Structures of HIV-1 RT-RNA/DNA ternary complexes with dATP and nevirapine reveal conformational flexibility of RNA/DNA: insights into requirements for RNase H cleavage.Das, K., Martinez, S.E., Bandwar, R.P., Arnold, E.
(2014) Nucleic Acids Res. 42: 8125-8137
- PubMed: 24880687
- DOI: 10.1093/nar/gku487
- Primary Citation of Related Structures:  4PQU, 4PUO, 4Q0B
- Also Cited By: 4R5P
- PubMed Abstract:
- Structural basis for the role of the K65R mutation in HIV-1 reverse transcriptase polymerization, excision antagonism, and tenofovir resistance.
Das, K.,Bandwar, R.P.,White, K.L.,Feng, J.Y.,Sarafianos, S.G.,Tuske, S.,Tu, X.,Clark, A.D.,Boyer, P.L.,Hou, X.,Gaffney, B.L.,Jones, R.A.,Miller, M.D.,Hughes, S.H.,Arnold, E.
(2009) J.Biol.Chem. 284: 35092
- HIV-1 reverse transcriptase complex with DNA and nevirapine reveals non-nucleoside inhibition mechanism.
Das, K.,Martinez, S.E.,Bauman, J.D.,Arnold, E.
(2012) Nat.Struct.Mol.Biol. 19: 253
- High-resolution structures of HIV-1 reverse transcriptase/TMC278 complexes: strategic flexibility explains potency against resistance mutations.
Das, K.,Bauman, J.D.,Clark, A.D.,Frenkel, Y.V.,Lewi, P.J.,Shatkin, A.J.,Hughes, S.H.,Arnold, E.
(2008) Proc.Natl.Acad.Sci.USA 105: 1466
- Crystal structure of HIV-1 reverse transcriptase in complex with a polypurine tract RNA:DNA.
Sarafianos, S.G.,Das, K.,Tantillo, C.,Clark, A.D.,Ding, J.,Whitcomb, J.M.,Boyer, P.L.,Hughes, S.H.,Arnold, E.
(2001) Embo J. 20: 1449
- Structural basis of HIV-1 resistance to AZT by excision.
Tu, X.,Das, K.,Han, Q.,Bauman, J.D.,Clark, A.D.,Hou, X.,Frenkel, Y.V.,Gaffney, B.L.,Jones, R.A.,Boyer, P.L.,Hughes, S.H.,Sarafianos, S.G.,Arnold, E.
(2010) Nat.Struct.Mol.Biol. 17: 1202
In synthesizing a double-stranded DNA from viral RNA, HIV-1 reverse transcriptase (RT) generates an RNA/DNA intermediate. RT also degrades the RNA strand and synthesizes the second DNA strand. The RNase H active site of RT functions as a nuclease to ...
In synthesizing a double-stranded DNA from viral RNA, HIV-1 reverse transcriptase (RT) generates an RNA/DNA intermediate. RT also degrades the RNA strand and synthesizes the second DNA strand. The RNase H active site of RT functions as a nuclease to cleave the RNA strand; however, the structural basis for endonucleolytic cleavage of the RNA strand remains elusive. Here we report crystal structures of RT-RNA/DNA-dATP and RT-RNA/DNA-nevirapine (NVP) ternary complexes at 2.5 and 2.9 Å resolution, respectively. The polymerase region of RT-RNA/DNA-dATP complex resembles DNA/DNA ternary complexes apart from additional interactions of 2'-OH groups of the RNA strand. The conformation and binding of RNA/DNA deviates significantly after the seventh nucleotide versus a DNA/DNA substrate. Binding of NVP slides the RNA/DNA non-uniformly over RT, and the RNA strand moves closer to the RNase H active site. Two additional structures, one containing a gapped RNA and another a bulged RNA, reveal that conformational changes of an RNA/DNA and increased interactions with the RNase H domain, including the interaction of a 2'-OH with N474, help to position the RNA nearer to the active site. The structures and existing biochemical data suggest a nucleic acid conformation-induced mechanism for guiding cleavage of the RNA strand.
Center for Advanced Biotechnology and Medicine, Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA.