Crystal Structure at 3.5 Å Resolution of HIV-1 Reverse Transcriptase Complexed with an Inhibitor

Abstract

A 3.5 angstrom resolution electron density map of the HIV-1 reverse transcriptase heterodimer complexed with nevirapine, a drug with potential for treatment of AIDS, reveals an asymmetric dimer. The polymerase (pol) domain of the 66-kilodalton subunit has a large cleft analogous to that of the Klenow fragment of Escherichia coli DNA polymerase I. However, the 51-kilodalton subunit of identical sequence has no such cleft because the four subdomains of the pol domain occupy completely different relative positions. Two of the four pol subdomains appear to be structurally related to subdomains of the Klenow fragment, including one containing the catalytic site. The subdomain that appears likely to bind the template strand at the pol active site has a different structure in the two polymerases. Duplex A-form RNA-DNA hybrid can be model-built into the cleft that runs between the ribonuclease H and pol active sites. Nevirapine is almost completely buried in a pocket near but not overlapping with the pol active site. Residues whose mutation results in drug resistance have been approximately located.

Prevalence and evolution of drug resistance HIV-1 variants in Henan, China

“…The targets of NRTIs and NNRTIs are different. When converted into the triphosphate forms by phosphorylation, NRTIs compete with natural triphosphate, incorporate into the DNA chain, and lead to the termination of viral DNA synthesis [16]. NNRTIs are a series compounds with multiple structures, which by binding to the hydrophobic region near the active sites of reverse transcriptase inhibit the activity of the enzyme [17].…”

Mutational studies of human immunodeficiency virus type 1 reverse transcriptase : the involvement of residues 183 and 184 in the fidelity of DNA synthesis

“…The three-dimensional structure of wild-type HIV-1 RT complexed with double-stranded DNA provides clues for the positioning Tyr-183 and Met-184 relative to the DNA polymerase active site [22,32,33]. The enzyme possesses a catalytic triad of three aspartic acid residues (at positions 110, 185 and 186) located in the 'palm' subdomain, which serves as the center of the catalytic site.…”

Cloning, expression, and purification of a catalytic fragment of moloney murine leukemia virus reverse transcriptase: Crystallization of nucleic acid complexes

“…Numerous crystal structures have been reported for HIV-I RT uncomplexed and complexed with a number of non-nucleoside inhibitors (Kohlstaedt et al, 1992;Jacobo-Molina et al, 1993;Jager et al, 1994;Unge et al, 1994;Ding et al, 1995aDing et al, , 1995bEsnouf et al, 1995;Ren et al, 1995;Rodgers et al, 1995;Hsiou, 1996). At present, one RT-nucleic acid complex has been reported at 3.0 8, resolution for HIV-I RT (Jacobo-Molina et al, 1993), which includes HIV-I RT, Fab, and an 18/19-mer oligonucleotide.…”