Pentacoordinated molecules .28. Computer simulation of ribonuclease action on uridylyl-(3'-5')-adenosine (Reprinted from J Am Chem Soc, vol 100, pg 7393, 1978)

The first step of the hydrolytic action of ribonuclease on the dinucleotide substrate UpA is investigated via molecular mechanics calculations. UpA coordinates were obtained by conformational minimization of the UpcA coordinates from the X-ray diffraction study of RNase-S with UpcA. Only the amino acid residues in the immediate vicinity of the active site were included in the calculations: histidine-12, histidine-119, and lysine-41. It is found that histidine-119 and lysine-41 may be moved into more favorable positions for contact with the phosphate group with little change in energy. The transphosphorylation step is initiated by decreasing the O-2, to Phosphorus distance while simultaneously increasing the O-5, to phosphorus distance, resulting in cleavage of the P-O-5, bond and formation of the 2',3'-cyclic intermediate. The phosphorus atom moves almost 2 Angstrom in forming this cyclic intermediate, bringing the phosphate unit within the hydrogen-bonding distance of lysine-41. Distances between the dinucleotide and the amino acid residues in both the initial structure and the cyclic intermediate support a proposed reaction mechanism involving hydrogen bonding. The reaction proceeds by an in-line attack of the O-2, oxygen atom on phosphorus and passes through a transition state which lies along the Berry coordinate. The transition-state structure is determined to be intermediate in geometry between a trigonal bipyramid and a square pyramid. Compatible with the enzyme catalysis, the computed ground state, transition state, and cyclic intermediate structures have comparable energies.