Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Letter
  • Published:

Crystal structure of thymine DNA glycosylase conjugated to SUMO-1

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.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Structure of SUMO-1–TDG.
Figure 2: Molecular interface between TDG and SUMO-1.
Figure 3: Model of a complex between SUMO-1–TDG and a DNA molecule containing an AP site.
Figure 4: DNA and SUMO-1 binding activity of TDG.

Similar content being viewed by others

References

  1. Johnson, E. S. Protein modification by SUMO. Annu. Rev. Biochem. 73, 355–382 (2004)

    Article  CAS  Google Scholar 

  2. Gill, G. SUMO and ubiquitin in the nucleus: different functions, similar mechanisms? Genes Dev. 18, 2046–2059 (2004)

    Article  CAS  Google Scholar 

  3. Seeler, J. S. & Dejean, A. Nuclear and unclear functions of SUMO. Nature Rev. Mol. Cell Biol. 4, 690–699 (2003)

    Article  CAS  Google Scholar 

  4. Kim, K. I., Baek, S. H. & Chung, C. H. Versatile protein tag, SUMO: its enzymology and biological function. J. Cell. Physiol. 191, 257–268 (2002)

    Article  CAS  Google Scholar 

  5. Mahajan, R., Delphin, C., Guan, T., Gerace, L. & Melchior, F. A small ubiquitin-related polypeptide involved in targeting RanGAP1 to nuclear pore complex protein RanBP2. Cell 88, 97–107 (1997)

    Article  CAS  Google Scholar 

  6. Hardeland, U. et al. Thymine DNA glycosylase. Prog. Nucleic Acid Res. Mol. Biol. 68, 235–253 (2001)

    Article  CAS  Google Scholar 

  7. Waters, T. R. & Swann, P. F. Kinetics of the action of thymine DNA glycosylase. J. Biol. Chem. 273, 20007–20014 (1998)

    Article  CAS  Google Scholar 

  8. Waters, T. R., Gallinari, P., Jiricny, J. & Swann, P. F. Human thymine DNA glycosylase binds to apurinic sites in DNA but is displaced by human apurinic endonuclease 1. J. Biol. Chem. 274, 67–74 (1999)

    Article  CAS  Google Scholar 

  9. Hardeland, U., Steinacher, R., Jiricny, J. & Schar, P. Modification of the human thymine-DNA glycosylase by ubiquitin-like proteins facilitates enzymatic turnover. EMBO J. 21, 1456–1464 (2002)

    Article  CAS  Google Scholar 

  10. Barrett, T. E. et al. Crystal structure of a G:T/U mismatch-specific DNA glycosylase: mismatch recognition by complementary-strand interactions. Cell 92, 117–129 (1998)

    Article  CAS  Google Scholar 

  11. Hardeland, U., Bentele, M., Jiricny, J. & Schar, P. Separating substrate recognition from base hydrolysis in human thymine DNA glycosylase by mutational analysis. J. Biol. Chem. 275, 33449–33456 (2000)

    Article  CAS  Google Scholar 

  12. Roberts, R. J. On base flipping. Cell 82, 9–12 (1995)

    Article  CAS  Google Scholar 

  13. Mol, C. D. et al. Crystal structure of human uracil-DNA glycosylase in complex with a protein inhibitor: protein mimicry of DNA. Cell 82, 701–708 (1995)

    Article  CAS  Google Scholar 

  14. Mol, C. D. et al. Crystal structure and mutational analysis of human uracil-DNA glycosylase: structural basis for specificity and catalysis. Cell 80, 869–878 (1995)

    Article  CAS  Google Scholar 

  15. Bayer, P. et al. Structure determination of the small ubiquitin-related modifier SUMO-1. J. Mol. Biol. 280, 275–286 (1998)

    Article  CAS  Google Scholar 

  16. Song, J., Durrin, L. K., Wilkinson, T. A., Krontiris, T. G. & Chen, Y. Identification of a SUMO-binding motif that recognizes SUMO-modified proteins. Proc. Natl Acad. Sci. USA 101, 14373–14378 (2004)

    Article  ADS  CAS  Google Scholar 

  17. Uchimura, Y., Nakamura, M., Sugasawa, K., Nakao, M. & Saitoh, H. Overproduction of eukaryotic SUMO-1- and SUMO-2-conjugated proteins in Escherichia coli. Anal. Biochem. 331, 204–206 (2004)

    Article  CAS  Google Scholar 

  18. Leslie, A. G. Integration of macromolecular diffraction data. Acta Crystallogr. D 55, 1696–1702 (1999)

    Article  CAS  Google Scholar 

  19. Collaborative Computational Project No. 4, The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D 50, 760–763 (1994)

    Article  Google Scholar 

  20. Vagin, A. & Teplyakov, A. MOLREP: an automated program for molecular replacement. J. Appl. Crystallogr. 30, 1022–1025 (1997)

    Article  CAS  Google Scholar 

  21. Mossessova, E. & Lima, C. D. Ulp1-SUMO crystal structure and genetic analysis reveal conserved interactions and a regulatory element essential for cell growth in yeast. Mol. Cell 5, 865–876 (2000)

    Article  CAS  Google Scholar 

  22. Jones, T. A., Zou, J. Y., Cowan, S. W. & Kjeldgaard, M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47, 110–119 (1991)

    Article  Google Scholar 

  23. Brunger, A. T. et al. Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D 54, 905–921 (1998)

    Article  CAS  Google Scholar 

  24. DeLano, W. L. PyMOLhttp://www.pymol.org (2002).

  25. Barrett, T. E. et al. Crystal structure of a thwarted mismatch glycosylase DNA repair complex. EMBO J. 18, 6599–6609 (1999)

    Article  CAS  Google Scholar 

Download references

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.

Author information

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
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Nobuo Maita
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Jun-Goo Jee
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Yasuhiro Uchimura
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Hisato Saitoh
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Kaoru Sugasawa
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Fumio Hanaoka
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Hidehito Tochio
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Hidekazu Hiroaki
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Masahiro Shirakawa
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Masahiro Shirakawa.

Ethics declarations

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.

Supplementary information

Supplementary Figure S1

Electron density map of SUMO1-TDG (DOC 745 kb)

Supplementary Figure S2

Limited proteolysis of TDG and SUMO1-TDG (DOC 539 kb)

Supplementary Figure S3

DNA and SUMO-1 binding activity of the full-length TDG (DOC 1491 kb)

Supplementary Table S1

Data collection and model refinement statistics (DOC 45 kb)

Supplementary Methods

Protein expression and purification (DOC 26 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

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

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature03634

This article is cited by

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing