title: RNA hydrolysis via an oxyphosphorane intermediate.
abstract: 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.
authors.affiliation: National Chemical Laboratory for Industry, Agency of Industrial Science & Technology, MITI, Tsukuba Science City, Japan.
authors.forename: T
authors.initials: T
authors.lastname: Uchimaru
authors.forename: J W
authors.initials: JW
authors.lastname: Storer
authors.forename: K
authors.initials: K
authors.lastname: Tanabe
authors.forename: M
authors.initials: M
authors.lastname: Uebayasi
authors.forename: S
authors.initials: S
authors.lastname: Nishikawa
authors.forename: K
authors.initials: K
authors.lastname: Taira
mesh_terms: 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
chemical_list: D001426:Bacterial Proteins; D012313:RNA; D012260:Ribonucleases; C019760:Bacillus amyloliquefaciens ribonuclease; D006163:Ribonuclease T1