Polymerase-tailored variations in the water-mediated and substrate-assisted mechanism for nucleotidyl transfer: insights from a study of T7 DNA polymerase.

ABSTRACT: The nucleotidyl transfer reaction catalyzed by DNA polymerases is the critical step governing the accurate transfer of genetic information during DNA replication, and its malfunctioning can cause mutations leading to human diseases, including cancer. Here, utilizing ab initio quantum mechanical/molecular mechanical calculations with free-energy perturbation, we carried out an extensive investigation of the nucleotidyl transfer reaction mechanism in the well-characterized high-fidelity replicative DNA polymerase from phage T7. Our defined mechanism entails an initial concerted deprotonation of a conserved crystal water molecule with protonation of the gamma-phosphate of the deoxynucleotide triphosphate(dNTP) via a solvent water molecule, and then the proton on the primer 3'-terminus is tran

SUBMITTER: Wang L 

PROVIDER: S-EPMC2801548 | biostudies-literature | 2009 Jun

REPOSITORIES: biostudies-literature