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Structure of UvrA nucleotide excision repair protein in complex with modified DNA

Nature Structural & Molecular Biology volume 18, pages 191–197 (2011)Cite this article

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Abstract

One of the primary pathways for removal of DNA damage is nucleotide excision repair (NER). In bacteria, the UvrA protein is the component of NER that locates the lesion. A notable feature of NER is its ability to act on many DNA modifications that vary in chemical structure. So far, the mechanism underlying this broad specificity has been unclear. Here, we report the first crystal structure of a UvrA protein in complex with a chemically modified oligonucleotide. The structure shows that the UvrA dimer does not contact the site of lesion directly, but rather binds the DNA regions on both sides of the modification. The DNA region harboring the modification is deformed, with the double helix bent and unwound. UvrA uses damage-induced deformations of the DNA and a less rigid structure of the modified double helix for indirect readout of the lesion.

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Figure 1: Binding and processing of the palindromic DNA substrate.
Figure 2: Structure of complex.
Figure 3: DNA binding.
Figure 4: Deformation of the DNA.
Figure 5: Comparison of Bst-UvrA–ADP and Tm-UvrA–DNA structures.

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Acknowledgements

We thank T. Sixma and J. Bujnicki for critical reading of the manuscript, M. Rychlik, M. Cybulska and J. Dyttus for excellent technical assistance, the staff of beamline 23-2 at European Synchrotron Radiation Facility (ESRF) and beamline 14-1 at Berliner Elektronenspeicherring-Gesellschaft für Synchrotronstrahlung (BESSY) for assistance with data collection, K. Górecka and M. Figiel for their help with data collection and P. Afonine and S. Ramón Maiques for help with structure refinement. This work was supported by a European Molecular Biology Organization Installation Grant to M.N. The access to ESRF was financed by the Polish Ministry of Science and Higher Education (project no. ESRF/73/2006). The research leading to these results has also received funding from the European Community's Seventh Framework Program under grant agreement no. 226716.

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Authors and Affiliations

  1. Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Warsaw, Poland

    Marcin Jaciuk, Elżbieta Nowak, Anna Tańska & Marcin Nowotny

  2. Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Warsaw, Poland

    Krzysztof Skowronek

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Contributions

M.J. purified Tm-UvrA, obtained its complex crystals and carried out the biochemical experiments. K.S. and E.N. carried out the biochemical experiments. A.T. carried out the initial expression and purification studies. M.N. collected the data. M.J., E.N. and M.N. refined and analyzed the structure. M.N. wrote the manuscript.

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Correspondence to Marcin Nowotny.

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Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–3, Supplementary Table 1 and Supplementary Methods (PDF 1911 kb)

Supplementary Video 1

Morphing between the DNA structure observed in the Tm-UvrA–DNA complex and the model of ideal B-form DNA to visualize the deformations of the DNA. The thymine residue with fluorescein modification is shown in orange. (MOV 2288 kb)

Supplementary Video 2

Tm-UvrA surface representation with morphing of the DNA structure as in Supplementary Video 1. Protein surface was added to visualize its complementarity with deformed DNA conformation. (MOV 3755 kb)

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Jaciuk, M., Nowak, E., Skowronek, K. et al. Structure of UvrA nucleotide excision repair protein in complex with modified DNA. Nat Struct Mol Biol 18, 191–197 (2011). https://doi.org/10.1038/nsmb.1973

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