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. 2006 Mar 15;34(5):1552–1563. doi: 10.1093/nar/gkl059

Figure 8.

Figure 8

The interaction of double-stranded DNA and ExoIII family AP endonuclease. A model for recognition of an AP site by the ExoIII family AP endonuclease. (A) Unbound forms of dsDNA containing an AP site (PDB ID: 1A9I) and human APE1 (PDB ID: 1BIX). The negative charge of the substrate DNA attracts the positively charged region of the enzyme. (B) An AP site recognition complex. When AP endonuclease encounters an AP site, the tryptophan residue in the vicinity of the catalytic site intercalates into an AP site pocket as an AP site ‘recognizer’. This recognition complex would immediately change into a reaction complex. (C) A cleavage reaction complex (PDB ID: 1DEW). To cleave on the 5′ side of the AP site, an abasic ribose ring is flipped out from the duplex interior and accommodated into a catalytic pocket with DNA kinking at the AP site.