Molecular dynamics and quantum chemical study of endonuclease v catalytic mechanism

Endonuclease V initiates repair of damaged DNA, that contains the thymine dimer, by cleavage of the glycosidic bond through the attack of an amine nucleophile. The transition state for this process is described using a series of model calculations that focus on the electronic characteristics that assist in stabilization of the transition state in the enzyme active site. The inherent geometrical and electronic features of the transition state are obtained in an in vacuo calculation which is then compared to situations where H-bond stabilization of the developing charge is included. The model of the endo V active site includes representations of the Glu-23 and Arg-26 residues. The guanidinium side chain of the arginine residue does not transfer a proton to the thymidine carbonyl in the developing anionic base even when optimizations are intitiated with a proton equidistant between the N of arginine and the O of the base. In the transition state structure, charge separation in the glycosidic bond does not significantly delocalize into the base or sugar, so the stabilization energy due to H-bonding is not large. The activation energy of the glycosidic cleavage catalyzed by a neutral amine is calculated to be about 30 kcal/mol.