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Recognition of DNA damage by the Rad4 nucleotide excision repair protein

Nature volume 449, pages 570575 (04 October 2007) | Download Citation

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Abstract

Mutations in the nucleotide excision repair (NER) pathway can cause the xeroderma pigmentosum skin cancer predisposition syndrome. NER lesions are limited to one DNA strand, but otherwise they are chemically and structurally diverse, being caused by a wide variety of genotoxic chemicals and ultraviolet radiation. The xeroderma pigmentosum C (XPC) protein has a central role in initiating global-genome NER by recognizing the lesion and recruiting downstream factors. Here we present the crystal structure of the yeast XPC orthologue Rad4 bound to DNA containing a cyclobutane pyrimidine dimer (CPD) lesion. The structure shows that Rad4 inserts a β-hairpin through the DNA duplex, causing the two damaged base pairs to flip out of the double helix. The expelled nucleotides of the undamaged strand are recognized by Rad4, whereas the two CPD-linked nucleotides become disordered. These findings indicate that the lesions recognized by Rad4/XPC thermodynamically destabilize the Watson–Crick double helix in a manner that facilitates the flipping-out of two base pairs.

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  • 04 October 2007

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Acknowledgements

We thank D. King for mass spectroscopic analysis; H. Erdjument-Bromage for N-terminal sequencing; the staff of the Advanced Photon Source ID-24 and 8-BM beamlines for help with data collection; M. Minto for administrative assistance; and Y. Goldgur, A. Wong, A. Smalls-Mantey, A. Rozenbaum and the members of the Pavletich laboratory for help and discussions. This work was supported by the NIH and the Howard Hughes Medical Institute. J.-H.M. was supported by the Leukemia & Lymphoma Society as a Special Fellow.

Coordinates and structure factors of the Rad4–Rad23 and Rad4–Rad23–DNA complexes have been deposited in the Protein Data Bank under accession code 2QSF (Rad4–Rad23), 2QSG (Rad4–Rad23 bound to CPD-mismatch DNA) and 2QSH (Rad4–Rad23 bound to mismatch-only DNA).

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Affiliations

  1. Structural Biology Program and,

    • Jung-Hyun Min
    •  & Nikola P. Pavletich
  2. Howard Hughes Medical Institute, Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA

    • Nikola P. Pavletich

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Reprints and permissions information is available at www.nature.com/reprints. The authors declare no competing financial interests.

Corresponding author

Correspondence to Nikola P. Pavletich.

Supplementary information

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    Supplementary Information

    This file contains Supplementary Tables 1–2, Supplementary Figures 1–7 with Legends, and Supplementary Discussion. Supplementary Table 1 contains crystallographic statistics. Supplementary Table 2 contains DNA sequences used for crystallization and EMSA. Supplementary Figures and Discussion contain detailed characterization/description of the Rad4–Rad23 complex and its apo- and DNA-bound crystal structures presented in the paper.

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https://doi.org/10.1038/nature06155

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