Figure 6

Structural overlay of PFV RNase H with different RNase H structures and HIV-1 RT. (A – D) Superposition of the lowest energy structure of PFV RNase H with different RNases H. (A) XMRV (PDB: 3V1O, Rmsd: 2.10 Å), the C-α positions of the three positively charged arginine (XMRV) or lysine (PFV) residues in the basic protrusion are highlighted as yellow (XMRV) or blue (PFV) spheres, (B) human (PDB: 2QK9, Rmsd: 2.35 Å), (C) B. halodurans (PDB: 1ZBF, Rmsd: 2.37 Å), and (D) HIV-1 (PDB: 1HRH, Rmsd: 1.90 Å). (E) Orientation of PFV and HIV-1 RNase H in the full length HIV-1 RT. Superposition of the RNase H domains from PFV (blue) (PDB: 2LSN) and HIV-1 (green) (PDB: 1HYS) in the full length HIV-1 RT (gray) (PDB: 1HYS) in complex with a DNA/RNA substrate (Rmsd: 1.85 Å). With regard to (D) the RNase H domains are turned vertically by 180°C. The enlargement shows the region harboring the C-helix (magenta) and the basic loop (orange) of PFV RNase H and the corresponding loop (dark green) derived from the connection domain of the p66 subunit of the heterodimeric HIV-1 p66/p51 RT. The RNA strand of nucleic acid substrate is colored in dark purple, the DNA strand is in light purple.