Crystal structure of HIV-1 reverse transcriptase in complex with a polypurine tract RNA:DNA

EMBO Journal

Volumn 20, Issue 6, 2001, Pages 1449-1461

  Sarafianos, Stefan G ^a   Das, Kalyan ^a   Tantillo, Chris ^a   Clark Jr , Arthur D ^a   Ding, Jianping ^a   Whitcomb, Jeannette M ^b   Boyer, Paul L ^c   Hughes, Stephen H ^c   Arnold, Edward ^a  

^a RUTGERS UNIVERSITY   (United States)

^b MONOGRAM BIOSCIENCES   (United States)

^c NATIONAL CANCER INSTITUTE   (United States)

Author keywords

HIV 1; Polypurine tract; Reverse transcriptase; RNA:DNA; RNase H

Indexed keywords

OLIGONUCLEOTIDE; RIBONUCLEASE H; RNA DIRECTED DNA POLYMERASE;

ARTICLE; BASE PAIRING; CATALYSIS; CRYSTAL STRUCTURE; HUMAN IMMUNODEFICIENCY VIRUS 1; POLYPURINE TRACT; PRIORITY JOURNAL; PROTEIN DEGRADATION; RNA STRUCTURE; VIRUS REPLICATION;

CRYSTALLOGRAPHY; DNA PRIMERS; HIV-1; HIV-1 REVERSE TRANSCRIPTASE; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; NUCLEIC ACID HYBRIDIZATION; OLIGODEOXYRIBONUCLEOTIDES; OLIGORIBONUCLEOTIDES; POLY A; POLY DA-DT; POLY T; PROTEIN STRUCTURE, QUATERNARY; PURINES; RIBONUCLEASE H, CALF THYMUS; SUBSTRATE SPECIFICITY; SURFACE PROPERTIES; SYNCHROTRONS; TRANSCRIPTION, GENETIC; VIRUS REPLICATION;

HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1; RNA VIRUSES;

EID: 0035868713     PISSN: 02614189     EISSN: None     Source Type: Journal    
DOI: 10.1093/emboj/20.6.1449     Document Type: Article

References (77)

1. DNA/RNA hybrid secondary structures
2. Structure of a stereoregular phosphorothioate DNA/RNA duplex
3. Characterization of the double stranded RNA dependent RNase activity associated with recombinant retroviruses
4. Nuclease activities of Moloney murine leukemia virus reverse transcriptase. Mutants with altered substrate specificities
5. Mechanism of RNA primer removal by the RNase H activity of avian myeloblastosis virus reverse transcriptase
6. A re-examination of the crystal structure of A-DNA using fiber diffraction data
7. A second origin of DNA plus-strand synthesis is required for optimal HIV replication
8. Crystallization of HIV-1 RT with and without nucleic acid substrates, inhibitors and an antibody Fab fragment
9. The crystal structure of the RNA/DNA hybrid r(GAAGAGAAGC), d(GCTTCTCTTC) shows significant differences to that found in solution
10. Crystal structure of the RNase H domain of HIV-1 RT
11. DNA structure from A to Z
12. ...the tyranny of the lattice ...
13. MPD and DNA bending in crystals and in solution
14. Protein-nucleic acid interactions and DNA conformation in a complex of HIV-1 RT with a double-stranded DNA template-primer
15. Structure and functional implications of the polymerase active site region in a complex of HIV-1 RT with double-stranded DNA and an antibody Fab fragment at 2.8 Å resolution
16. Structure of a DNA:RNA hybrid duplex. Why RNase H does not cleave pure RNA
17. Solution structure of r(gaggacug):d(CAGTCCTC) hybrid: Implications for the initiation of HIV-1 (+)-strand synthesis
18. Use of an oligoribonucleotide containing the polypurine tract sequence as a primer by HIV RT
19. Conferring RNA polymerase activity to a DNA polymerase: A single residue controls substrate selection
20. Effects of mutations in the polymerase domain on the polymerase, RNase H and strand transfer activities of HIV-1 RT
21. Similarities and differences in the RNase H activities of HIV-1 RT and Moloney murine leukemia virus RT
22. Truncating α-helix E' of p66 HIV RT modulates RNase H function and impairs DNA strand transfer
23. Mutating a conserved motif of the HIV-1 RT palm subdomain alters primer utilization
24. HIV-1 RT: Spatial and temporal relationship between the polymerase and RNase H activities
25. HIV-1 RT-associated RNase H cleaves RNA/RNA in arrested complexes: Implications for the mechanism by which RNase H discriminates between RNA/RNA and RNA/DNA
26. Localization of the active site of HIV-1 RT-associated RNase H domain on a DNA template using site-specific generated hydroxyl radicals
27. Comparison of the thermodynamic stabilities and solution conformations of DNA.RNA hybrids containing purine-rich and pyrimidine-rich strands with DNA and RNA duplexes
28. Solution structures of DNA.RNA hybrids with purine-rich and pyrimidine-rich strands: Comparison with the homologous DNA and RNA duplexes
29. Structure of a DNA analog of the primer for HIV-1 RT second strand synthesis
30. Plus-strand DNA synthesis of the yeast retrotransposon Ty1 is initiated at two sites, PPT1 next to the 3′ LTR and PPT2 within the pol gene. PPT1 is sufficient for Ty1 transposition
31. The structure of an RNA/DNA hybrid: A substrate of the RNase activity of HIV- 1 RT
32. Redesignation of the RNase D activity associated with retroviral RT as RNase H*
33. Structure of a covalently trapped catalytic complex of HIV-1 RT: Implications for drug resistance
34. HIV-1 RT. Template binding, processivity, strand displacement synthesis and template switching
35. Mutations in the central polypurine tract of HIV-1 result in delayed replication
36. Crystal structure of RNase H from Thermus thermophilus HB8 refined at 2.8 Å resolution
37. Crystal structure of HIV-1 RT complexed with double-stranded DNA at 3.0 Å resolution shows bent DNA
38. Enzymatic activity and protein stability of E. coli RNase HI
39. Three-dimensional structure of RNase H from E. coli
40. Co-crystal structure of TBP recognizing the minor groove of a TATA element
41. Crystal structure at 3.5 Å resolution of HIV-1 RT complexed with an inhibitor
42. NMR assignments and solution conformation of the DNA.RNA hybrid duplex d(GTGAACTT).r(AAGUUCAC)
43. The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids
44. Crystal and molecular structure of r(CGCGAAUUAGCG): An RNA duplex containing two G(anti).A(anti) base pairs
45. Cleavage of single strand RNA adjacent to RNA-DNA duplex regions by Escherichia coli RNase H1
46. Structure and conformation of helical nucleic acids: Analysis program (SCHNAaP)
47. Specificities involved in the initiation of retroviral plus-strand DNA
48. Processing of X-ray diffraction data collected in oscillation mode
49. Mutations within the primer grip region of HIV-1 RT result in loss of RNase H function
50. New parameters for the refinement of nucleic acid containing structures
51. Sequence and structural determinants required for priming of plus-strand DNA synthesis by the HIV-1 polypurine tract
52. Alanine-scanning mutations in the 'primer grip' of p66 HIV-1 RT result in selective loss of RNA priming activity
53. Residues in the αH and αI helices of the HIV-1 RT thumb subdomain required for the specificity of RNase H-catalyzed removal of the polypurine tract primer
54. The sequence features important for plus strand priming by HIV-1 RT
55. Plus-strand priming by Moloney murine leukemia virus. The sequence features important for cleavage by RNase H
56. Involvement of retrovirus RT-associated RNase H in the initiation of strong-stop (+) DNA synthesis and the generation of the long terminal repeat
57. Nucleosome cores reconstituted from poly(dA-dT) and the octamer of histones
58. Torsion angle dynamics: Reduced variable conformational sampling enhances crystallographic structure refinement
59. Crystal structure of an IHF-DNA complex: A protein-induced DNA U-turn
60. The solution structure of the r(gcg)d(TATACCC):d(GGGTATACGC) Okazaki fragment contains two distinct duplex morphologies connected by a junction
61. Lamivudine (3TC) resistance in HIV-1 RT involves steric hindrance with β-branched amino acids
62. Point mutations in conserved amino acid residues within the C-terminal domain of HIV-1 reverse transcriptase specifically repress RNase H function
63. HIV-1 RT-associated ribonuclease H displays both endonuclease and 3′→5′ exonuclease activity
64. Purification and characterization of an active HIV-1 RNase H domain
65. NMR structure of the chimeric hybrid duplex r(gcaguggc).r(gcca)d(CTGC) comprising the tRNA-DNA junction formed during initiation of HIV-1 reverse transcription
66. Domain structure of the Moloney murine leukemia virus RT: Mutational analysis and separate expression of the DNA polymerase and RNase H activities
67. Reverse transcriptase and the generation of retroviral DNA
68. Mutations within the RNase H domain of HIV-1 RT abolish virus infectivity
69. Enzymatic analysis of two HIV-1 RT mutants with mutations in carboxyl-terminal amino acid residues conserved among retroviral RNase H
70. Molecular structure of r(GCG)d(TATACGC): A DNA-RNA hybrid helix joined to double helical DNA
71. Recognition of the four Watson-Crick base pairs in the DNA minor groove by synthetic ligands
72. Interaction of HIV-1 RNase H with polypurine tract containing RNA-DNA hybrids
73. Crystal structure and conformation of a DNA-RNA hybrid duplex with a polypurine RNA strand: D(TTCTTBr5CTTC)-r(GAAGAAGAA)
74. Structure of RNase H phased at 2 Å resolution by MAD analysis of the selenomethionyl protein
75. The isolated RNase H domain of murine leukemia vires RT. Retention of activity with concomitant loss of specificity
76. 2