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 e xcision of deoxyribose 5-phosphate from DNA at an interaction interfac e 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 dis plays a low pK(a) (5.7) due to proximity to Lys-35. In a proposed mech anism, Lys-68 protonates the hemiacetal O4' and His-34 stabilizes the protonated aldehyde-type species. possibly accepting the proton. In on e of two possible mechanisms, Lys-68 or Lys-72 forms a Schiffs base wi th 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 phosphomon oester leaving group in either case. (C) 1997 Elsevier Science Ltd.