RNA hydrolysis via an oxyphosphorane intermediate.
From calculations of a model reaction scheme for base-catalyzed RNA hydrolysis, a pentacoodinate dianionic intermediate 2a (Storer, et al., J. Am. Chem. Soc., 1991, 113, 5216-5219) as well as two transition states, TS1 and TS2, to the intermediate have been located by ab initio calculations at the 3-21G* level. Although the intermediate, which has the well depth on the order of kBT, is unlikely to be kinetically significant, the overall rate-limiting transition state structure TS2 obtained at 3-21G* level is very close to the corresponding structure at the STO-3G level; it has an extended P-O(5') bond breaking character. These gas-phase calculation results are used to qualitatively interpret mutagenesis results of Barnase and RNase T1 where water molecules are absent from the active site.
Uchimaru
T
T
National Chemical Laboratory for Industry, Agency of Industrial Science & Technology, MITI, Tsukuba Science City, Japan.
Storer
J W
JW
Tanabe
K
K
Uebayasi
M
M
Nishikawa
S
S
Taira
K
K
D001426:Bacterial Proteins; D002384:Catalysis; D006863:Hydrogen-Ion Concentration; D006868:Hydrolysis; D008958:Models, Molecular; D012313:RNA / Q000737:chemistry*; D006163:Ribonuclease T1 / Q000494:pharmacology; D012260:Ribonucleases / Q000494:pharmacology; D013816:Thermodynamics
D001426:Bacterial Proteins; D012313:RNA; D012260:Ribonucleases; C019760:Bacillus amyloliquefaciens ribonuclease; D006163:Ribonuclease T1