ , B ₂ , and P ₂ sites. dTpdAp and pdTpdAp inhibited RNase A action more markedly than dTpdA, indicating the contribution of 3'- and 5'-terminal phosphate groups attached to dTpdA to the affinity of RNase A. The ³¹ P NMR spectra of RNase A-dTpdAp and pdTpdAp complexes excluded the possible interaction of the monoester type phosphate of the inhibitors with the P ₁ site of RNase A, thus indicating the binding of the 3'-side phosphates with the P ₂ subsite of RNase A. The effects of pA, Ap, and adenosine on the RNase A-s ⁴ Up complex were studied by difference spectroscopy. The results indicated the binding of Ap at the B ₂ and P ₂ sites of RNase A without affecting the RNase A-s ⁴ Up complex. The rates of enzymatic cleavage of UpApA and UpApG were 2.47 and 5.17 times larger than that of UpA, respectively and were different from each other. This supports the existence of the B ³ site besides the P ₂ site in the active site of RNase A. These results clearly indicated the presence of P ₂ and B ₂ sites in RNase A in addition to the P ₀ , B ₁ , P ₁ , and B ₂ sites previously reported.