AP Endonucleases

Cytosine deamination (G ) Spontaneous/ chemicals Uracil glycosylase AP endonuclease DNA polymerase DNA ligase... 

This enzyme (also known as DNA-(apurmic or apyrimid-inic site) lyase, AP endonuclease class I, E. coli endonuclease III, Phage-T4 UV endonuclease, and Micrococcus luteus UV endonuclease) catalyzes the cleavage of the phosphodiester bond in a lyase-type reaction, not hydro-... 

Ter (Replication termination) xthA AP endonuclease holE DNA polymerase III subunit... 

DNA glycosylases 971 AP site 971 AP endonucleases 972 DNA photolyases 974 recombinational DNA repair 976 error-prone translesion DNA synthesis 976 SOS response 976 homologous genetic recombination 978... 

Pyrimidine dimers and other forms of DNA damage can be removed by a general excision repair mechanism. The first reaction in this form of repair involves forming nicks about the damaged region of the DNA. In (a) we see the mode of incision of UV-irradiated DNA by the pyrimidine-dimer-specific glycosylase and AP endonuclease... 

Nucleotide excision and base removal followed by the action of apurinic-apyrimidine endonucleases (AP endonucleases) are the two types of excision repair that currently are thought to occur. A number of nucleotides are excised from the damaged DNA strand. After excision, the correct complementary bases are replaced by polymerase action, with the intact strand as template. Finally, the new strand is attached covalently to the adjacent undamaged old strand by the enzyme DNA ligase. 

Figure 22.2. Enzymatic and chemical cleavage of DNA strand at the AP site. AP sites are chemically unstable, undergoing spontaneous P-elimination leading to DNA strand break at the 3 side of the AP site. Only the AP endonuclease generates a 3 terminus at the strand break that can be used by a DNA polymerase for DNA synthesis. The p-elimination reaction can also be catalyzed by AP lyases. The fate of the baseless deoxyribose is highlighted.

Figure 22.9. The 3 end of DNA strand breaks induced by ionization radiation often contains a phosphate or phosphoglycolate group. These groups can be removed by an AP endonuclease.

The removal of an altered base by the glycosylase results in the formation of an abasic site (AP site) (sometimes also referred to as an apurinic or apyrimidinic site). The AP site is acted upon by an AP endonuclease that makes an incision in the damaged strand by hydrolyzing the phosphodiester bond 5 to the AP site (Figure 23.5). Alternatively, some glycosylases have an associated lyase activity that incises... 

E. coli possesses a second AP endonuclease, endonuclease IV. It is encoded by the nfo gene, and it is also referred to as Nfo. Nfo only comprises about 10% of the AP endonuclease activity in the cell. It acts in the same way that XthA does and... 

Figure 23.7. Structure of an AP site (center) and structures produced by 5 AP endonuclease activity (left) or lyase activity (right). These are formed in double-strand DNA, but only one strand is represented in the figure. 5 AP-endonuclease activity results in the formation of a 5 -deoxyribose-phosphate end (5 -dRP), which must be subsequently processed by a dRPase (see text). Lyase activity results in the formation of 3 -unsaturated aldehydic a, P, 4-hydroxy-2-pentenal end, which must be subsequently acted upon by a 5 AP endonuclease. (Reproduced with permission from Boiteux, S., and Guillet, M. Abasic sites in DNA repair and biological consequences in Saccharomyces cerevisiae. DNA Repair 3,1-12, 2004.)...

Fung H, Kow YW, Van Houten B, et al. 1998. Asbestos increases mammalian AP-endonuclease gene expression, protein levels, and enzyme activity in mesothelial cells. Cancer Res 58 189-194. 

Finally, in addition to nucleotide excision repair and base excision repair, an alternative repair pathway exists to remove PyroPyr and (6 ) photoproducts in some organisms, including Schizosaccharomyces pombe. In this alternative pathway, an enzyme called UV dimer endonuclease cleaves DNA immediately 5 to the damaged lesion. The damage is then removed by a 5 to 3 exonuclease (26, 27). Additionally, AP endonucleases, like Nfo in E. coli and APEl in humans, have the ability to incise immediately 5 to nonbulky lesions caused by oxidative damage and initiate excision of the lesion by a 5 to 3 exonuclease (28). 

Figure 5 Base excision repair in mammalian cells. In base excision repair, the damaged nucleotide is removed in a two-step process. A glycosylase cleaves the glycosidic bond of the damaged base, releasing it, and then AP lyase and AP endonuclease cleave the phosphodlester bonds on either side of the abasic site, which releases the deoxyribose.

The catalytic action of these glycosylases results in formation of a nucleotide that has lost its base. The result is an apyrimidinic site (AF site). The AP site consists only of a nesidueofdwxyribose-phosphate. What happens next in the DNArepair pathway The deoxyribosc-phosphate is subsequently snipped out of the strand of DNA by an enzyme called etidottuclease. The full name for the enzyme is AP endonuclease (APE). The action of AP endonuclease results in a small gap in the double-stranded DMA helix, which is then filled in by DNA polymerase to yield repaired DNA. 

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