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Complexes of HIV-1 RT, NNRTI and RNA/DNA hybrid reveal a structure compatible with RNA degradation.

Lapkouski M, Tian L, Miller JT, Le Grice SF, Yang W - Nat. Struct. Mol. Biol. (2013)

Bottom Line: The enzyme structure also differs from all previous RT-DNA complexes.These observations indicate that an RT-nucleic acid complex may adopt two structural states, one competent for DNA polymerization and the other for RNA degradation.RT mutations that confer drug resistance but are distant from the inhibitor-binding sites often map to the unique RT-hybrid interface that undergoes conformational changes between two catalytic states.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA.

ABSTRACT
Hundreds of structures of type 1 human immunodeficiency virus (HIV-1) reverse transcriptase (RT) have been determined, but only one contains an RNA/DNA hybrid. Here we report three structures of HIV-1 RT complexed with a non-nucleotide RT inhibitor (NNRTI) and an RNA/DNA hybrid. In the presence of an NNRTI, the RNA/DNA structure differs from all prior nucleic acid-RT structures including the RNA/DNA hybrid. The enzyme structure also differs from all previous RT-DNA complexes. Thus, the hybrid has ready access to the RNase-H active site. These observations indicate that an RT-nucleic acid complex may adopt two structural states, one competent for DNA polymerization and the other for RNA degradation. RT mutations that confer drug resistance but are distant from the inhibitor-binding sites often map to the unique RT-hybrid interface that undergoes conformational changes between two catalytic states.

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Related in: MedlinePlus

Structural comparison of WT22Efv and RT–DNA–Nvp (3V81)29. (a) Pairwise comparisons of RT in the 3V81 structure with RT complexed with Nevirapine (3QIP14), an RT ternary complex (1RTD26), and our WT22Efv (4B3O). The Cα-Cα vector maps are shown after superposition of p51 subunits and colored as in Fig. 2. Domain movements of 3V81 relative to others are indicated by black arrowheads. (b) Comparison of the entire RT–DNA–Nvp complex (3V81) with an RT–DNA–dNTP ternary complex (3KK227). Upon superposition of the nucleic acids, both of which are crosslinked to p66 via Q258C, not only are the DNAs highly similar, but also are the RT proteins except for the p66 fingers and palm subdomains as indicated by the grey arrowhead. The protein and DNA are color coded as indicated, and the NNRTI (Nvp) is shown as purple spheres.
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Figure 3: Structural comparison of WT22Efv and RT–DNA–Nvp (3V81)29. (a) Pairwise comparisons of RT in the 3V81 structure with RT complexed with Nevirapine (3QIP14), an RT ternary complex (1RTD26), and our WT22Efv (4B3O). The Cα-Cα vector maps are shown after superposition of p51 subunits and colored as in Fig. 2. Domain movements of 3V81 relative to others are indicated by black arrowheads. (b) Comparison of the entire RT–DNA–Nvp complex (3V81) with an RT–DNA–dNTP ternary complex (3KK227). Upon superposition of the nucleic acids, both of which are crosslinked to p66 via Q258C, not only are the DNAs highly similar, but also are the RT proteins except for the p66 fingers and palm subdomains as indicated by the grey arrowhead. The protein and DNA are color coded as indicated, and the NNRTI (Nvp) is shown as purple spheres.

Mentions: Structural comparison with the recently reported RT–DNA–NNRTI complex29 (PDB: 3V81) turned out to be not as revealing. Perhaps due to the crosslinking between RT and DNA and the procedure of soaking NNRTI into a preformed RT–DNA co-crystal, the protein structure of 3V81 is more similar to that of the RT–DNA–dNTP ternary complex than to that in either the RT–NNRTI complex or our WT22Efv structure (Fig. 3a).


Complexes of HIV-1 RT, NNRTI and RNA/DNA hybrid reveal a structure compatible with RNA degradation.

Lapkouski M, Tian L, Miller JT, Le Grice SF, Yang W - Nat. Struct. Mol. Biol. (2013)

Structural comparison of WT22Efv and RT–DNA–Nvp (3V81)29. (a) Pairwise comparisons of RT in the 3V81 structure with RT complexed with Nevirapine (3QIP14), an RT ternary complex (1RTD26), and our WT22Efv (4B3O). The Cα-Cα vector maps are shown after superposition of p51 subunits and colored as in Fig. 2. Domain movements of 3V81 relative to others are indicated by black arrowheads. (b) Comparison of the entire RT–DNA–Nvp complex (3V81) with an RT–DNA–dNTP ternary complex (3KK227). Upon superposition of the nucleic acids, both of which are crosslinked to p66 via Q258C, not only are the DNAs highly similar, but also are the RT proteins except for the p66 fingers and palm subdomains as indicated by the grey arrowhead. The protein and DNA are color coded as indicated, and the NNRTI (Nvp) is shown as purple spheres.
© Copyright Policy
Related In: Results  -  Collection

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Figure 3: Structural comparison of WT22Efv and RT–DNA–Nvp (3V81)29. (a) Pairwise comparisons of RT in the 3V81 structure with RT complexed with Nevirapine (3QIP14), an RT ternary complex (1RTD26), and our WT22Efv (4B3O). The Cα-Cα vector maps are shown after superposition of p51 subunits and colored as in Fig. 2. Domain movements of 3V81 relative to others are indicated by black arrowheads. (b) Comparison of the entire RT–DNA–Nvp complex (3V81) with an RT–DNA–dNTP ternary complex (3KK227). Upon superposition of the nucleic acids, both of which are crosslinked to p66 via Q258C, not only are the DNAs highly similar, but also are the RT proteins except for the p66 fingers and palm subdomains as indicated by the grey arrowhead. The protein and DNA are color coded as indicated, and the NNRTI (Nvp) is shown as purple spheres.
Mentions: Structural comparison with the recently reported RT–DNA–NNRTI complex29 (PDB: 3V81) turned out to be not as revealing. Perhaps due to the crosslinking between RT and DNA and the procedure of soaking NNRTI into a preformed RT–DNA co-crystal, the protein structure of 3V81 is more similar to that of the RT–DNA–dNTP ternary complex than to that in either the RT–NNRTI complex or our WT22Efv structure (Fig. 3a).

Bottom Line: The enzyme structure also differs from all previous RT-DNA complexes.These observations indicate that an RT-nucleic acid complex may adopt two structural states, one competent for DNA polymerization and the other for RNA degradation.RT mutations that confer drug resistance but are distant from the inhibitor-binding sites often map to the unique RT-hybrid interface that undergoes conformational changes between two catalytic states.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA.

ABSTRACT
Hundreds of structures of type 1 human immunodeficiency virus (HIV-1) reverse transcriptase (RT) have been determined, but only one contains an RNA/DNA hybrid. Here we report three structures of HIV-1 RT complexed with a non-nucleotide RT inhibitor (NNRTI) and an RNA/DNA hybrid. In the presence of an NNRTI, the RNA/DNA structure differs from all prior nucleic acid-RT structures including the RNA/DNA hybrid. The enzyme structure also differs from all previous RT-DNA complexes. Thus, the hybrid has ready access to the RNase-H active site. These observations indicate that an RT-nucleic acid complex may adopt two structural states, one competent for DNA polymerization and the other for RNA degradation. RT mutations that confer drug resistance but are distant from the inhibitor-binding sites often map to the unique RT-hybrid interface that undergoes conformational changes between two catalytic states.

Show MeSH
Related in: MedlinePlus