Table 1.
Amino-acid motifs used to align HIV-1 protease and reverse transcriptase sequences
| Motifa | Positions | Functionb | % Conserved in HIV-1c | % Conserved in HIV-2 |
|---|---|---|---|---|
| Protease | ||||
| PQ(I|V)T | 1-4 | Dimer interface | >99 | 0 |
| DTG | 25-27 | Active site | 100 | 100 |
| GCTLN | 94-98 | Dimer interface | >99 | 0 |
| RT | ||||
| PISP | 1-4 | Part of protease/RT cleavage site | >99 | 0 |
| QWPL(T|S) | 23-27 | β1-αA turn | >99 | 100 |
| D(V|I)GDA | 110-114 | Active site | >99 | 100 |
| QY(.)DD(L|I) | 182-187 | Active site | >99 | 100 |
| WMG(Y|F)) | 229-232 | β12-α13 turn | >99 | 100 |
a
I|V, “I” means that either I or V is acceptable at that position; (.), any amino acid is acceptable at the position.
b
DTG constitutes the active site of the protease. The three catalytic aspartates (D) at codons 110, 185 and 186 constitute the active site of the RT.
c
Each motif not only is highly conserved among HIV-1 RT and protease, but also is not found at any other position within these two genes.