Structure and functional implications of the polymerase active site region in a complex of HIV-1 RT with a double-stranded DNA template-primer and an antibody Fab fragment at 2.8 A resolution.Ding, J., Das, K., Hsiou, Y., Sarafianos, S.G., Clark Jr., A.D., Jacobo-Molina, A., Tantillo, C., Hughes, S.H., Arnold, E.
(1998) J.Mol.Biol. 284: 1095-1111
- PubMed: 9837729
- DOI: 10.1006/jmbi.1998.2208
- Also Cited By: 1SUQ, 1SV5
- PubMed Abstract:
- Crystal Structure of Human Immunodeficiency Virus Type 1 Reverse Transcriptase Complexed with Double-Stranded DNA at 3.0 A Resolution Shows Bent DNA
Jacobo-Molina, A.,Ding, J.,Nanni, R.G.,Clark Junior, A.D.,Lu, X.,Tantillo, C.,Williams, R.L.,Kamer, G.,Ferris, A.L.,Clark, P.,Hizi, A.,Hughes, S.H.,Arnold, E.
(1993) Proc.Natl.Acad.Sci.USA 90: 6320
- Structure of HIV-1 RT/TIBO R 86183 Complex Reveals Similarity in the Binding of Diverse Nonnucleoside Inhibitors
Ding, J.,Das, K.,Moereels, H.,Koymans, L.,Andries, K.,Janssen, P.A.,Hughes, S.H.,Arnold, E.
(1995) Nat.Struct.Mol.Biol. 2: 407
- Structure of HIV-1 Reverse Transcriptase in a Complex with the Non-Nucleoside Inhibitor Alpha-Apa R 95845 at 2.8 A Resolution
Ding, J.,Das, K.,Tantillo, C.,Zhang, W.,Clark Junior, A.D.,Jessen, S.,Lu, X.,Hsiou, Y.,Jacobo-Molina, A.,Andries, K.,Pauwels, R.,Moereels, H.,Koymans, L.,Janssen, P.A.J.,Smith Junior, R.H.,Koepke, M.K.,Michejda, C.J.,Hughes, S.H.,Arnold, E.
(1995) Structure 3: 365
- Structure of HIV-1 Reverse Transcriptase/DNA Complex at 7 A Resolution Showing Active Site Locations
Arnold, E.,Jacobo-Molina, A.,Nanni, R.G.,Williams, R.L.,Lu, X.,Ding, J.,Clark Junior, A.D.,Zhang, A.,Ferris, A.L.,Clark, P.,Hizi, A.,Hughes, S.H.
(1992) Nature 357: 85
- Structure of Unliganded HIV-1 Reverse Transcriptase at 2.7 A Resolution: Implications of Conformational Changes for Polymerization and Inhibition Mechanisms
Hsiou, Y.,Ding, J.,Das, K.,Clark Junior, A.D.,Hughes, S.H.,Arnold, E.
(1996) Structure 4: 853
- Crystallization of Human Immunodeficiency Virus Type 1 Reverse Transcriptase with and without Nucleic Acid Substrates, Inhibitors, and an Antibody Fab Fragment
Clark Junior, A.D.,Jacobo-Molina, A.,Clark, P.,Hughes, S.H.,Arnold, E.
(1995) Methods Enzymol. 262: 171
The structure of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) complexed with a 19-mer/18-mer double-stranded DNA template-primer (dsDNA) and the Fab fragment of monoclonal antibody 28 (Fab28) has been refined at 2.8 A resolu ...
The structure of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) complexed with a 19-mer/18-mer double-stranded DNA template-primer (dsDNA) and the Fab fragment of monoclonal antibody 28 (Fab28) has been refined at 2.8 A resolution. The structures of the polymerase active site and neighboring regions are described in detail and a number of novel insights into mechanisms of polymerase catalysis and drug inhibition are presented. The three catalytically essential amino acid residues (Asp110, Asp185, and Asp186) are located close to the 3' terminus of the primer strand. Observation of a hydrogen bond between the 3'-OH of the primer terminus and the side-chain of Asp185 suggests that the carboxylate of Asp185 could act as a general base in initiating the nucleophilic attack during polymerization. Nearly all of the close protein-DNA interactions involve atoms of the sugar-phosphate backbone of the nucleic acid. However, the phenoxyl side-chain of Tyr183, which is part of the conserved YMDD motif, has hydrogen-bonding interactions with nucleotide bases of the second duplex base-pair and is predicted to have at least one hydrogen bond with all Watson-Crick base-pairs at this position. Comparison of the structure of the active site region in the HIV-1 RT/dsDNA complex with all other HIV-1 RT structures suggests that template-primer binding is accompanied by significant conformational changes of the YMDD motif that may be relevant for mechanisms of both polymerization and inhibition by non-nucleoside inhibitors. Interactions of the "primer grip" (the beta12-beta13 hairpin) with the 3' terminus of the primer strand primarily involve the main-chain atoms of Met230 and Gly231 and the primer terminal phosphate. Alternative positions of the primer grip observed in different HIV-1 RT structures may be related to conformational changes that normally occur during DNA polymerization and translocation. In the vicinity of the polymerase active site, there are a number of aromatic residues that are involved in energetically favorable pi-pi interactions and may be involved in the transitions between different stages of the catalytic process. The protein structural elements primarily responsible for precise positioning of the template-primer (including the primer grip, template grip, and helices alphaH and alphaI of the p66 thumb) can be thought of functioning as a "translocation track" that guides the relative movement of nucleic acid and protein during polymerization.
Center for Advanced Biotechnology and Medicine (CABM) and Rutgers University Chemistry Department, 679 Hoes Lane, Piscataway, NJ, 08854-5638, USA.