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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.

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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.

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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.)

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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

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  1. Mengli Cai
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Correspondence to Angela M. Gronenborn or G. Marius Clore.

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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

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