(A) Base excision repair. This pathway starts with a DNA glycosylase. Here the enzyme uracil DNA glycosylase removes an accidentally deaminated cytosine in DNA. After the action of this glycosylase (or another DNA glycosylase that recognizes a different kind of damage), the sugar phosphate with the missing base is cut out by the sequential action of AP endonuclease and a phosphodiesterase. (These same enzymes begin the repair of depurinated sites directly.) The gap of a single nucleotide is then filled by DNA polymerase and DNA ligase. The net result is that the U that was created by accidental deamination is restored to a C. The AP endonuclease derives its name from the fact that it recognizes any site in the DNA helix that contains a deoxyribose sugar with a missing base; such sites can arise either by the loss of a purine (apurinic sites) or by the loss of a pyrimidine (apyrimidinic sites). (B) Nucleotide excision repair. After a multienzyme complex has recognized a bulky lesion such as a pyrimidine dimer (see Figure 5-48), one cut is made on each side of the lesion, and an associated DNA helicase then removes the entire portion of the damaged strand. The multienzyme complex in bacteria leaves the gap of 12 nucleotides shown; the gap produced in human DNA is more than twice this size. The nucleotide excision repair machinery can recognize and repair many different types of DNA damage.