Deoxyribose phosphate excision by the N-terminal domain of the polymerase beta: the mechanism revisited

A reaction mechanism for the 5'-RP excision activity of the 8kDa domain, which focuses on a catalytic groove near its helix-hairpin-helix motif is presented. It is proposed that the additional contacts between amino acid residues in the catalytic groove and the dRP group may be responsible for the 8kDa domain recognition of the preincised AP. Results demonstrate that the binding affinity of the 8kDa domain for the nicked AP site is much higher than that for the AP nucleotide without nicking, indicating that the 5'-phosphate was necessary for recognition.