AP endonuclease

An AP endonuclease is an enzyme that cuts a strand of DNA on the 5'-side of an AP (apurinic/apyrimidinic) site, as part of DNA base excision repair (BER). Mg 2+ is required for activity of most of them (not for EndoIV of E. coli).

Mechanism
First DNA glycosylases recognize and excise the damaged bases from the sugar phosphate backbone of the DNA. It does this by cleaving the N-glycosydic bond between the target base and deoxyribose. What is left is an abasic site (or AP,apurinic/apyrimidinic). The group of enzymes called AP-endonucleases recognize the abasic site and make an incision at the 5' or 3' phosphodiester of the AP site which generates a nucleotide gap. It is then filled by polymerization (DNA polymerase I) and ligation (DNA ligase) of the new nucleotide to the existing DNA sequence. Endonucleases, in general, are sometimes referred to as "molecular scissors" because they "cut" a strand of DNA.