Structure of the ribonuclease•uridine-vanadate transition state analogue complex by Raman difference spectroscopy:: Mechanistic implications

Raman difference spectroscopy is used to assess changes in the internal bonding of the oxygens of a drop VO2- group when that group is incorporated into a complex also involving RNase A, uridine, and a water molecule (the RNase/UVO2/H2O complex). We find that the strengths of the nonbridging V chemical anion O bonds are decreased by 0.055 vu and their bond lengths are decreased 0.012 Angstrom, based on the stretching frequency changes of nonbridging V chemical anion O bonds upon formation of the enzymic RNase/UVO2/H2O complex from the cyclic vanadate diester in solution. The bond lengths are 1.638 Angstrom for the solution complex and 1.650 Angstrom for the enzymic complex. The values found for the bond lengths are about 0.15 Angstrom shorter than those found previously in crystallographic studies. Assuming the RNase/UVO2/H2O adduct is a reasonably good transition state analogue, our Raman results suggest that the RNase-catalyzed hydrolysis of uridine 2',3'-cyclic phosphate proceeds via an S(N)2-like process. The process also may involve a small associative character, since the summed bond strength of nonbridging P chemical anion O bonds is reduced by only 0.11-0.22 vu in the transition state compared with the ground state, which means the summed bond strength of the P chemical anion O bonds of the entering and leaving groups is correspondingly increased.