Amino acid substitution in the active site of DNA polymerase β explains the energy barrier of the nucleotidyl transfer reaction.

ABSTRACT: DNA polymerase β (pol β) is a bifunctional enzyme widely studied for its roles in base excision DNA repair, where one key function is gap-filling DNA synthesis. In spite of significant progress in recent years, the atomic level mechanism of the DNA synthesis reaction has remained poorly understood. Based on crystal structures of pol β in complex with its substrates and theoretical considerations of amino acids and metals in the active site, we have proposed that a nearby carboxylate group of Asp256 enables the reaction by accepting a proton from the primer O3'group, thus activating O3'as the nucleophile in the reaction path. Here, we tested this proposal by altering the side chain of Asp256 to Glu and then exploring the impact of this conservative change on the reaction. The D256E enzyme i

SUBMITTER: Batra VK 

PROVIDER: S-EPMC3918438 | biostudies-literature | 2013 May

REPOSITORIES: biostudies-literature