Structural template for (a) retroviral proteases compared to that for (b) the aspartic protease family. In the symmetrical retroviral dimer (a), loops A1 and A2 are shown in yellow in each monomer, shown as stereo pairs. In the single-chain aspartic protease (b), the corresponding loops are labeled A1 and A2 in the left-side domain and A3 and A4 in the right-side domain. Likewise, loops B1 and B2 in (a) are shown in blue in each monomer of the retroviral dimer, and the analogous loops in blue are labeled B1, B2, B3, and B4 in the single-chain enzymes. Loops B1 in the retroviral enzymes and B1 and B3 in the single-chain enzymes contain the catalytic residues. Helical segments C1 and C2 (red) in (a) are mirrored by segments C1-C4 in (b). Finally, loop D1 in the retroviral monomers provides a double flap structure in (a), whereas the 'half loops' D2' provide the four strands that form a β sheet at the bottom of the dimer. In (b), loop D1 provides the flap on one side only, whereas D3 on the other side is pointing outward. Loops D2 and D4 provide the center of the β sheet at the bottom of these enzymes. (c) Movement of flaps in the retroviral protease during ligand binding. This stereo pair shows the movement that occurs upon binding of a ligand to the active site of HIV-1 protease. The 'empty' enzyme structure is shown as a green ribbon and the enzyme following binding is shown as an orange ribbon. The flap residues move downward by approximately 8 Å.
Dunn et al. Genome Biology 2002 3:reviews3006.1 doi:10.1186/gb-2002-3-4-reviews3006