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

Demetrios T. Braddock, John M. Louis, James L. Baber, David Levens and G. Marius Clore
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Demetrios T. Braddock: Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health
John M. Louis: Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health
James L. Baber: Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health
David Levens: National Cancer Institute, National Institutes of Health
G. Marius Clore: Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health

Nature, 2002, vol. 415, issue 6875, 1051-1056

Abstract: 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.

Date: 2002
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DOI: 10.1038/4151051a

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