Multimerization of HIV-1 integrase hinges on conserved SH3-docking platforms

Meytal Galilee; Akram Alian

To characterize the peptide binding site(s), we solved the 2.0 Å crystal structure of HIV-1 IN CCD in complex with the peptide (table-1). Except for the Cterminal pair of residues (Ser-Tyr), well-defined electron densities show binding of the peptide molecule to two sites, which we call site-1 and site-2 ( Figure 2A ). By examining available structures of various IN functional multimers (4) (5) (6) (7) (8) we underscore the conservation of these two CCD/CTD docking platforms ( Figure 2B ). Site-1 is at the tetrameic interface and is formed by a CTD from a flanking protomer docking at the carboxyl-terminus of CCD α4 of an inner protomer ( Figure 2B & 1B) . Forming site-2 is the docking of a CTD of another flanking protomer into the amino-terminus of the same α4 ( Figure 2B & 2C). The surface area buried upon peptide binding at site-2 is ~ 100 Å 2 larger than that at site-1 (744 as compared to 650 Å 2 ). Peptide binding at site-2 also involves a higher number of interacting residues at the interface (26 as compared to 17 at site-1). Side chains of two residues of the peptide (Trp1 and Tyr3 at site-1 and Ser10 and Tyr14 at site-2) participate in direct hydrogen bonds with the CCD (to side chains of Glu69 and Asp167 at site-1, and to carbonyl oxygen of Val79 and Ala80 at site-2). Additional hydrogen bonds were directly formed with the backbone of the peptide (one in site-1 and three in site-2), and water molecules mediated additional interactions at each site (two in site-1 and one in site-2) ( Figure 2D ). Interestingly, Ala80 carbonyl oxygen of CCD at site-2, which makes a hydrogen bond with the peptide, also makes a hydrogen bond (2.93 Å) with Lys266 of CTD in the HIV-1 IN functional multimers (discussed below and Figure 4B ). It has been shown that the positive charge at this Lys266 position is crucial for viral replication in which a Lys266Ala or Lys266Glu produced replication defective viruses (23) .