Based on its genomic diversity, the human immunodeficiency virus type 1 (HIV-1) has been classified into three groups, M (major), N (nonmajor), and O (other/outlier) (16
). Group M has been further defined into nine clades (clades A to D, F to H, and J and K) and a number of subclades and circulating recombinant forms (CRFs). HIV-1 protease is one of the major proteins targeted for anti-HIV drug development. The pol
gene, which codes for protease, differs by 10 to 15% between clades (7
), and sequence diversity within HIV-1 clades has been an important area of study in recent years due to its possible role in altering resistance pathways within the protease (1
). In particular, the HIV-1 CRF01_AE protease acquires nelfinavir resistance via an alternative mutational pathway (1
), making the detailed study of non-B proteases strongly warranted.
Structural studies of clade B protease have led to the successful development of a number of protease inhibitors (PIs). However, the majority of HIV-1 infection cases in the world result from non-clade B variants, and there is limited evidence that non-clade B variants respond differently to currently available PIs (3
). Although a large number of clade B protease structures have been solved over the years, to date, very little structural information is available for non-B HIV proteases. The first non-clade B protease structures for clade F were published recently by Sanches et al. (18
), and the crystallization of clade C PI complexes has been reported by Coman et al. (4
). We present here the crystal structure of an inactive HIV-1 CRF01_AE protease variant (D25N) in complex with a decameric peptide corresponding to the p1-p6 cleavage site within the Gag and Gag-Pro-Pol polyproteins. CRF01_AE was one of the first CRFs to be identified and is now the predominant HIV-1 variant in Southeast Asia (12
). The protease was derived from a Japanese patient isolate and has 10 amino acid substitutions (R14K, K20R, E35D, M36I, R41K, P63L, V64I, H69K, L89M, and I93L) compared to that of clade B (Fig. ).
FIG. 1. (A) Amino acid sequence alignment of the CRF01_AE protease with the clade B protease. Positions where sequences differ are indicated in red. (B) CRF01_AE protease in complex with p1-p6 (green). Amino acid changes in monomer A (cyan) are indicated in red, (more ...)