Structural and functional studies of SUMO ylation and poly-ubiquitination

• Project/Area Number: 16370052
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Structural biochemistry
• Research Institution: Kyoto University
• Principal Investigator: SHIRAKAWA Masahiro Kyoto University, Department of Molecular Engineering, Professor (00202119)
• Project Period (FY): 2004 – 2005
• Project Status: Completed (Fiscal Year 2005)
• Budget Amount: ¥15,000,000 (Direct Cost: ¥15,000,000); Fiscal Year 2005: ¥7,100,000 (Direct Cost: ¥7,100,000); Fiscal Year 2004: ¥7,900,000 (Direct Cost: ¥7,900,000)
• Keywords: SUMO / protein modification / DNA repair / protein structure determination / X-ray crystallography / ユビキチン / ポリユビキチン / NMR / 立体構造

Research Abstract

Attachment of SUMO (Small ubiquitin-like modifier) family proteins is a post-translational modification that regulates the functions, structures or localizations of modified proteins, and regulates a vast arrays of cellular functions, such as transcription, DNA repair and regulation of chromatin structures. One of the target proteins, Thymine DNA glycosylase (TDG) is an DNA glycosylase that is thought to excise mismatch base from DNA containing G-U or G-T base pairs. SUMO-1 or SUMO-2/3 attachment of TDG has been proposed to promote its dissociation from DNA containing an abasic site.
We have determined the crystal structure of the central region of TDG, which involves the catalytic core domain and the SUMOylation site, conjugated to SUMO-1 (SUMO-1-TDG) or SUMO-3 (SUMO-3-TDG). The structure of SUMO-1-TDG shows that the central region of TDG interacts SUMO-1 through both covalent and non-covalent contacts, which seemingly induces a structural rearrangement in a region of TDG. A model building assumes that this possible structural change may create a protrusion on the protein surface, which is positioned so as to make a steric clash with DNA bound to TDG. The structure of SUMO-3-TDG is similar to that of SUMO-1-TDG.

Research Products

• [Journal Article] The structure of the third intracellular loop of the muscarinic acetylcholine receptor M2 subtype. (2006)
  • Author(s): Ichiyama S., Oka Y., Haga, K., Kojima, S., Tateishi, Y., Shirakawa, M., Haga, T.
  • Journal Title: FEBS Letter 580 Pages: 23-26
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Crystal Structure of thymine DNA glycosylase conjugated to SUMO-1. (2006)
  • Author(s): Baba, D., Maita, N., Jee, J. -G., Uchimura, Y., Saitoh, H., Sugasawa, K., Hanaoka, F., Tochio, H., Hiroaki, H., Shirakawa, M.
  • Journal Title: Nature 435 Pages: 979-982
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] The structure of the third intracellular loop of the muscarinic acetylcholine receptor M2 subtype. (2006)
  • Author(s): Ichiyama, S., Oka, Y., Haga, K, Kojima, S., Tateishi, Y., Shirakawa. M., Haga, T.
  • Journal Title: FEBSLetter 580 Pages: 23-26
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Crystal Structure of thymine DNA glycosylase conjugated to SUMO-1. (2006)
  • Author(s): Baba, D., Maita, N., Jee, J.-G., Uchimura, Y., Saitoh, H., Sugasawa, K, Hanaoka, R, Tochio, H., Hiroaki, H., Shirakawa, M.
  • Journal Title: Nature 435 Pages: 979-982
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Crystal Structure of thymine DNA glycosylase conjugated to SUMO-1. (2006)
  • Author(s): Baba, D., Maita, N., Jee, J.-G., Uchimura, Y., Saitoh, H., Sugasawa, K., Hanaoka, F., Tochio, H., Hiroaki, H., Shirakawa, M.
  • Journal Title: Nature 435 Pages: 979-982
• [Journal Article] The UBL-UBA protein KPC2 is required for degradation of p27 at G1 phase. (2005)
  • Author(s): Hara, T., Kamura, T., Kotoshiba, S., Fujiwara, K., Onoyama, I., Shirakawa, M., Nakayama, K. -l.
  • Journal Title: Molecular and Cellular Biology 25 Pages: 9292-9303
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Molecular mechanism of a temperature-sensitive phenotype in peroxisomal biogenesis disorder. (2005)
  • Author(s): Hashimoto, K., Kato, Z., Nagase, T., Shimozawa, N., Kuwata, K., Omoya, K., Li, A., Matsukuma, E., Yamamoto, Y., Ohnishi, H., Tochio, H., Shirakawa, M., Suzuki, Y., Wanders, R. J. A., Kondo, N.
  • Journal Title: Pediatric Research 58 Pages: 263-9
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Structural characterization of the MIT domain from human Vps4b. (2005)
  • Author(s): Takasu, H., Jee, J. G., Ohno, A., Goda, N., Fujiwara, K., Tochio, H., Shirakawa, M., Hiroaki, H.
  • Journal Title: Biochemical and Biophysical Research Communications 334 Pages: 460-465
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Plc1p, Arg82p, and Kcs1p, enzymes involved in inositol pyrophosphate synthesis, are essential for phosphate regulation and polyphosphate accumulation in Saccharomyces cerevisiae. (2005)
  • Author(s): Auesukaree, C., Tochio, H., Shirakawa. M., Kaneko, Y., Harashima, S.
  • Journal Title: Journal of Biological Chemistry 280 Pages: 25127-25133
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Structure of the UBA domain of Dsk2p in complex with Ubiquitin : Molecular Determinants for Ubiquitin Recognition (2005)
  • Author(s): Ohno, A., Jee, J-G, Fujiwara, K., Tenno, T., Goda, N., Tochio, H., Kobayashi, H., Hiroaki, H., Shirakawa, M.
  • Journal Title: Structure 13 Pages: 521-532
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Backbone (1)H, (13)C, and (15)E. coli nickel binding protein NikA. (2005)
  • Author(s): Rajesh, S., Heddle, J. G., Kurashima-Ito, K., Nietlispach, D., Shirakawa. M., Tame, J. R., Ito, Y.
  • Journal Title: J Biomolecular NMR 32 Pages: 177-177
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] K.-I. The UBL-UBA protein KPC2 is required for degradation of p27 at Gl phase. (2005)
  • Author(s): Hara, T., Kamura, T., Kotoshiba, S., Fujiwara, K., Onoyama, I., Shirakawa, M., Nakayama
  • Journal Title: Molecular and Cellular Biology 25 Pages: 9292-9303
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Molecular mechanism of a temperature-sensitive phenotype in peroxisomal biogenesis disorder. (2005)
  • Author(s): Hashimoto, K., Kato, Z., Nagase, T., Shimozawa, N., Kuwata, K., Omoya, K.,Li, A., Matsukuma, B., Yamamoto, Y., Ohnishi, H., Tochio, H., Shirakawa. M..Suzuki. Y, Wanders, R. J. A., Kondo, N.
  • Journal Title: Pediatric Research 58 Pages: 263-9
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Structural characterization of the MIT domain from human Vps4b. (2005)
  • Author(s): Takasu, H., Jee, J. G., Ohno, A., Goda, N., Fujiwara, K, Tochio, H., Shirakawa. M.., Hiroaki, H.
  • Journal Title: Biochemical and Biophysical Research Communications 334 Pages: 460-465
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Plclp, Arg82p, and Kcslp, enzymes involved in inositol pyrophosphate synthesis, are essential for phosphate regulation and polyphosphate accumulation in Saccharomyces cerevisiae. (2005)
  • Author(s): Auesukaree, C, Tochio, H., Shirakawa. M.. Kaneko, Y., Harashima, S.
  • Journal Title: Journal of Biological Chemistry 280 Pages: 25127-25133
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Structure of the UBA domain of Dsk2p in complex with Ubiquitin: Molecular Determinants for Ubiquitin Recognition. (2005)
  • Author(s): Ohno, A., Jee, J-G, Fujiwara, K, Tenno, T., Goda, N., Tochio, H., Kobayashi, H., Hiroaki, H., Shirakawa, M.
  • Journal Title: Structure 13 Pages: 521-532
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Backbone (l)H, (13)C, and (15) B, coli nickel binding protein NikA. (2005)
  • Author(s): Rajesh, S., Heddle, J. G., Kurashima-Ito, K, Nietlispach, D., Shirakawa. M.. Tame, J. R., Ito, Y.
  • Journal Title: J Biomolecular NMR 32 Pages: 177-177
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Structural characterization of MIT domain from human Vps4b.. (2005)
  • Author(s): Takasu, H., Jee, J.G., Ohno, A., Goda, N., Fujiwara, K., Tochio, H., Shirakawa, M., Hiroaki, H.
  • Journal Title: Biochemical and Biophysical Research Communication 334 Pages: 460-465
• [Journal Article] Molecular mechanism of a temperature-sensitive phenotype in peroxisomal biogenesis disorder (2005)
  • Author(s): Hashimoto, K., Kato, Z., Nagase, T., Shimozawa, N., Kuwata, K., Omoya, K., Li, A., Matsukuma, E., Yamamoto, Y., Ohnishi, H., Tochio, H., Shirakawa, M., Suzuki, Y., Wanders, R.J.A., Kondo, N.
  • Journal Title: Pediatric Research, 58 Pages: 263-269
• [Journal Article] Plc1p, Arg28p, and Kcs1p, enzymes involved in inositol pyrophosphate synthesis, are essential for phosphate regulation and polyphosphate accumulation in Saccharomyces cerevisiae (2005)
  • Author(s): Auseukaree, C., Tochio, H., Shirakawa, M., Kaneko, Y., Harashima, S.
  • Journal Title: Journal of Biological Chemistry 280 Pages: 25127-25133
• [Journal Article] Backbone (1)H, (13)C, and (15) E.coli nickel binding protein NikA. (2005)
  • Author(s): Rajesh, S., Heddle, J.G., Kurashima-Ito, K., Nietlispach, D., Shirakawa, M., Tame, J.R., Ito, Y.
  • Journal Title: J Biomolecular NMR 32 Pages: 177-177
• [Journal Article] p53 suppresses c-Myb-induced trans-activation and transformation by recruiting the corepressor mSin3A. (2004)
  • Author(s): Tanikawa, J., Nomura, T., Macmillan, E. M., Shinagawa, T. Jin, W., Kokura K., Baba, D., Shirakawa, M., Gonda, T. J., Ishii, S.
  • Journal Title: Journal of Biological Chemistry 279 Pages: 55393-55400
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Two-Metal Ion, Ni(II) and Cu(II), Binding a-Helical Coiled-coil Peptide. (2004)
  • Author(s): Tanaka, T., Mizuno, T., Fukui, S., Hiroaki, H., Oku. J., Kanaori, K., Tajima, K., Shirakawa, M.
  • Journal Title: Journal of American Chemical Society 126 Pages: 14023-14028
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Structure of the N-terminal domain of PEX1 AAA-ATPase : characterization of a putative adaptor-binding domain. (2004)
  • Author(s): Shiozawa, K., Maita, N., Tomii, K., Seto, A., Goda N., Akiyama, Y., Shimizu, T., Shirakawa, M., Hiroaki, H.
  • Journal Title: Journal of Biological Chemistry 279 Pages: 50060-50068
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Crystallographic characterization of the N-terminal domain of PEX1. (2004)
  • Author(s): Shiozawa, K., Maita, N., Tomii, K., Seto, A., Goda, N., Akiyama, Y., Shimizu, T., Shirakawa, M., Hiroaki, H.
  • Journal Title: Acta Crystallography D Biological Crystallography 60 Pages: 2098-2099
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Structural basis for distinct roles of Lys63-and Lys48-linked polyubiquitin chains. (2004)
  • Author(s): Tenno, T., Fujiwara, K., Tochio, H., Iwai, K., Morita, E. H., Hayashi, H., Murata, S., Hiroaki, H., Sato, M., Tanaka, K., Shrakawa, M.
  • Journal Title: Genes to Cells 9 Pages: 865-875
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Small ubiquitin-like modifier 1 (SUMO-1)modification of the synergy control motif of Ad4 binding protein/steroidogenic factor 1 (Ad4BP/SF-1)regulates synergistic transcription between Ad4BP/SF-1 and Sox9. (2004)
  • Author(s): Komatsu, T., Mizusaki, H., Mukai T., Ogawa, H., Baba, D., Shirakawa, M., Hatakeyama, S., Nakayama, K. I., Yamamoto, H., Kikuchi, A., Morohashi, K.
  • Journal Title: Molecular Endocrinology 18 Pages: 2451-2462
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] MUTYH prevents OGG1 or APEX1 from inappropriately processing its substrate or reaction product with its C-terminal domain. (2004)
  • Author(s): Tominaga, Y., Ushijima, Y., Tsuchimoto, D., Mishima, M., Shirakawa, M., Hirano, Sakumi, K., Nakabeppu, Y.
  • Journal Title: Nucleic Acid Research 15 Pages: 3198-3211
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Structure of human MTH1, a Nudix family hydrolase that selectively degrades oxidized purine nucleoside triphosphates. (2004)
  • Author(s): Mishima, M., Sakai, Y., Itoh, N., Kamiya, H., Furuichi, M., Takahashi, M., Yamagata, Y., Iwai, S., Nakabeppu, Y., Shirakawa, M.
  • Journal Title: Journal of Biological Chemistry 279 Pages: 33806-33815
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] High-throughput expression vector of isotopically labeled peptides for use in NMR studies. (2004)
  • Author(s): Teeno, T., Goda, N., Tateishi, Y., Tochio, H., Mishima, M., Shirakawa, M., Hiroaki, H.
  • Journal Title: Protein Engineering, Design & Selection 17 Pages: 305-314
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Paramagnetic NMR study of Cu^<2+> IDA complex locatization on a protein surface and its application to elucidate long distance information. (2004)
  • Author(s): Nomura, M., Kobayashi, T., Kohno, T., fujiwara, K., Tenno, T., Shirakawa, M., Ishizaki, I., Yamamoto, K., Matsuyama, T., Mishima, M., Kojima, C.
  • Journal Title: FEBS Letters 566 Pages: 157-161
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Intracellular phosphate serves as a signal for the regulation of the PHO pathway in Saccaromyces cerevisiae. (2004)
  • Author(s): Auesukaree, C., Homma, T., Tochio, H., Shirakawa, M., Kaneko, Y., Harashima, S.
  • Journal Title: Journal of Biological Chemistry 279 Pages: 17289-17294
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] p53 suppresses c-Myb-induced trans-activation and transformation by recruiting the corepressor mSin3A. (2004)
  • Author(s): Tanikawa, J., Nomura, T., Macmillan, E. M., Shinagawa, T., Jin, W., Kokura, K, Baba, D., Shirakawa. M.. Gonda, T. J., Ishii, S.
  • Journal Title: Journal of Biological Chemistry 279 Pages: 55393-55400
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Two-Metal Ion, Ni(II) and Cu(II), Binding a-Helical Coiled-coil Peptide. (2004)
  • Author(s): Tanaka, T., Mizuno, T., Fukui, S., Hiroaki, H., Oku, J., Kanaori, K., Tajima, K. Shirakawa, M.
  • Journal Title: Journal of American Chemical Society 126 Pages: 14023-14028
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Structure of the N-terminal domain of PEX1 AAA-ATPase : characterization of a putative adaptor-binding domain. (2004)
  • Author(s): Shiozawa, K. Maita, N., Tomii, K, Seto, A., Goda, N., Akiyama, Y., Shimizu, T., Shirakawa. M.. Hiroaki, H.
  • Journal Title: Journal of Biological Chemistry 279 Pages: 50060-50068
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Crystallographic characterization of the N-terminal domain of PEX1. (2004)
  • Author(s): Shiozawa, K, Maita, N., Tomii, K., Seto, A., Goda, N., Akiyama, Y., Shimizu, T., Shirakawa. M., Hiroaki, H.
  • Journal Title: Ada Crystallography D Biological Crystallography Pages: 2098-2099
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Structural basis for distinct roles of Lys63- and Lys48-linked polyubiquitin chains. (2004)
  • Author(s): Tenno, T., Fujiwara, K., Tochio, H., Iwai, K, Morita, E. H., Hayashi, H., Murata, S., Hiroaki, H., Sato, M., Tanaka, K, Shirakawa. M.
  • Journal Title: Genes to Cells 9 Pages: 865-875
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Small ubiquitiirlike modifier 1 (SUMO-1) modification of the synergy control motif of Ad4 binding protein/steroidogenic factor 1 (Ad4BP/SF-1) regulates synergistic transcription between Ad4BP/SF-1 and Sox9. (2004)
  • Author(s): Komatsu, T., Mizusaki, H., Mukai, T., Ogawa, H., Baba, D., Shirakawa. M.. Hatakeyama, S., Nakayama, K. I., Yamamoto, H., Kikuchi, A., Morohashi, K.
  • Journal Title: Molecular Endocrinology 18 Pages: 2451-2462
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] MUTYH prevents OGG1 or APEX1 from inappropriately processing its substrate or reaction product with its Oterminal domain. (2004)
  • Author(s): Tominaga, Y., Ushijima, Y., Tsuchimoto, D., Mishima, M., Shirakawa. M.. Hirano, Sakumi, K., Nakabeppu, Y.
  • Journal Title: Nucleic Acid Research 15 Pages: 3198-3211
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Structure of human MTH1, a Nudix family hydrolase that selectively degrades oxidized purine nucleoside triphosphates. (2004)
  • Author(s): Mishima, M., Sakai, Y., Itoh, N., Kamiya, H., Furuichi, M., Takahashi, M., Yamagata, Y., Iwai, S., Nakabeppu, Y., Shirakawa. M.
  • Journal Title: Journal of Biological Chemistry 279 Pages: 33806-33815
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] High-throughput expression vector of isotopically labeled peptides for use in NMR studies. (2004)
  • Author(s): Tenno, T., Goda, N., Tateishi, Y., Tochio, H., Mishima, M., Shirakawa, M, Hiroaki, H
  • Journal Title: Protein Engineering, Design & Selection 17 Pages: 305-314
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Paramagnetic NMR study of Cu^<2+> ID A complex locatization on a protein surface and its application to elucidate long distance information. (2004)
  • Author(s): Nomura, M., Kobayashi, T., Kohno, T., fujiwara, K., Tenno, T., Shirakawa, M.. Ishizaki, I., Yamamoto, K, Matsuyama, T., Mishima, M., Kojima, C.
  • Journal Title: FEBS Letters 566 Pages: 157-161
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Intracellular phosphate serves as a signal for the regulation of the PHO pathway in Saccaromyces cerevisiae. (2004)
  • Author(s): Auesukaree, G, Homma, T., Tochio, H., Shirakawa. M., Kaneko, Y., Harashima, S.
  • Journal Title: Journal of Biological Chemistry 279 Pages: 17289-17294
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] p53 suppresses c-Myb-induced trans-activation and transformation by recrulting the corepressor in Sin3 A (2004)
  • Author(s): Tanikawa, J., Nomura, T., Macmillan, E.M., Shinagawa, T., Jin, W., Kokura, K., Baba, D., Shirakawa, M., Gorda, T.J., Tshii, S.
  • Journal Title: Journal of Biological Chemistry 279 Pages: 55393-55400
• [Journal Article] Structure of the N-terminal domain of PEX1 AAA-Atpase : characterization of a putative adaptor-binding domain (2004)
  • Author(s): Shirakawa, K., Makita, N., Tomii, K., Seto, A., Goda, N., Akiyama, Y., Shimizu, T., Shirakawa, M., Hiroaki, H.
  • Journal Title: Journal of Biological Chemistry 279 Pages: 50060-50068
• [Journal Article] Structural basis for distinct roles of Lys63- and Lys48- linked polyubiquitin chains (2004)
  • Author(s): tenno, T., Fujiwara, K., Tochio, H., Inai, K., Morita, E.H., Hayashi, H., Murata, S., Hiroaki, H., Sato, M., Tanaka, K., Shirakawa, M.
  • Journal Title: Genes to Cells 9 Pages: 865-875
• [Journal Article] Small ubiquitin-like modifier 1(SUMO-1) modification of the synergy control motif of Ad4 binding protein-steroidogenetic factor 1(Ad4Bp/St-1) regulates synergistic transcription between Ad4BP-SF-1 and Sox9 (2004)
  • Author(s): Komatsu, T., Mizusaki, H., Mukai, T., Ogawa, H., Baba, D., Shirakawa, M., Hatakeyama, S., Nakayama, K.I., Yamamoto, H., Kikuchi, A., Morohashi, K.
  • Journal Title: Molecular Endocrinology 18 Pages: 2451-2462
• [Journal Article] Structure of human MTH1, a Nudix family hydrolase that selectively degrades oxidized purine nucleoside triphosphates (2004)
  • Author(s): Nishima, M., Sakai, Y., Itoh, N., Kamiya H., Furuichi, M., Takahashi, M., Yamagata, Y., Inai, S., Nakabeppu, Y., Shirakawa, M.
  • Journal Title: Journal of Biological Chemistry 279 Pages: 33806-33815
• [Journal Article] Structure of the UBA domain of Dsk2p in complex with Ubiquitin : Molecular Determinants for Ubiquitin Recognition
  • Author(s): Ohno, A., Jee, J-G, Fujimura, K., Tenno, T., Goda, N., Tochio, H., Kobayashi, H., Hiroaki, H., Shirakawa, M.
  • Journal Title: Structure (印刷中)