Characterization of a DNA binding domain in the C-terminus of HIV-1 integrase by deletion mutagenesis

The integrase (IN) protein of human immunodeficiency virus type 1 (HIV-1) catalyzes site-specific cleavage of 2 bases from the viral long terminal repeat (LTR) sequence yet it binds DNA with little DNA sequence specificity. We have previously demonstrated that the C-terminal half of IN (amino acids 154–288) possesses a DNA binding domain. In order to further characterize this region, a series of clones expressing truncated forms of IN as N-terminal fusion proteins in E.coli were constructed and analyzed by Southwestern blotting. Proteins containing amino acids 1 – 263, 1 – 248 and 170 – 288 retained the ability to bind DNA, whereas a protein containing amino acids 1 – 180 showed no detectable DNA binding. This defines a DNA binding domain contained within amino acids 180 – 248. This region contains an arrangement of 9 lysine and arginine residues each separated by 2 – 4 amino acids (KxxxKxxxKxxxxRxxxRxxRxxxxKxxxKxxxK), spanning amino acids 211 – 244, which is conserved in all HIV-1 isolates. A clone expressing full-length IN with a C-terminal fusion of 16 amino acids was able to bind DNA comparably to a cloned protein with a free C-terminus, and an IN-specific monoclonal antibody which recognizes an epitope contained within amino acids 264 – 279 was unable to block DNA binding, supporting the evidence that a region necessary for binding lies upstream of amino acid 264.