IN belongs, both mechanistically and structurally, to the superfamily of polynucleotidyl transferases 10 and is composed of 288 amino acids that form the 32 kDa protein. Retroviruses encode their enzymes (protease, reverse transcriptase and integrase) with the POL gene with the 3´end encoding for IN.
IN is composed of 3 structurally independent, functional domains (see figure 1).:
1. The N-terminal domain (NTD) encompasses amino acids 1–50 and contains two histidine residues (His12 and His16) and two cysteine residues (Cys40 and Cys43), all of which are absolutely conserved and form a HHCC zinc-finger motif. Single mutations of any of these four residues reduce IN enzymatic activity. The HHCC zinc-finger motif chelates one zinc atom per IN monomer. The NTD is required for higher order multimer formation which appears to be its primary role. The multimerization requires zinc atom that stabilizes the fold.
2. The catalytic core domain (CCD), which encompasses amino acids 51- 212, contains the active site of IN but it can't catalyze integration in the absence of NTD and CTD (the C-terminal domain). CCD contains three absolutely conserved negatively charged amino acids; D64, D116 and E152. These amino acids form the DDE motif that coordinate divalent metal ions (Mg or Mn). These metal ions are essential for the catalysis of integration. CCD has a mixed β and α structure with five β-sheets and six α helices that are linked by flexible loops. The flexible loops allow conformational changes that are required for 3´processing of the viral DNA and strand transfer (STF) reactions which are two key steps of the integration reaction. CCD is essential for these steps and substitution of any of the residues in the DDE motif dramatically inhibits the activity of IN.
3. The C-terminal domain (CTD), which encompasses amino acids 213–288, binds DNA nonspecifically and its interaction with NTD and CCD is required for IN 3´-processing and strand-transfer activities. CTD is the least conserved of the three domains.
IN acts as a multimer and dimerization is required for the 3´-processing step, with tetrameric IN catalyzing the strand-transfer reaction.