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 cellular factor BAF responsible for protecting retroviral DNA from autointegration

Nature Structural Biology volume 5, pages 903–909 (1998)Cite this article

Abstract

The solution structure of the human barrier-to-autointegration factor, BAF, a 21,000 Mr dimer, has been solved by NMR, including extensive use of dipolar couplings which provide a priori long range structural information. BAF is a highly evolutionarily conserved DNA binding protein that is responsible for inhibiting autointegration of retroviral DNA, thereby promoting integration of retroviral DNA into the host chromosome. BAF is largely helical, and each subunit is composed of five helices. The dimer is elongated in shape and the dimer interface comprises principally hydrophobic contacts supplemented by a single salt bridge. Despite the absence of any sequence similarity to any other known protein family, the topology of helices 3–5 is similar to that of a number of DNA binding proteins, with helices 4 and 5 constituting a helix-turn-helix motif. A model for the interaction of BAF with DNA that is consistent with structural and mutagenesis data is proposed.

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

Figure 1: Sequence alignment of human, mouse, zebrafish and C. elegans BAF, together with a summary of the secondary structure.
Figure 2: Examples of strips taken from the 3D 13C-separated/12C-filtered NOE spectrum recorded on a 1:1 mixture of 13C/14N and 12C/15N labeled BAF in D2O, illustrating intersubunit NOEs from protons attached to 13C (in the indirect dimension) to protons attached to 12C (in the acquisition dimension).
Figure 3: Stereoviews of BAF.
Figure 4
Figure 5: Model for the binding of a BAF monomer to DNA.

Similar content being viewed by others

References

  1. Katz, R.A. & Skalka, A.M. The retroviral enzymes. Annu. Rev. Biochem. 63, 133–173 (1994).

    Article  CAS  Google Scholar 

  2. Brown, P.O., Bowerman, B., Varmus, H.E., and Bishop, J.M. Correct integration of retroviral DNA in vitro. Cell 49, 347–356 (1987).

    Article  CAS  Google Scholar 

  3. Ellison, V., Abrams, H., Roe, T., Lifson, J., and Brown, P. Human immunodeficiency virus integration in a cell-free system. J. Virol. 64, 2711– 2715 (1990).

    CAS  PubMed  PubMed Central  Google Scholar 

  4. Farnet, C.M. and Haseltine, W.A. Integration of human immunodeficiency virus type 1 DNA in vitro. Proc. Natl. Acad. Sci. USA 87, 4164–4168 (1990).

    Article  CAS  Google Scholar 

  5. Lee, M.S. & Craigie, R. Protection of retroviral DNA from autointegration: involvement of a cellular factor. Proc. Natl. Acad. Sci. USA 91, 9823–9827 (1994).

    Article  CAS  Google Scholar 

  6. Lee, M.S. & Craigie, R. A previously unidentified host protein protects retroviral DNA from autointegration. Proc. Natl. Acad. Sci. USA 95, 1528–1533 ( 1998).

    Article  CAS  Google Scholar 

  7. Clore, G.M., Gronenborn, A.M., Szabo, A. & Tjandra, N. Determining the magnitude of the fully asymmetric diffusion tensor from heteronuclear relaxation data in the absence of structural information. J. Am. Chem. Soc. 120, 4889–4890 ( 1998).

    Article  CAS  Google Scholar 

  8. Clore, G.M. & Gronenborn, A.M. Structures of larger proteins in solution: three- and four-dimensional heteronuclear NMR spectroscopy. Science 252, 1390–1399 ( 1991).

    Article  CAS  Google Scholar 

  9. Clore, G. M. & Gronenborn, A. M. Determining the structures of larger proteins and protein complexes by NMR. Trends Biotech. 16, 22–34 ( 1998).

    Article  CAS  Google Scholar 

  10. Bax, A. & Grzesiek, S. Methdological advances in protein NMR Acc. Chem. Res. 26, 131– 138 (1993).

    Article  CAS  Google Scholar 

  11. Tjandra, N., Omichinski, J. G., Gronenborn, A. M., Clore, G. M. & Bax, A. Use of dipolar 1H-15N and 1H-13C couplings in the structure determination of magnetically oriented macromolecules in solution. Nature Struct. Biol. 4, 732–728 (1997).

    Article  CAS  Google Scholar 

  12. Pabo, C.O. & Sauer, R.T. Transcription factors: structural families and principles of DNA recognition. Annu. Rev. Biochem. 61, 1053–1095 ( 1992).

    Article  CAS  Google Scholar 

  13. Schumacher, S. et al. Solution structure of the Mu end DNA-binding Iß subdomain of phage Mu transposase: modular DNA recognition by two tethered domains. EMBO J. 16, 7532– 7541 (1997).

    Article  CAS  Google Scholar 

  14. Wilson, D.S., Guenther, B., Desplan, C. & Kuriyan, J. High-resolution crystal structure of a paired (PAX) class cooperative homeodomain dimer on DNA. Cell 82, 709– 719 (1995).

    Article  CAS  Google Scholar 

  15. Luger, K., Maeder, A.W., Richmond, R.K., Sargent, D.F. & Richmond, T.J. X-ray structure of the nucleosome core particle at 2.8 Å resolution. Nature 389 , 251–259 (1997).

    Article  CAS  Google Scholar 

  16. Xie, X. et al. Structural similarity between TAFS and the hetrotetrameric core of the histone octamer. Nature 380, 316– 322 (1996).

    Article  CAS  Google Scholar 

  17. Cai, M. et al. An efficient and cost-effective isotope labeling protocol for proteins expressed in Escherichia coli. J. Biomol. NMR 11, 97–102 (1998).

    Article  CAS  Google Scholar 

  18. Delaglio, F. et al. NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J. Biomol. NMR 6, 277– 293 (1995).

    Article  CAS  Google Scholar 

  19. Garrett, D. S., Powers, R., Gronenborn, A. M. & Clore, G. M. A common sense approach to peak picking in two-, three- and four-dimensional spectra using automatic computer analysis of contour diagrams. J. Magn. Reson. 95, 214–220 (1991).

    CAS  Google Scholar 

  20. Bax, A. et al. Measurement of homo- and hetero-nuclear J couplings from quantitative J correlation. Meth. Enz. 239, 79– 106 (1994).

    Article  CAS  Google Scholar 

  21. Pelton, J.G., Torchia, D.A., Meadow, M.D. & Roseman, S. Tautomeric states of the active-site histidines of phosphorylated and unphosphorylated IIIGlc, a signal transducing protein from Escherichia coli , using two-dimensional heteronuclear NMR techniques. Protein Sci. 2, 543–558 ( 1993).

    Article  CAS  Google Scholar 

  22. Tjandra, N. & Bax, A. Direct measurement of distances and angles in biomolecules by NMR in dilute liquid crystalline medium. Science 278, 1111–1114 ( 1997).

    Article  CAS  Google Scholar 

  23. Ottiger, M., Delaglio, F. & Bax, A. Measurement of J and dipolar couplings from simplified two-dimensional NMR spectra. J. Magn. Reson. 131, 173–178 (1998).

    Article  Google Scholar 

  24. Bewley, C.A. et al. Solution structure of cyanovirin-N, a potent HIV-inactivating protein. Nature Struct. Biol. 5, 571– 578 (1998).

    Article  CAS  Google Scholar 

  25. Clore, G. M., Gronenborn, A. M. & Bax, A. A robust method for determining the magnitude of the fully asymmetric alignment tensor of oriented macromolecules in the absence of structural information. J. Magn. Reson. 133, 216–221 (1998).

    Article  CAS  Google Scholar 

  26. Grzesiek, S. & Bax, A. The importance of not saturating H 2O in protein NMR: application to sensitivity enhancement and NOE measurements . J. Am. Chem. Soc. 115, 12593– 12594 (1993).

    Article  CAS  Google Scholar 

  27. Tjandra, N., Wingfield, P.T., Stahl, S.J. & Bax, A. Anisotropic rotational diffusion of perdeuterated HIV protease from 15N NMR relaxation measurements at two magnetic fields. J. Biomol. NMR. 8, 273–284 ( 1996

    Article  CAS  Google Scholar 

  28. Nilges, M. A calculational strategy for the structure determination of symmetric dimers by 1H-NMR. Proteins Struct. Funct. Genet. 17, 297–309 (1993).

    Article  CAS  Google Scholar 

  29. Nilges, M., Gronenborn, AM., Brünger, A. T. & Clore G. M. Determination of three-dimensional structures of proteins by simulated annealing with interproton distance restraints: application to crambin, potato carboxypeptidase inhibitor and barley serine proteinase inhibitor 2. Prot. Engng. 2, 27–38 (1988).

    Article  CAS  Google Scholar 

  30. Brünger, A.T. et al. Crystallography and NMR system (CNS): a new software suite for macromolecular structure determination. Acta Crystallogr. D in the press (1998).

  31. Clore, G.M. & Gronenborn, A.M. New methods of structure refinement for macromolecular structure determination by NMR. Proc. Natl. Acad. Sci. USA 95, 5891–5898 (1998).

    Article  CAS  Google Scholar 

  32. Clore, G. M., Gronenborn, A. M. & Tjandra, N. Direct structure refinement against residual dipolar couplings in the presence of rhombicity of unknown magnitude. J. Magn. Reson. 131, 159–162 (1998).

    Article  CAS  Google Scholar 

  33. Brooks, B.R. et al. CHARMM: a program for macromolecular energy minimization and dynamics calculations. J. Comput. Chem. 4, 187–217 (1993).

    Article  Google Scholar 

  34. Koradi, R., Billeter, M. & Wuthrich, K. MOLMOL: a program for display and analysis of macromolecular structures. J. Mol. Graph. 14 51-5, 29– 32 (1996).

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

    Article  Google Scholar 

  36. Holm, L. & Sander, C. Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233, 123–138 (1993).

    Article  CAS  Google Scholar 

  37. Laskowski, R. A., MacArthur, M. W., Moss, D. S. & Thornton, J. M. PROCHECK: A program to check the stereochemical quality of protein structures . J. Appl. Crystallogr. 26, 283– 291 (1993).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank D.S. Garrett and F. Delaglio for software support; R. Tschudin for hardware supprot; L. Pannel for mass spectrometry; M. Krause for deriving the C. elegans BAF sequence from genomic and EST sequences in the databases; and C. Bewley, D. Garrett, K. Frank, M. Ottiger and N. Tjandra for useful discussions. This work was supported by the AIDS Targeted Antiviral Program of the Office of the Director of the National Institutes of Health (G.M.C., A.M.G. and R.C.)

Author information

Authors and Affiliations

  1. Laboratories of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, 20892-0520, Maryland, USA

    Mengli Cai, Angela M. Gronenborn & G. Marius Clore

  2. Laboratories of Molecular Biology, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, 20892-0520, Maryland, USA

    Ying Huang, Ronglan Zheng, Shui-Qing Wei, Rodolfo Ghirlando, Myung Soo Lee & Robert Craigie

Authors
  1. Mengli Cai
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Ying Huang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Ronglan Zheng
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Shui-Qing Wei
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Rodolfo Ghirlando
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Myung Soo Lee
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Robert Craigie
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Angela M. Gronenborn
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. G. Marius Clore
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Angela M. Gronenborn or G. Marius Clore.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Cai, M., Huang, Y., Zheng, R. et al. Solution structure of the cellular factor BAF responsible for protecting retroviral DNA from autointegration. Nat Struct Mol Biol 5, 903–909 (1998). https://doi.org/10.1038/2345

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/2345

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