Structure of the unbound form of HIV-1 subtype A protease: comparison with unbound forms of proteases from other HIV subtypes

Abstract

The crystal structure of the unbound form of HIV-1 subtype A protease (PR) has been determined to 1.7 A resolution and refined as a homodimer in the hexagonal space group P6(1) to an R(cryst) of 20.5%. The structure is similar in overall shape and fold to the previously determined subtype B, C and F PRs. The major differences lie in the conformation of the flap region. The flaps in the crystal structures of the unbound subtype B and C PRs, which were crystallized in tetragonal space groups, are either semi-open or wide open. In the present structure of subtype A PR the flaps are found in the closed position, a conformation that would be more anticipated in the structure of HIV protease complexed with an inhibitor. The amino-acid differences between the subtypes and their respective crystal space groups are discussed in terms of the differences in the flap conformations.

Figure 1

Ribbon diagram of the homodimer of the HIV-1 subtype A PR structure. Catalytic aspartic acids are shown as sticks. Blue spheres indicate amino acids that vary between subtype A PR and subtype B PR (numbers refer to amino-acid positions). Features of the PR structure are as labeled. This figure was generated using PyMOL (DeLano, 2002 ▶).

Figure 2

Stereo 2|F _o| − |F _c| OMIT map centered on the active site of HIV-1 subtype A PR. The map is contoured at 1.3σ and includes a 4 Å radius buffer around flap residues and water positions. All atoms of the flap (residues 46–55 and 46′–55′), the active-site aspartates Asp25 and Asp25′ and two waters (depicted as red spheres) were omitted from the calculation of the map.

Figure 3

Stereo superposition of unbound PR homodimers. (a) Complete PR homodimers, (b) close-up of the flap regions shown in (a) viewed down the twofold axis. Color code: green, dimers in tetragonal space groups with semi-open flaps; red, dimers in tetragonal space groups with wide-open flaps; blue, dimers in the hexagonal space group P6₁ with closed flaps. Note that the tips of the flaps invert between the semi-open and closed conformations. PDB coordinates were as used in Fig. 5 ▶. This figure was generated using PyMOL (DeLano, 2002 ▶).

Figure 4

Sequences of HIV-1 PR structures.

Figure 5

Pairwise r.m.s.d.s of C^α—C^α distances (Å).

Figure 6

Stereo figure showing the crystal contacts of HIV-1 subtypes. (a) Wide open (PDB code 2pc0; Heaslet et al., 2007 ▶), (b) semi-open (PDB code 2hb2; Heaslet et al., 2007 ▶) and (c) closed (PDB code 3ixo). PDB coordinates were as used in Fig. 7 ▶. Colored spheres represent the amino acids involved in contacts. A contact is calculated from the sum of atomic radii. This figure was generated using PyMOL (DeLano, 2002 ▶).

Figure 7

Packing contacts (colored cells represent crystal-packing contacts).