Characterization of a catalytically slow AP lyase activity in DNA polymerase gamma and other family A DNA polymerases

Mitochondrial DNA polymerase gamma (pol gamma) is active in base excision r epair of AP (apurinic/apyrimidinic) sites in DNA. Usually AP site repair in volves cleavage on the 5' side of the deoxyribose phosphate by AP endonucle ase. Previous experiments suggested that DNA pol gamma acts to catalyze the removal of a S'-deoxyribose phosphate (dRP) group in addition to playing t he conventional role of a DNA polymerase. We confirm that DNA pol gamma is an active dRP lyase and show that other members of the family A of DNA poly merases including Escherichia coli DNA pol I also possess this activity. Th e dRP lyase reaction proceeds by formation of a covalent enzyme-DNA interme diate that is converted to an enzyme-dRP intermediate following elimination of the DNA. Both intermediates can be cross-linked with NaBH4. For both DN A pol gamma and the Klenow fragment of pol I, the enzyme-dRP intermediate i s extremely stable. This limits the overall catalytic rate of the dRP lyase , so that family A DNA polymerases, unlike pol beta, may only be able to ac t as dRP lyases in repair of AP sites when they occur at low frequency in D NA.