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Crystal structure of the RNA-dependent RNA polymerase from hepatitis C virus reveals a fully encircled active site

Nature Structural Biology volume 6, pages 937–943 (1999)Cite this article

Abstract

Various classes of nucleotidyl polymerases with different transcriptional roles contain a conserved core structure. Less is known, however, about the distinguishing features of these enzymes, particularly those of the RNA-dependent RNA polymerase class. The 1.9 Å resolution crystal structure of hepatitis C virus (HCV) nonstructural protein 5B (NS5B) presented here provides the first complete and detailed view of an RNA-dependent RNA polymerase. While canonical polymerase features exist in the structure, NS5B adopts a unique shape due to extensive interactions between the fingers and thumb polymerase subdomains that serve to encircle the enzyme active site. Several insertions in the fingers subdomain account for intersubdomain linkages that include two extended loops and a pair of antiparallel α-helices. The HCV NS5B apoenzyme structure reported here can accommodate a template:primer duplex without global conformational changes, supporting the hypothesis that this structure is essentially preserved during the reaction pathway. This NS5B template:primer model also allows identification of a new structural motif involved in stabilizing the nascent base pair.

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Figure 1: Overall structure of HCV NS5B RNA-dependent RNA polymerase.
Figure 2: Comparison of polymerase structures and sequences.
Figure 3: Details of the HCV NS5B active site and intersubdomain linkages in stereo.
Figure 4: A hypothetical model for an HCV NS5B–template:primer–rNTP complex.

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References

  1. World Health Organization. Weekly Epidemiological Record 72, 341–344 (1997).

  2. Rice, C.M. In Fields virology 3rd edn (eds Fields, B.N., Knipe, D.N. & Howley, P.M.) 931–959 (Lippincott–Raven Publishers, Philadelphia; 1996).

    Google Scholar 

  3. Takamizawa, A. et al. J. Virol. 65, 1105–1113 (1991).

    CAS  PubMed  PubMed Central  Google Scholar 

  4. Hwang, S.B., Park, K.-J., Kim, Y.-S., Sung, Y.C. & Lai, M.M.C. Virology 227, 439–446 (1997).

    Article  CAS  Google Scholar 

  5. Yamashita, T. et al. J. Biol. Chem. 273, 15479–15486 (1998).

    Article  CAS  Google Scholar 

  6. Poch, O., Sauvaget, I., Delarue, M. & Tordo, N. EMBO J. 8, 3867–3874 (1989).

    Article  CAS  Google Scholar 

  7. Behrens, S.E., Tomei, L. & De Francesco, R. EMBO J. 15, 12–22 (1996).

    Article  CAS  Google Scholar 

  8. Lohmann, V., Korner, F., Herian, U. & Bartenschlager, R. J. Virol. 71, 8416–8428 (1997).

    CAS  PubMed  PubMed Central  Google Scholar 

  9. Ferrari, E. et al. J. Virol. 73, 1649–1654 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  10. Ishido, S., Fujita, T. & Hotta, H. Biochem. Biophys. Res. Commun. 244, 35–40 (1998).

    Article  CAS  Google Scholar 

  11. Joyce, C.M. & Steitz, T.A. Annu. Rev. Biochem. 63, 777–822 (1994).

    Article  CAS  Google Scholar 

  12. Sousa, R. Trends Biochem. Sci. 21, 186–190 (1996).

    Article  CAS  Google Scholar 

  13. Doublié, S., Sawaya, M.R. & Ellenberger, T. Structure 7, R31–R35 (1999).

    Article  Google Scholar 

  14. Jäger, J., Smerdon, S.J., Wang, J., Boisvert, D.C. & Steitz, T.A. Structure 2, 869–876 (1994).

    Article  Google Scholar 

  15. Li, Y., Korolev, S. & Waksman, G. EMBO J. 17, 7514–7525 (1998).

    Article  CAS  Google Scholar 

  16. Hansen, J.L., Long, A.M. & Schultz, S.C. Structure 5, 1109–1122 (1997).

    Article  CAS  Google Scholar 

  17. Huang, H., Chopra, R., Verdine, G.L. & Harrison, S.C. Science 282, 1669–1675 (1998).

    Article  CAS  Google Scholar 

  18. Ollis, D.L., Brick, P., Hamlin, R., Xuong, N.G. & Steitz, T.A. Nature 313, 762–766 (1985).

    Article  CAS  Google Scholar 

  19. Kornberg, A. DNA replication. (Freeman, San Francisco; 1980).

    Google Scholar 

  20. Johnson, M.S., McClure, M.A., Feng, D.F., Gray, J. & Doolittle, R.F. Proc. Natl. Acad. Sci. USA 83, 7648–7652 (1986).

    Article  CAS  Google Scholar 

  21. Jeruzalmi, D. & Steitz, T.A. EMBO J. 17, 4101–4113 (1998).

    Article  CAS  Google Scholar 

  22. Beese, L.S. & Steitz, T.A. EMBO J. 10, 25–33 (1991).

    Article  CAS  Google Scholar 

  23. Gao, G., Orlova, M., Georgiadis, M.M., Hendrickson, W.A. & Goff, S.P. Proc. Natl. Acad. Sci. USA 94, 407–411 (1997).

    Article  CAS  Google Scholar 

  24. Jacobo-Molina, A. et al. Proc. Natl. Acad. Sci. USA 90, 6320–6324 (1993).

    Article  CAS  Google Scholar 

  25. Wang, J. et al. Cell 89, 1087–1099 (1997).

    Article  CAS  Google Scholar 

  26. Doublié, S., Tabor, S., Long, A.M., Richardson, C.C. & Ellenberger, T. Nature 391, 251–258 (1998).

    Article  Google Scholar 

  27. Kiefer, J.R., Mao, C., Braman, J.C. & Beese, L.S. Nature 391, 304–307 (1998).

    Article  CAS  Google Scholar 

  28. Lohmann, V., Roos, A., Korner, F., Koch, J.O. & Bartenschlager, R. Virology 249, 108–118 (1998).

    Article  CAS  Google Scholar 

  29. Doublié, S. Methods Enzymol. 276, 523–530 (1997).

    Article  Google Scholar 

  30. Hendrickson, W.A. & Ogata, C.M. Methods Enzymol. 276, 494–523 (1997).

    Article  CAS  Google Scholar 

  31. Otwinowski, Z. & Minor, W. Methods Enzymol. 276, 307–326 (1997).

    Article  CAS  Google Scholar 

  32. Bailey, S. Acta Crystallogr. D 50, 760–763 (1994).

    Article  Google Scholar 

  33. Miller, R., Gallo, S.M., Khalak, H.G. & Weeks, C.M. J. Appl. Crystallogr. 27, 613–621 (1994).

    Article  CAS  Google Scholar 

  34. de La Fortelle, E. & Bricogne, G. Methods Enzymol. 276, 472–494 (1996).

    Article  Google Scholar 

  35. Jones, T.A., Zou, J.Y., Cowan, S.W. & Kjeldgaard, M. Acta Crystallogr. A 47, 110–119 (1991).

    Article  Google Scholar 

  36. Brünger, A.T. X-PLOR: a system for X-ray crystallography and NMR. (Yale University Press, New Haven, Connecticut; 1992).

    Google Scholar 

  37. Kleywegt, G.J. & Brünger, A.T. Structure 4, 897–904 (1996).

    Article  CAS  Google Scholar 

  38. Nicholls, A., Sharp, K.A. & Honig, B. Proteins 11, 281–296 (1991).

    Article  CAS  Google Scholar 

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Acknowledgements

We thank T. Fischmann, A. Hruza, P. Reichert and the IMCA-CAT staff for assistance with crystallization and synchrotron data collection.

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Authors and Affiliations

  1. Department of Structural Chemistry, Schering-Plough Research Institute, Kenilworth, 07033, New Jersey, USA

    Charles A. Lesburg, Michael B. Cable, Anthony F. Mannarino & Patricia C. Weber

  2. Department of Antiviral Therapy, Schering-Plough Research Institute, Kenilworth, 07033, New Jersey, USA

    Eric Ferrari & Zhi Hong

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  1. Charles A. Lesburg
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  2. Michael B. Cable
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  4. Zhi Hong
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Correspondence to Patricia C. Weber.

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Lesburg, C., Cable, M., Ferrari, E. et al. Crystal structure of the RNA-dependent RNA polymerase from hepatitis C virus reveals a fully encircled active site. Nat Struct Mol Biol 6, 937–943 (1999). https://doi.org/10.1038/13305

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