X-ray analysis of HIV-1 proteinase at 2.7 Å resolution confirms structural homology among retroviral enzymes

Abstract

Knowledge of the tertiary structure of the proteinase from human immunodeficiency virus HIV-1 is important to the design of inhibitors that might possess antiviral activity and thus be useful in the treatment of AIDS. The conserved Asp-Thr/Ser-Gly sequence in retroviral proteinases suggests that they exist as dimers similar to the ancestor proposed for the pepsins. Although this has been confirmed by X-ray analyses of Rous sarcoma virus and HIV-1 proteinases, these structures have overall folds that are similar to each other only where they are also similar to the pepsins. We now report a further X-ray analysis of a recombinant HIV-1 proteinase at 2.7 A resolution. The polypeptide chain adopts a fold in which the N- and C-terminal strands are organized together in a four-stranded beta-sheet. A helix precedes the single C-terminal strand, as in the Rous sarcoma virus proteinase and also in a synthetic HIV-1 proteinase, in which the cysteines have been replaced by alpha-aminobuytric acid. The structure reported here provides an explanation for the amino acid invariance amongst retroviral proteinases, but differs from that reported earlier in some residues that are candidates for substrate interactions at P3, and in the mode of intramolecular cleavage during processing of the polyprotein.

A procedure for detecting structural domains in proteins

“…Figure 4 shows details of the interface region, from which it is clear that Leu-6 enables the two potentially separate cores to merge. Although the detection of a single hydrophobic core leads to this domain assignment, a single core passing through the interface is in line with earlier analyses of the HIV proteinase, which also noted this characteristic (Lapatto et al, 1989).…”

“…Figure 4 shows details of the interface region, from which it is clear that Leu-6 enables the two potentially separate cores to merge. Although the detection of a single hydrophobic core leads to this domain assignment, a single core passing through the interface is in line with earlier analyses of the HIV proteinase, which also noted this characteristic (Lapatto et al, 1989).A second case where automated assignments yield unanticipated results is in lactate dehydrogenase, where core residues also span the domain interface. As a result, the Rossmann fold domain is merged with the second domain (see Appendix 1).…”

Crystal structure of a complex of HIV‐1 protease with a dihydroxyethylene‐containing inhibitor: Comparisons with molecular modeling

“…5A; Kinemage 2). Although the apoenzyme of HIV-1 PR is strictly symmetric under conditions of the investigation of its crystals reported previously (Lapatto et al, 1989;Navia et al, 1989;Wlodawer et al, 1989), most of the inhibitors studied so far are asymmetric, and thus the two molecules in the protein dimer of the resulting complex are nonequivalent. It was reported that this asymmetry is present even in the complexes of protease with quasisymmetric inhibitors Bone et al, 1991).…”

Conformational instability of the N‐ and C‐terminal lobes of porcine pepsin in neutral and alkaline solutions

“…The substrate binding cleft and the catalytic aspartic residues are located between these lobes (for review, see Davies [1990]). On the other hand, the retroviral aspartic proteases, including the HIV protease, are homodimers with the substrate binding cleft and the active-site aspartic residues equally contributed by the two monomers (Foundling et al, 1989;Lapatto et al, 1989;Miller et al, 1989;Wlodawer et al, 1383Fitzgerald et al, 1990). It has been proposed that the internally homologous lobes of pepsin and other eukaryotic aspartic proteases are evolutionarily derived by gene duplication and fusion, and that a primordial aspartic protease would have a homodimeric structure (Tang et al, 1978).…”