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Science 5 April 1991:
Vol. 252. no. 5002, pp. 88 - 95
DOI: 10.1126/science.1707186
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Articles

Science, Vol 252, Issue 5002, 88-95
Copyright © 1991 by American Association for the Advancement of Science

articles

Crystal structure of the ribonuclease H domain of HIV-1 reverse transcriptase

JF Davies 2nd, Z Hostomska, Z Hostomsky, Jordan SR, and DA Matthews

Agouron Pharmaceuticals, Inc., La Jolla, CA 92037.

The crystal structure of the ribonuclease (RNase) H domain of HIV-1 reverse transcriptase (RT) has been determined at a resolution of 2.4 A and refined to a crystallographic R factor of 0.20. The protein folds into a five-stranded mixed beta sheet flanked by an asymmetric distribution of four alpha helices. Two divalent metal cations bind in the active site surrounded by a cluster of four conserved acidic amino acid residues. The overall structure is similar in most respects to the RNase H from Escherichia coli. Structural features characteristic of the retroviral protein suggest how it may interface with the DNA polymerase domain of p66 in the mature RT heterodimer. These features also offer insights into why the isolated RNase H domain is catalytically inactive but when combined in vitro with the isolated p51 domain of RT RNase H activity can be reconstituted. Surprisingly, the peptide bond cleaved by HIV-1 protease near the polymerase-RNase H junction of p66 is completely inaccessible to solvent in the structure reported here. This suggests that the homodimeric p66-p66 precursor of mature RT is asymmetric with one of the two RNase H domains at least partially unfolded.


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J. Biol. Chem. 272, 8602-8610
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Expression, Purification, and Characterization of an Active RNase H Domain of the Hepatitis B Viral Polymerase.
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Thermal Stability of Escherichia coli Ribonuclease HI and Its Active Site Mutants in the Presence and Absence of the Mg2+ Ion. PROPOSAL OF A NOVEL CATALYTIC ROLE FOR Glu48.
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Retroviral Integrase, Putting the Pieces Together.
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J. Biol. Chem. 271, 19633-19636
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The Putative Substrate Recognition Loop of Escherichia coli Ribonuclease H Is Not Essential for Activity.
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J. Biol. Chem. 271, 19883-19887
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Differential Effects of Moloney Murine Leukemia Virus Reverse Transcriptase Mutations on RNase H Activity in Mg[IMAGE] and Mn[IMAGE].
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J. Biol. Chem. 271, 1448-1454
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Unity in Transposition Reactions.
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Science 270, 253
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Truncating alpha-Helix E` of p66 Human Immunodeficiency Virus Reverse Transcriptase Modulates RNase H Function and Impairs DNA Strand Transfer.
M. Ghosh, K. J. Howard, C. E. Cameron, S. J. Benkovic, S. H. Hughes, and S. F. J. Le Grice (1995)
J. Biol. Chem. 270, 7068-7076
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Crystal structure of the catalytic domain of HIV-1 integrase: similarity to other polynucleotidyl transferases.
F Dyda, A. Hickman, T. Jenkins, A Engelman, R Craigie, and D. Davies (1994)
Science 266, 1981-1986
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Metalloenzymes, structural motifs, and inorganic models.
K. Karlin (1993)
Science 261, 701-708
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Two DNA Polymerases: HIV Reverse Transcriptase and the Klenow Fragment of Escherichia coli DNA Polymerase I.
T.A. Steitz, S. Smerdon, J. Jager, J. Wang, L.A. Kohlstaedt, J.M. Friedman, L.S. Beese, and P.A. Rice (1993)
Cold Spring Harb Symp Quant Biol 58, 495-504
   Abstract »    PDF »
Structure-Based Strategies for Drug Design and Discovery.
I. D. Kuntz (1992)
Science 257, 1078-1082
   Abstract »    PDF »
Another piece of the HIV puzzle falls into place.
A Wlodawer (1992)
Science 256, 1766
   PDF »
Crystal structure at 3.5 A resolution of HIV-1 reverse transcriptase complexed with an inhibitor.
L. Kohlstaedt, J Wang, J. Friedman, P. Rice, and T. Steitz (1992)
Science 256, 1783-1790
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Mutational Analysis of the Pyrococcus furiosus Holliday Junction Resolvase Hjc Revealed Functionally Important Residues for Dimer Formation, Junction DNA Binding, and Cleavage Activities.
K. Komori, S. Sakae, H. Daiyasu, H. Toh, K. Morikawa, H. Shinagawa, and Y. Ishino (2000)
J. Biol. Chem. 275, 40385-40391
   Abstract »    Full Text »    PDF »
Co-crystal of Escherichia coli RNase HI with Mn2+ Ions Reveals Two Divalent Metals Bound in the Active Site.
E. R. Goedken and S. Marqusee (2001)
J. Biol. Chem. 276, 7266-7271
   Abstract »    Full Text »    PDF »
Probing Contacts between the Ribonuclease H Domain of HIV-1 Reverse Transcriptase and Nucleic Acid by Site-specific Photocross-linking.
J. W. Rausch, B. K. Sathyanarayana, M. K. Bona, and S. F. J. Le Grice (2000)
J. Biol. Chem. 275, 16015-16022
   Abstract »    Full Text »    PDF »


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