Crystal Structure of SUMO-3-modified Thymine-DNA Glycosylase

Journal of Molecular Biology

Volumn 359, Issue 1, 2006, Pages 137-147

  Baba, Daichi ^a,b   Maita, Nobuo ^c   Jee, Jun Goo ^d   Uchimura, Yasuhiro ^e   Saitoh, Hisato ^e   Sugasawa, Kaoru ^f,g   Hanaoka, Fumio ^f,g,h   Tochio, Hidehito ^a   Hiroaki, Hidekazu ^a   Shirakawa, Masahiro ^b,g,i  

^a YOKOHAMA CITY UNIVERSITY   (Japan)

^b KYOTO UNIVERSITY   (Japan)

^c KYUSHU UNIVERSITY   (Japan)

^d NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES   (United States)

^e KUMAMOTO UNIVERSITY   (Japan)

^f Japan Science and Technology Agency   (Japan)

^g JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

^h OSAKA UNIVERSITY   (Japan)

ⁱ RIKEN YOKOHAMA INSTITUTE   (Japan)

Author keywords

DNA repair; post translational protein modification; SUMO

Indexed keywords

SUMO 1 PROTEIN; THYMINE DNA GLYCOSYLASE;

AMINO ACID SEQUENCE; ARTICLE; BINDING AFFINITY; CONTROLLED STUDY; CRYSTAL STRUCTURE; DNA BINDING; ESCHERICHIA COLI; GENE TARGETING; MOLECULAR DYNAMICS; NONHUMAN; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN MODIFICATION; PROTEIN STRUCTURE;

EID: 33646174474     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2006.03.036     Document Type: Article

References (38)

1. Hay R.T. SUMO: a history of modification. Mol. Cell 18 (2005) 1-12
2. Johnson E.S. Protein modification by SUMO. Annu. Rev. Biochem. 73 (2004) 355-382
3. Seeler J.S., and Dejean A. Nuclear and unclear functions of SUMO. Nature Rev. Mol. Cell. Biol. 4 (2003) 690-699
4. Gill G. SUMO and ubiquitin in the nucleus: different functions, similar mechanisms?. Genes Dev. 18 (2004) 2046-2059
5. Mahajan R., Delphin C., Guan T., Gerace L., and Melchior F. A small ubiquitin-related polypeptide involved in targeting RanGAP1 to nuclear pore complex protein RanBP2. Cell 88 (1997) 97-107
6. Girdwood D., Bumpass D., Vaughan O.A., Thain A., Anderson L.A., Snowden A.W., et al. P300 transcriptional repression is mediated by SUMO modification. Mol. Cell 11 (2003) 1043-1054
7. Yang S.H., and Sharrocks A.D. SUMO promotes HDAC-mediated transcriptional repression. Mol. Cell 13 (2004) 611-617
8. Ishov A.M., Sotnikov A.G., Negorev D., Vladimirova O.V., Neff N., Kamitani T., et al. PML is critical for ND10 formation and recruits the PML-interacting protein daxx to this nuclear structure when modified by SUMO-1. J. Cell Biol. 147 (1999) 221-234
9. Seeler J.S., Marchio A., Losson R., Desterro J.M., Hay R.T., Chambon P., and Dejean A. A common properties of nuclear body protein SP100 and TIF1alpha chromatin factor: role of SUMO modification. Mol. Cell. Biol. 21 (2001) 3314-3324
10. Hardeland U., Steinacher R., Jiricny J., and Schar P. Modification of the human thymine-DNA glycosylase by ubiquitin-like proteins facilitates enzymatic turnover. EMBO J. 21 (2002) 1456-1464
11. Hong Y., Rogers R., Matunis M.J., Mayhew C.N., Goodson M.L., Park-Sarge O.K., and Sarge K.D. Regulation of heat shock transcription factor 1 by stress-induced SUMO-1 modification. J. Biol. Chem. 276 (2001) 40263-40267
12. Goodson M.L., Hong Y., Rogers R., Matunis M.J., Park-Sarge O.K., and Sarge K.D. SUMO-1 modification regulates the DNA binding activity of heat shock transcription factor 2, a promyelocytic leukemia nuclear body associated transcription factor. J. Biol. Chem. 276 (2001) 18513-18518
13. Kim K.I., Baek S.H., and Chung C.H. Versatile protein tag, SUMO: its enzymology and biological function. J. Cell Physiol. 191 (2002) 257-268
14. Guo D., Li M., Zhang Y., Yang P., Eckenrode S., Hopkins D., et al. A functional variant of SUMO4, a new I kappa B alpha modifier, is associated with type 1 diabetes. Nature Genet. 36 (2004) 837-841
15. Vertegaal A.C., Ogg S.C., Jaffray E., Rodriguez M.S., Hay R.T., Andersen J.S., et al. A proteomic study of SUMO-2 target proteins. J. Biol. Chem. 279 (2004) 33791-33798
16. Zhao Y., Kwon S.W., Anselmo A., Kaur K., and White M.A. Broad spectrum identification of cellular small ubiquitin-related modifier (SUMO) substrate proteins. J. Biol. Chem. 279 (2004) 20999-21002
17. Saitoh H., and Hinchey J. Functional heterogeneity of small ubiquitin-related modifiers SUMO-1 versus SUMO-2/3. J. Biol. Chem. 275 (2000) 6252-6258
18. Macauley M.S., Errington W.J., Okon M., Scharpf M., Mackereth C.D., Schulman B.A., and McIntosh L.P. Structural and dynamic independence of isopeptide-linked RanGAP1 and SUMO-1. J. Biol. Chem. 279 (2004) 49131-49137
19. Pichler A., Knipscheer P., Oberhofer E., van Dijk W.J., Korner R., Olsen J.V., et al. SUMO modification of the ubiquitin-conjugating enzyme E2-25K. Nature Struct. Mol. Biol. 12 (2005) 264-269
20. Reverter D., and Lima C.D. Insights into E3 ligase activity revealed by a SUMO-RanGAP1-Ubc9-Nup358 complex. Nature 435 (2005) 687-692
21. Baba D., Maita N., Jee J.G., Uchimura Y., Saito H., Sugasawa K., et al. Crystal structure of thymine DNA glycosylase conjugated to SUMO-1. Nature 435 (2005) 979-982
22. Hardeland U., Bentele M., Lettieri T., Steinacher R., Jiricny J., and Schar P. Thymine DNA glycosylase. Prog. Nucl. Acid Res. Mol. Biol. 68 (2001) 235-253
23. Tornaletti S., and Pfeifer G.P. Complete and tissue-independent methylation of CpG sites in the p53 gene: implications for mutations in human cancers. Oncogene 10 (1995) 1493-1499
24. Waters T.R., and Swann P.F. Kinetics of the action of thymine DNA glycosylase. J. Biol. Chem. 273 (1998) 20007-20014
25. Waters T.R., Gallinari P., Jiricny J., and 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 (1999) 67-74
26. Song J., Durrin L.K., Wilkinson T.A., Krontiris T.G., and Chen Y. Identification of a SUMO-binding motif that recognizes SUMO-modified proteins. Proc. Natl Acad. Sci. USA 101 (2004) 14373-14378
27. Barrett T.E., Savva R., Panayotou G., Barlow T., Brown T., Jiricny J., and Pearl L.H. Crystal structure of a G:T/U mismatch-specific DNA glycosylase: mismatch recognition by complementary-strand interactions. Cell 92 (1998) 117-129
28. Huang W.C., Ko T.P., Li S.S., and Wang A.H. Crystal structures of the human SUMO-2 protein at 1.6 Å and 1.2 Å resolution: implication on the functional differences of SUMO proteins. Eur. J. Biochem. 271 (2004) 4114-4122
29. Tatham M.H., Jaffray E., Vaughan O.A., Desterro J.M., Botting C.H., Naismith J.H., and Hay R.T. Polymeric chains of SUMO-2 and SUMO-3 are conjugated to protein substrates by SAE1/SAE2 and Ubc9. J. Biol. Chem. 276 (2001) 35368-35374
30. Gallinari P., and Jiricny J. A new class of uracil-DNA glycosylases related to human thymine-DNA glycosylase. Nature 383 (1996) 735-738
31. Song J., Zhang Z., Hu W., and Chen Y. Small ubiquitin-like modifier (SUMO) recognition of a SUMO binding motif: a reversal of the bound orientation. J. Biol. Chem. 280 (2005) 40122-40129
32. Hannich J.T., Lewis A., Kroetz M.B., Li S.J., Heide H., Emili A., and Hochstrasser M. Defining the SUMO-modified proteome by multiple approaches in Saccharomyces cerevisiae. J. Biol. Chem. 280 (2005) 4102-4110
33. Uchimura Y., Nakamura M., Sugasawa K., Nakao M., and Saitoh H. Overproduction of eukaryotic SUMO-1- and SUMO-2-conjugated proteins in Escherichia coli. Anal. Biochem. 331 (2004) 204-206
34. Leslie A.G. Integration of macromolecular diffraction data. Acta Crystallog. sect. D 55 (1999) 1696-1702
35. Collaborative Computational Project, Number 4. The CCP4 suite: programs for protein crystallography. Acta Crystallog. sect. D 50 (1994) 760-763
36. Vagin A., and Teplyakov A. MOLREP: an automated program for molecular replacement. J. Appl. Crystallog. 30 (1997) 1022-1025
37. Jones T.A., Zou J.Y., Cowan S.W., and Kjeldgaard M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallog. sect. A 47 (1991) 110-119
38. Brunger A.T., Adams P.D., Clore G.M., DeLano W.L., Gros P., Grosse-Kunstleve R.W., et al. Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallog. sect. D 54 (1998) 905-921