Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Structure of the hepatitis C virus RNA helicase domain

Nature Structural Biology volume 4, pages 463–467 (1997)Cite this article

Abstract

Helicases are nucleotide triphosphate (NTP)-dependent enzymes responsible for unwinding duplex DNA and RNA during genomic replication. The 2.1 Å resolution structure of the HCV helicase from the positive-stranded RNA hepatitis C virus reveals a molecule with distinct NTPase and RNA binding domains. The structure supports a mechanism of helicase activity involving initial recognition of the requisite 3′ single-stranded region on the nucleic acid substrate by a conserved arginine-rich sequence on the RNA binding domain. Comparison of crystallographically independent molecules shows that rotation of the RNA binding domain involves conformational changes within a conserved TATPP sequence and untwisting of an extended antiparallel β-sheet. Location of the TATPP sequence at the end of an NTPase domain β-strand structurally homologous to the ‘switch region’ of many NTP-dependent enzymes offers the possibility that domain rotation is coupled to NTP hydrolysis in the helicase catalytic cycle.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Similar content being viewed by others

References

  1. Jin, L. & Peterson, D.L. Expression, isolation, and characterization of the hepatitis C virus APTase/RNA helicase. Arch. Biochem. Biophys. 323, 47–53 (1995).

    Article  CAS  Google Scholar 

  2. Kim, D.W., Gwack, Y., Han, J.H. & Choe, J. C-Terminal domain of the hepatitis C virus N53 protein contains an RNA helicase activity. Biochem. Biophys. Res. Comm. 215, 160–166 (1995).

    Article  CAS  Google Scholar 

  3. Kadare, G. & Haenni, A.-L. Virus-encoded RNA helicase. J. Virol. 71, 2583–2590 (1997).

    CAS  PubMed  PubMed Central  Google Scholar 

  4. Gorbalenya, A.E. & Koonin, E.V. Helicases: amino acid sequence comparisons and structure-function relationships. Curr. Opin. Struct. Biol. 3, 419–429 (1993).

    Article  CAS  Google Scholar 

  5. Walker, J.E., Saraste, M., Runswick, M.J. & Gay, N.J. Distantly related sequences in the a- and b-subunits of ATP synthetase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold. EMBO J. 1, 945–951 (1982).

    Article  CAS  Google Scholar 

  6. Kanai, A., Tanabe, K. & Kohara, M. Poly(U) binding activity of hepatitis C virus NS3 protein, a putative RNA helicase. FEBS Letters 376, 221–224 (1995).

    Article  CAS  Google Scholar 

  7. Schmid, S.R. & Linder, P. D-E-A-D protein family of putative RNA helicases. Mol. Microbiol. 6, 283–292 (1992).

    Article  CAS  Google Scholar 

  8. Fuller-Pace, F.V. RNA helicase: modulators of RNA structure. Trends Cell Biol. 4, 271–274 (1994).

    Article  CAS  Google Scholar 

  9. Gross, C.H. & Shuman, S. Mutational analysis of vaccinia virus nucleoside triphosphate phosphohydrolase II, a DExH box RNA helicase. J. Virol. 69, 4727–4736 (1995).

    CAS  PubMed  PubMed Central  Google Scholar 

  10. Schulz, G.E. Binding of nucleotides by proteins. Curr. Opin. Struct. Biol. 2, 61–67 (1992).

    Article  CAS  Google Scholar 

  11. Yoshida, M. & Amano, T. A common topology of proteins catalyzing ATP-triggered reactions. FEBS Letts. 359, 1–5 (1995).

    Article  CAS  Google Scholar 

  12. Subramanya, H.S., Bird, L.E., Brannigan, J.A. & Wigley, D.B. Crystal structure of a DExx box DNA helicase. Nature 384, 379–383 (1996).

    Article  CAS  Google Scholar 

  13. Pause, A., Methot, N. & Sonenberg, N. The HRIGRXXR region of the DEAD box RNA helicase eukaryotic translation initiationfactor 4A is required for RNA binding and ATP hydrolysis. Mol. Cell Biol. 13, 6789–6798 (1993).

    Article  CAS  Google Scholar 

  14. Gross, C.H. & Shuman, S. QRxGRxGRxxxG motif of the vaccinia virus DExH box RNA helicase NPH-II is required for ATP hydrolysis and RNA unwinding but not for RNA binding. J. Virol. 70, 1706–1713 (1996).

    CAS  PubMed  PubMed Central  Google Scholar 

  15. Suzich, J.A. et al. Hepatitis C Virus NS3 protein polynucleotide-stimulated nucleoside triphosphatase and comparison with the related pestivirus and flavivirus enzymes. J. Virol. 67, 6152–6158 (1993).

    CAS  PubMed  PubMed Central  Google Scholar 

  16. Fernandez, A. & Garcia, J.A. The RNA helicase Cl from plum pox potyvirus has two regions involved in binding to RNA. FEBS Letts 388, 206–210 (1996).

    Article  CAS  Google Scholar 

  17. Tai, C., Chi, W., Chen, D. & Hwang, L. The helicase activity associated with hepatitis C virus nonstructural protein 3 (NS3). J. Virol. 70, 8477–8484 (1996).

    CAS  PubMed  PubMed Central  Google Scholar 

  18. Gross, C.H. & Shuman, S. Vaccinia virus RNA helicase: nucleic acid specificity in duplex unwinding. J. Virol. 70, 2615–2619 (1996).

    CAS  PubMed  PubMed Central  Google Scholar 

  19. Matson, S.W. & Kaiser-Rogers, K.A. DNA helicases. Ann. Rev. Biochem. 59, 289–329 (1990).

    Article  CAS  Google Scholar 

  20. Lohman, T.M. & Bjornson, K.P. Mechanisms of helicase-catalyzed DNA unwinding. Ann. Rev. Biochem. 65, 169–214 (1996).

    Article  CAS  Google Scholar 

  21. Preugschat, F., Averett, D.R., Clarke, B.E. & Porter, D.J.T. A steady-state and pre-steady-state kinetic analysis of the NTPase activity associated with the hepatitis C virus NS3 helicase domain. J. Biol. Chem. 271, 24449–24457 (1996).

    Article  CAS  Google Scholar 

  22. Kim, J.L. et al. Crystal structure of the hepatitis C virus NS3 protease domain complexed with a synthetic NS4A cofactor peptide. Cell 87, 343–355 (1996).

    Article  CAS  Google Scholar 

  23. Love, R.A. et al. The crystal structure of hepatitis C virus NS3 proteinase reveals a trypsin-like fold and a structural zinc binding site. Cell 87, 331–342 (1996).

    Article  CAS  Google Scholar 

  24. Failla, C., Tomei, L. & DeFrancesco, R. Both NS3 and NS4A are required for proteolytic processing of hepatitis C virus nonstructural proteins. J. Virology 68, 3753–3760 (1994).

    CAS  PubMed  Google Scholar 

  25. Lin, C., Thomson, J.A. & Rice, C.M. A central region in the hepatitis C virus NS4A protein allows formation of an active NS3-NS4A serine proteinase complex in vivo and in vitro. J. Virol. 69, 4373–4380 (1995).

    CAS  PubMed  PubMed Central  Google Scholar 

  26. Shimizu, Y. & et al. Identification of the sequence on NS4A required for the enhanced cleavage of the NS5A/5B site by hepatitis C virus NS3 protease. J. Virol. 70, 127–132 (1996).

    CAS  PubMed  PubMed Central  Google Scholar 

  27. CCP4. The CCP4 suite: program for protein crystallography. Acta Crystallogr. D50, 760–763 (1994).

  28. Sack, J.S. CHAIN: a crystallographic modeling program. J. Mol. Graphics 6, 224–225 (1988).

    Article  Google Scholar 

  29. Kraulis, P.J. Molscript: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24, 946–950 (1991).

    Article  Google Scholar 

  30. Nicholls, A. GRASP: graphical representation and analysis of surface properties, (Columbia University, New York, 1993).

    Google Scholar 

  31. Brünger, A.T. X-PLOR, Version 3.1 manual: a system for X-ray crystallography and NMR (Yale University Press, New Haven, USA, 1993).

    Google Scholar 

  32. Hodel, A., Kim, S.H. & Brünger, A.T. Model bias in macromolecular crystal structures. Acta Crystallogr. A48, 851–859 (1992).

    Article  CAS  Google Scholar 

  33. Read, R.J. Improved Fourier coefficients for maps using phases from partial structures with errors. Acta Crystallogr. A42, 140–149 (1986).

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Structural Chemistry and Virology Departments, Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, New Jersey, 07033, USA

    Nanhua Yao, T. Hesson, M. Cable, Z. Hong, A.D. Kwong, H.V. Le & Patricia C. Weber

Authors
  1. Nanhua Yao
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. T. Hesson
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. M. Cable
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Z. Hong
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. A.D. Kwong
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. H.V. Le
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Patricia C. Weber
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Patricia C. Weber.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Yao, N., Hesson, T., Cable, M. et al. Structure of the hepatitis C virus RNA helicase domain. Nat Struct Mol Biol 4, 463–467 (1997). https://doi.org/10.1038/nsb0697-463

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nsb0697-463

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing