Insights into the mechanism of the beta-elimination catalyzed by the N-terminal domain of DNA polymerase beta

The N-terminal domain of DNA polymerase beta carries an activity for excision of deoxyribose 5-phosphate from DNA at an interaction interface that includes a helix-hairpin-helix motif containing Lys-68 and Lys-72 and an adjacent Omega loop containing His-34 and Lys-35. His-34 displays a low pK(a) (5.7) due to proximity to Lys-35. In a proposed mechanism, Lys-68 protonates the hemiacetal O4' and His-34 stabilizes the protonated aldehyde-type species. possibly accepting the proton. In one of two possible mechanisms, Lys-68 or Lys-72 forms a Schiffs base with the substrate. His-34 can function in C2' deprotonation for the Lys-68 Schiff's base intermediate, while the proton would be transferred to water for the Lys-72 Schiffs base. Lys-35 stabilizes the phosphomonoester leaving group in either case. (C) 1997 Elsevier Science Ltd.