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

Jin An Feng, Chiquito J. Crasto, Yoshihiro Matsumoto

Research output: Contribution to journalReview article

29 Scopus citations


DNA polymerase β (Pol β) is one of the key enzymes in the base excision repair pathway. The amino-terminal 8 kDa domain of Pol β has an activity for excising a 5'-deoxyribose phosphate (dRP) group from preincised apurine/apyrimidine (AP) sites. Recent biochemical studies have identified the catalytic center of the 8 kDa domain and provided new insight into the mechanism of DNA repair by DNA polymerase β. By incorporating both structural and biochemical data, we present here a reaction mechanism for the 5'-dRP excision activity of the 8 kDa domain. This mechanism focuses on a catalytic groove near the helix-hairpin-helix (HhH) motif of the 8 kDa domain. Our model shows that the dRP group of the AP site can be stabilized in the catalytic groove through extensive interactions with the residues of the groove and be positioned close to the active center, Lys72, which catalyzes a β-elimination reaction by forming a Schiff base with the C1' of the dRP group.

Original languageEnglish
Pages (from-to)9605-9611
Number of pages7
Issue number27
StatePublished - Jul 7 1998


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