Figure 3

Mapping of the nucleic acid-binding sites within the HIV-1 integrase (IN) catalytic site. Panel A: Structural superimposition between the crystal structures of HIV-1 IN catalytic core domain (PDB accession code: 1QS4; in yellow) and Tn5 transposase in complex with donor DNA (PDB: 1MM8; protein in green; DNA: in violet). The catalytic triads of IN and Tn5 transposase are shown in red and black, respectively. Panel B: transposition of Tn5 donor DNA (carbon backbone in cyan) to a crystal structure (PDB:1QS4) of HIV-1 IN in complex with 1-(5-chloroindol-3-yl)-3-(tetrazoyl)-1,3-propandione-ene (5CITEP; carbon backbone in yellow). HIV-1 DNA-interacting residues Q148 and K159 are shown as sticks. Hydrogens have been removed for better clarity. The metal ion crystallized with IN is shown in magenta. Panel C: Structural superimposition between the crystal structures of HIV-1 IN catalytic core domain (in yellow), and Bacillus halodurans RNAse H in complex with an RNA/DNA hybrid (PDB: 1ZBL; protein: in cyan; nucleic acid: in smudge green). The catalytic triads of IN and RNAse H are shown in red and black, respectively. Panel D: Transposition of B. halodurans RNA/DNA hybrid (carbon backbone in green) to HIV-1 IN. Putative DNA-interacting residues, K136 and K159 (from right to left) are shown as sticks. A phosphate (in yellow) co crystallized with IN (PDB: 2B4J) had been added by superimposing the 2B4J structure to the IN structure (PDB: 1QS4) used as reference structure in this part of the present study.