Fig. 7: The induced space-filling model for APE1 in processing various duplex DNAs. | Nature Communications

Fig. 7: The induced space-filling model for APE1 in processing various duplex DNAs.

From: APE1 distinguishes DNA substrates in exonucleolytic cleavage by induced space-filling

Fig. 7

Based on the positions of cleavage sites in dsDNA substrates, they are classified into two groups, a terminal binding and b middle binding. c The close-up view of the product pocket and AP site-containing dsDNA (PDB entry: 5DFI). Only the AP site (orange), upstream and downstream phosphoryl group, and a downstream nucleotide (black) of the substrate dsDNA is shown. e The close-up view of the product pocket and the 1-nt mismatched nicked dsDNA (PDB entry: 5WN5). Only the leaving group (blue) and a downstream nucleotide (black) of the substrate dsDNA is shown. d Superposition of the leaving group in 1-nt mismatched nicked dsDNA (blue) and the AP site (orange), upstream and downstream phosphoryl group, and a downstream nucleotide (black) in the AP site-containing dsDNA. The base region of the leaving group is overlapped to the downstream phosphoryl group near the AP site. f EMSA measurements of wild-type and double mutant (R176A/M269A) mAPE1 binding with matched 1-nt gapped dsDNA. The band of protein–DNA complex with a lower molecular weight is not observed in the binding of mAPE1 double mutant. f Source data are provided as a Source Data file.

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