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The Mu repressor–DNA complex contains an immobilized 'wing' within the minor groove

Nature Structural Biology volume 8, pages 84–90 (2001)Cite this article

Abstract

We have determined the solution structure of the complex between the 'winged-helix' enhancer binding domain of the Mu repressor protein and its cognate DNA site. The structure reveals an unusual use for the 'wing' which becomes immobilized upon DNA binding where it makes intermolecular hydrogen bond contacts deep within the minor groove. Although the wing is mobile in the absence of DNA, it partially negates the large entropic penalty associated with its burial by maintaining a small degree of structural order in the DNA-free state. Extensive contacts are also formed between the recognition helix and the DNA, which reads the major groove of a highly conserved region of the binding site through a single base-specific hydrogen bond and van der Waals contacts.

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Figure 1: a, Schematic showing the operator sites (O1, O2 and O3) within the Mu transposon.
Figure 2: Representative NMR spectra of residues at the protein–DNA interface.
Figure 3: The NMR solution structure of the MuR-DBD–DNA complex.
Figure 4: Protein–DNA contacts observed in the MuR-DBD–DNA complex.
Figure 5: The wing becomes ordered in the presence of DNA.

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Acknowledgements

We thank G. Daughdrill and the staff at the Pacific Northwest National Laboratory for assistance in operating their 800 MHz NMR spectrometer. We also thank K. Connolly for preparation of the Mu repressor expression plasmid and U. Ilangovan for useful discussions. This work was supported by grants from the US Department of Energy and National Institutes of Health.

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  1. Department of Chemistry and Biochemistry, Molecular Biology Institute and the UCLA-DOE Laboratory of Structural Biology and Molecular Medicine, University of California, Los Angeles, 405 Hilgard Ave, Los Angeles, 90095, California, USA

    Jonathan M. Wojciak, Junji Iwahara & Robert T. Clubb

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Correspondence to Robert T. Clubb.

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Wojciak, J., Iwahara, J. & Clubb, R. The Mu repressor–DNA complex contains an immobilized 'wing' within the minor groove. Nat Struct Mol Biol 8, 84–90 (2001). https://doi.org/10.1038/83103

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