Human DNA polymerase η (Pol η) is an enzyme involved in the repair of DNA mutations that cause skin cancer. In addition to the two Mg2+ ions aligning the active site, recent experiments suggest that a third Mg2+ ion could play an essential catalytic role. We investigated the role of this third metal ion with quantum mechanical/molecular mechanical (QM/MM) free energy simulations of the phosphoryl transfer reaction and a proposed self-activating proton transfer from the incoming nucleotide to the pyrophosphate leaving group. The simulations with only two metal ions in the active site support a sequential mechanism, with phosphoryl transfer followed by relatively fast proton transfer. The simulations with three metal ions in the active site suggest that the third metal ion may play a catalytic role through electrostatic interactions with the leaving group. These electrostatic interactions stabilize the product, making the phosphoryl transfer reaction more thermodynamically favorable with a lower free energy barrier relative to the activated state, and also inhibit the subsequent proton transfer. The possibility that Mg2+-bound hydroxide acts as the base deprotonating the nucleophile is also explored.

Exploring the role for the third active-site metal ion in DNA polymerase ETA with QM/MM free-energy simulations

2019 Spring National Meeting

The official archive and repository for all ACS Meetings & Expositions abstracts and select posters or presentations.