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Structure of the LexA–DNA complex and implications for SOS box measurement

Abstract

The eubacterial SOS system is a paradigm of cellular DNA damage and repair, and its activation can contribute to antibiotic resistance1,2,3. Under normal conditions, LexA represses the transcription of many DNA repair proteins by binding to SOS ‘boxes’ in their operators. Under genotoxic stress, accumulating complexes of RecA, ATP and single-stranded DNA (ssDNA) activate LexA for autocleavage. To address how LexA recognizes its binding sites, we determined three crystal structures of Escherichia coli LexA in complex with SOS boxes. Here we report the structure of these LexA–DNA complexes. The DNA-binding domains of the LexA dimer interact with the DNA in the classical fashion of a winged helix–turn–helix motif. However, the wings of these two DNA-binding domains bind to the same minor groove of the DNA. These wing–wing contacts may explain why the spacing between the two half-sites of E. coli SOS boxes is invariant.

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Figure 1: Overall structure of the E. coli LexA–DNA complex.
Figure 2: Binding of the E. coli LexA–DNA complex.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

Atomic coordinates and structure factor files have been deposited with the Protein Data Bank under the accession codes 3JSO (A22), 3JSP (B22) and 3K3R (C29).

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Acknowledgements

We thank E. Harris and O. Adekeye for help with crystal growth and optimization; Y.-L. C. Leung for advice on DNA-binding assays; S. Montaño and other members of the Rice laboratory for help and discussions; the staffs at beamlines BioCARS 14, SBC 19-ID and 19-BM, and LS-CAT 21-ID-F at the Advanced Photon Source, Argonne National Laboratory, for helping with the synchrotron X-ray data collection. The research is supported in part by National Institutes of Health grant GM058827.

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Authors

Contributions

A.P.P.Z. grew the crystals, determined the structure and performed the affinity assays. Y.Z.P. assisted greatly with cloning, protein purification, and crystal screening and optimization. P.R. designed and directed the project and assisted in crystallographic data collection and structure determination. A.P.P.Z. and P.A.R. wrote the manuscript.

Corresponding author

Correspondence to Phoebe A. Rice.

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The authors declare no competing financial interests.

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This file contains Supplementary Tables 1-3, Supplementary Figures 1-5 with legends and References. (PDF 1906 kb)

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Zhang, A., Pigli, Y. & Rice, P. Structure of the LexA–DNA complex and implications for SOS box measurement. Nature 466, 883–886 (2010). https://doi.org/10.1038/nature09200

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