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Structure and dynamics of KH domains from FBP bound to single-stranded DNA

Nature volume 415, pages 1051–1056 (2002)Cite this article

Abstract

Gene regulation can be tightly controlled by recognition of DNA deformations that are induced by stress generated during transcription1,2,3. The KH domains of the FUSE-binding protein (FBP), a regulator of c-myc expression1,4, bind in vivo and in vitro to the single-stranded far-upstream element (FUSE), 1,500 base pairs upstream from the c-myc promoter4,5,6. FBP bound to FUSE acts through TFIIH at the promoter4. Here we report the solution structure of a complex between the KH3 and KH4 domains of FBP and a 29-base single-stranded DNA from FUSE. The KH domains recognize two sites, 9–10 bases in length, separated by 5 bases, with KH4 bound to the 5′ site and KH3 to the 3′ site. The central portion of each site comprises a tetrad of sequence 5′d-ATTC for KH4 and 5′d-TTTT for KH3. Dynamics measurements show that the two KH domains bind as articulated modules to single-stranded DNA, providing a flexible framework with which to recognize transient, moving targets.

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Figure 1: Structural analysis of the FBP3/4-ssDNA complex.
Figure 2: Structure of the FBP3/4–ssDNA complex.
Figure 3: Interdomain motion in the FBP3/4–M29 ssDNA complex, a, 15N-{1H} NOE values as a function of residue number.

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Acknowledgements

We thank D. Garrett and F. Delaglio for software support; C. A. Bewley, M. Caffrey, W. A. Eaton, J. Kuszewski, L. Murphy, C. Schwieters, A. Szabo and N. Tjandra for discussions; and C. A. Bewley for critically reading the manuscript. This work was supported in part by the AIDS Targeted Antiviral Program of the Office of the Director of the National Institutes of Health (to G.M.C.).

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Authors and Affiliations

  1. Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, 20892, Maryland, USA

    Demetrios T. Braddock, John M. Louis, James L. Baber & G. Marius Clore

  2. Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, 20892, Maryland, USA

    Demetrios T. Braddock & David Levens

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  1. Demetrios T. Braddock
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Braddock, D., Louis, J., Baber, J. et al. Structure and dynamics of KH domains from FBP bound to single-stranded DNA. Nature 415, 1051–1056 (2002). https://doi.org/10.1038/4151051a

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