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:

Solution structure of the origin DNA-binding domain of SV40 T-antigen

Nature Structural Biology volume 3, pages 1034–1039 (1996)Cite this article

Abstract

The structure of the domain from simian virus 40 (SV40) large T-antigen that binds to the SV40 origin of DNA replication (T-ag-OBD131–260) has been determined by nuclear magnetic resonance spectroscopy. The overall fold, consisting of a central five-stranded antiparallel β-sheet flanked by two α-helices on one side and one α-helix and one 310-helix on the other, is a new one. Previous mutational analyses have identified two elements, termed A (∼152–155) and B2 (203–207), as essential for origin-specific recognition. These elements form two closely juxtaposed loops that define a continuous surface on the protein. The addition of a duplex oligonucleotide containing the origin recognition pentanucleotide GAGGC induces chemical shift changes and slows amide proton exchange in resonances from this region, indicating that this surface directly contacts the DNA.

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. Jacob, F., Brenner, S. & Cuzin, F. On the regulation of DNA replication in bacteria Cold Spring Harbor Sym. Quant Biol. 28, 329–348 (1963).

    Article  CAS  Google Scholar 

  2. Stillman, B. Replicator renaissance Nature 366, 506–507 (1993).

    Article  CAS  Google Scholar 

  3. Kornberg, A. & Baker, T.A. DNA Replication (W.H. Freeman and Co., New York, 1992).

    Google Scholar 

  4. Tegtmeyer, P. Simian virus 40 deoxyribonucleic acid synthesis: the viral replicon. J. Virol. 10, 591–598 (1972).

    CAS  PubMed  PubMed Central  Google Scholar 

  5. Borowiec, J.A., Dean, F.B., Bullock, P.A. & Hurwitz, J. Binding and unwinding-how T antigen engages the SV40 origin of DNA replication Cell 60, 181–184 (1990).

    Article  CAS  Google Scholar 

  6. Fanning, E. & Knippers, R. Structure and function of simian virus 40 large tumor antigen. Ann. Rev. Biochem. 61, 55–85 (1992).

    Article  CAS  Google Scholar 

  7. Brünger, A.T. X-PLOR: A System for X-ray Crystallography and NMR X-PLOR Version 3.1 Manual (Yale University Press, New Haven, CT.) (1992).

    Google Scholar 

  8. Wun-Kim, K. et al. The DNA-binding domain of simian virus 40 tumor antigen has multiple functions. J. Virol. 67, 7608–7611 (1993).

    CAS  PubMed  PubMed Central  Google Scholar 

  9. Wun-Kim, K. & Simmons, D.T. Mapping of helicase and helicase substrate-binding domains on simian virus 40 large T antigen J. Virol. 64, 2014–2020 (1990).

    CAS  PubMed  PubMed Central  Google Scholar 

  10. Simmons, D.T., Loeber, G. & Tegtmeyer, P. Four major sequence elements of simian virus 40 large T antigen coordinate its specific and nonspecific DNA binding. J. Virol. 64, 1973–1983 (1990).

    CAS  PubMed  PubMed Central  Google Scholar 

  11. Simmons, D.T., Wun-Kim, K. & Young, W. Identification of simian virus 40 T-antigen residues important for specific and nonspecific binding to DNA and for helicase activity. J. Virol. 64, 4858–4865 (1990).

    CAS  PubMed  PubMed Central  Google Scholar 

  12. Tjian, R. The binding site on SV40 DNA for a T-antigen related protein. Cell 13, 165–179 (1978).

    Article  CAS  Google Scholar 

  13. Bax, A., Ikura, M., Kay, I.E., Torchia, D.A. & Tschudin, R. Comparison of different modes of two-dimensional reverse-correlation NMR for the study of proteins J. Magn. Reson. 86, 304–318 (1990).

    CAS  Google Scholar 

  14. Lian, L.Y., Barsukov, I.L., Sutcliffe, M.J., Sze, K.H. & Roberts, G.C.K. Protein-Ligand Interactions: Exchange Processes and Determination of Ligand Conformation and Protein-Ligand Contacts Meth. Enzym. 239, 657–700 (1994).

    Article  CAS  Google Scholar 

  15. Cleland, W.W. & Kreevoy, M.M. Low-barrier hydrogen bonds and enzymatic catalysis Science 264, 1887–1890 (1994).

    Article  CAS  Google Scholar 

  16. Frey, P.A., Whitt, S.A. & Tobin, J.B. A low-barrier hydrogen bond in the catalytic triad of serine proteases Science 264, 1927–1930 (1994).

    Article  CAS  Google Scholar 

  17. Holm, L. & Sander, C. Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 170, 123–138 (1993).

    Article  Google Scholar 

  18. Bernstein, F.C. et al. The protein data bank: a computer-based archival file for macromolecular structures J. Mol. Biol. 112, 535–542 (1977).

    Article  CAS  Google Scholar 

  19. Abola, E.E., Bernstein, F.C., Bryant, S.H., Koetzle, T.F. & Weng, J. “Protein Data Bank” in crystallographic databases-information content, software systems, scientific applications Data commission of the Int'l union of crystallography, Bonn/Cambridge/Chester 107–132 (1987).

  20. Avis, J.M. et al. Solution structure of the N-terminal RNP domain of U1A protein: the role of the C-terminal residues in structure stability and RNA binding. J. Mol. Biol. 257, 398–411 (1996).

    Article  CAS  Google Scholar 

  21. Hegde, R.S., Grossman, S.R., Laimins, L.A. & Sigler, P.B. Crystal structure at 1.7 Å of the bovine papillomavirus-1 E2 DNA-binding domain bound to its DNA target. Nature 359, 505–512 (1992).

    Article  CAS  Google Scholar 

  22. Bochkarev, A. et al. Crystal structure of the DNA-binding domain of the Epstein-barr virus origin-binding protein, EBNA1, bound to DNA Cell 84, 791–800 (1996).

    Article  CAS  Google Scholar 

  23. Harrison, S.C. A structural taxonomy of DNA-binding domains Nature 353, 715–719 (1991).

    Article  CAS  Google Scholar 

  24. Kay, L.E., Ikura, M., Tschudin, R. & Bax, A. Three-dimensional triple-resonance NMR spectroscopy of isotopically enriched proteins J. Magn. Reson. 89, 496–514 (1990).

    CAS  Google Scholar 

  25. Bax, A. & Ikura, M. An efficient 3D NMR technique for correlating the proton and 15N backbone amide resonances with the alpha-carbon of the preceding residue in uniformly 15N/13C enriched proteins J. Biomolec. NMR 1, 99–104 (1991).

    Article  CAS  Google Scholar 

  26. Farmer II, B.T., Venters, R.A., Spicer, L.D., Wittekind, M.G. & Müller, L. A refocused and optimized HNCA: increased sensitivity and resolution in large macromolecules. J. Biomolec. NMR 2, 195–202 (1992).

    Article  CAS  Google Scholar 

  27. Farmer II, B.T. Optimized triple resonance applied to peptides labeled only with 15N. The HN(CO)(CA) experiment J. Magn. Reson. 94, 413–418 (1991).

    CAS  Google Scholar 

  28. Kay, L.E. & Bax, A. New methods for the measurement of NH-CαH coupling constants in 15N-labeled proteins J. Magn. Reson. 86, 110–126 (1990).

    CAS  Google Scholar 

  29. Vuister, G.W. & Bax, A. Quantitative J correlation: a new approach for measuring homonuclear three-bond J(HNHα) coupling constants in 15N-enriched proteins J. Am. Chem. Soc. 115, 7772–7777 (1993).

    Article  CAS  Google Scholar 

  30. Carson, M. Ribbon models of macromolecules J. Mol. Graphics 5, 103–106 (1987).

    Article  CAS  Google Scholar 

  31. Nicholls, A.J., Sharp, K.A. & Honig, B. Protein folding and association: insights from interfacial and thermodynamic properties of hydrocarbons. Proteins Struct. Funct. Genet. 11, 281–296 (1991).

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Biochemistry, Tufts University School of Medicine, 136 Harrison Avenue, Boston, Massachusetts, 02111, USA

    Xuelian Luo, David G. Sanford, Peter A. Bullock & William W. Bachovchin

Authors
  1. Xuelian Luo
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. David G. Sanford
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Peter A. Bullock
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. William W. Bachovchin
    View author publications

    You can also search for this author in PubMed Google Scholar

Rights and permissions

Reprints and permissions

About this article

Cite this article

Luo, X., Sanford, D., Bullock, P. et al. Solution structure of the origin DNA-binding domain of SV40 T-antigen. Nat Struct Mol Biol 3, 1034–1039 (1996). https://doi.org/10.1038/nsb1296-1034

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nsb1296-1034

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