Figure 6.

Structural basis of integrase 3′ processing and strand transfer activities. (A) Structure of the manganese-bound SSC (pdb code 4E7I). The DNA and integrase backbones are colored magenta and green, respectively; red and orange sticks are oxygen and phosphorus atoms, respectively. Gray and red spheres are manganese ions and water molecules, respectively, with the nucleophilic water labeled W_Nuc. Black dashed lines indicate metal ion interactions; the red dashed line connects the nucleophile and scissile phosphodiester bond. (B) Overlay of metal ion-bound TCC (pdb code 4E7K; DNA and protein in green) and STC (pdb code 4E7L; elements painted in cyan) structures. Both sets of metal ions are shown; the 3.8 Å spacing between ions in the TCC contracts to 3.2 Å in the STC (85). The curved black line indicates the displacement of the viral-target DNA phosphodiester bond after strand transfer relative to the scissile bond in target DNA. Other labeling is the same as in panel A.