Crystal structure of thymine DNA glycosylase conjugated to SUMO-1 (original) (raw)

Nature volume 435, pages 979–982 (2005)Cite this article

Abstract

Members of the small ubiquitin-like modifier (SUMO) family can be covalently attached to the lysine residue of a target protein through an enzymatic pathway similar to that used in ubiquitin conjugation1, and are involved in various cellular events that do not rely on degradative signalling via the proteasome or lysosome2,3,4,5. However, little is known about the molecular mechanisms of SUMO-modification-induced protein functional transfer. During DNA mismatch repair, SUMO conjugation of the uracil/thymine DNA glycosylase TDG promotes the release of TDG from the abasic (AP) site created after base excision, and coordinates its transfer to AP endonuclease 1, which catalyses the next step in the repair pathway6. Here we report the crystal structure of the central region of human TDG conjugated to SUMO-1 at 2.1 Å resolution. The structure reveals a helix protruding from the protein surface, which presumably interferes with the product DNA and thus promotes the dissociation of TDG from the DNA molecule. This helix is formed by covalent and non-covalent contacts between TDG and SUMO-1. The non-covalent contacts are also essential for release from the product DNA, as verified by mutagenesis.

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Acknowledgements

This work was supported by grants to M.S. from the Japanese Ministry of Education, Science, Sports and Culture, and Japan Science and Technology Agency.

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Author notes

  1. Jun-Goo Jee
    Present address: Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, 20892, USA

Authors and Affiliations

  1. Graduate School of Integrated Science, Yokohama City University, Yokohama, 230-0045, Japan
    Daichi Baba, Nobuo Maita, Hidehito Tochio, Hidekazu Hiroaki & Masahiro Shirakawa
  2. Japan Biological Informatics Consortium, Tokyo, 104-0032, Japan
    Nobuo Maita
  3. RIKEN Genomic Sciences Center, Yokohama, Kanagawa, 230-0045, Japan
    Jun-Goo Jee & Masahiro Shirakawa
  4. Department of Regeneration Medicine, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, 860-0811, Japan
    Yasuhiro Uchimura & Hisato Saitoh
  5. Cellular Physiology Laboratory, Discovery Research Institute, RIKEN, Wako, 351-0198, Japan
    Kaoru Sugasawa & Fumio Hanaoka
  6. SORST, Japan Science and Technology Agency, 332-0012, Saitama, Kawaguchi, Japan
    Kaoru Sugasawa & Fumio Hanaoka
  7. Graduate School of Frontier Biosciences, Osaka University, Suita, 565-0871, Japan
    Fumio Hanaoka
  8. Graduate School of Engineering, Kyoto University, Kyoto, 615-8510, Japan
    Masahiro Shirakawa
  9. CREST, Japan Science and Technology Corporation, Kawaguchi, 332-0012, Saitama, Japan
    Masahiro Shirakawa

Authors

  1. Daichi Baba
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  2. Nobuo Maita
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  3. Jun-Goo Jee
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  4. Yasuhiro Uchimura
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  5. Hisato Saitoh
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  6. Kaoru Sugasawa
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  7. Fumio Hanaoka
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  8. Hidehito Tochio
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  9. Hidekazu Hiroaki
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  10. Masahiro Shirakawa
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Corresponding author

Correspondence toMasahiro Shirakawa.

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Competing interests

Atomic coordinates of SUMO-1–TDG have been deposited in the Protein Data Bank under the accession number 1WYW. Reprints and permissions information is available at npg.nature.com/reprintsandpermissions. The authors declare no competing financial interests.

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Baba, D., Maita, N., Jee, JG. et al. Crystal structure of thymine DNA glycosylase conjugated to SUMO-1.Nature 435, 979–982 (2005). https://doi.org/10.1038/nature03634

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