The structure of cytidilyl(2',5')adenosine when bound to pancreatic ribonuclease S

The three-dimensional structure of the RNase S complex with the synthetic dinucleoside monophosphate cytidilyl(2′,5′)adenosine(C₂,p₅,A) is determined using difference Fourier techniques at 2.0 Å resolution in conjunction with computer graphic model-building and energy minimization. The latter has been carried out as a function of the rigid body parameters of the dinucleoside monophosphate and the dihedral angles of the nucleoside portion as well as of relevent amino acids in the active site of the enzyme.The bound dinucleoside monophosphate is found to assume an extended conformation, with the adenine and cytidine bases nearly perpendicular. The bases form specific hydrogen bonds with groups in the active site. Although the atoms involved in the recognition of the pyrimidine base by the enzyme are the same as in the pyrimidine bases of UMP, CMP and UpcA, the details of the binding are different. The adenosine moiety blocks most of the various positions that His119 occupies in the native enzyme and forces it into one well-defined position. One of the His119 ring protons is in contact with O(5′) (the leaving group), O(1′) of the adenine ribose and with a free phosphoryl oxygen. No strong charge contacts with the phosphate group are observed.We show how combining X-ray data with computer graphic model-building, electron density fitting and energy calculations leads to the model we propose and discuss in detail the enzyme-nucleic acid interactions.