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 *help |
¥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.
|
Report
(3 results)
Research Products
(49 results)
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[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
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Peer Reviewed
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[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.
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Journal Title
Nature 435
Pages: 979-982
Description
「研究成果報告書概要(和文)」より
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Peer Reviewed
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[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
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-
[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.
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Journal Title
Nature 435
Pages: 979-982
Description
「研究成果報告書概要(欧文)」より
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[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.
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Journal Title
Nature 435
Pages: 979-982
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[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.
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Journal Title
Molecular and Cellular Biology 25
Pages: 9292-9303
Description
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[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.
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Journal Title
Pediatric Research 58
Pages: 263-9
Description
「研究成果報告書概要(和文)」より
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[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.
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Journal Title
Biochemical and Biophysical Research Communications 334
Pages: 460-465
Description
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[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
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[Journal Article] Structure of the UBA domain of Dsk2p in complex with Ubiquitin : Molecular Determinants for Ubiquitin Recognition2005
Author(s)
Ohno, A., Jee, J-G, Fujiwara, K., Tenno, T., Goda, N., Tochio, H., Kobayashi, H., Hiroaki, H., Shirakawa, M.
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Journal Title
Structure 13
Pages: 521-532
Description
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[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.
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Journal Title
J Biomolecular NMR 32
Pages: 177-177
Description
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[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
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[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.
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Journal Title
Pediatric Research 58
Pages: 263-9
Description
「研究成果報告書概要(欧文)」より
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[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
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[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
Related Report
-
[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
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[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
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[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
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-
[Journal Article] Molecular mechanism of a temperature-sensitive phenotype in peroxisomal biogenesis disorder2005
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
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[Journal Article] Plc1p, Arg28p, and Kcs1p, enzymes involved in inositol pyrophosphate synthesis, are essential for phosphate regulation and polyphosphate accumulation in Saccharomyces cerevisiae2005
Author(s)
Auseukaree, C., Tochio, H., Shirakawa, M., Kaneko, Y., Harashima, S.
-
Journal Title
Journal of Biological Chemistry 280
Pages: 25127-25133
Related Report
-
[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
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[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.
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Journal Title
Journal of Biological Chemistry 279
Pages: 55393-55400
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[Journal Article] Two-Metal Ion, Ni(II) and Cu(II), Binding a-Helical Coiled-coil Peptide.2004
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Tanaka, T., Mizuno, T., Fukui, S., Hiroaki, H., Oku. J., Kanaori, K., Tajima, K., Shirakawa, M.
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Journal Title
Journal of American Chemical Society 126
Pages: 14023-14028
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[Journal Article] Structure of the N-terminal domain of PEX1 AAA-ATPase : characterization of a putative adaptor-binding domain.2004
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Shiozawa, K., Maita, N., Tomii, K., Seto, A., Goda N., Akiyama, Y., Shimizu, T., Shirakawa, M., Hiroaki, H.
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Journal Title
Journal of Biological Chemistry 279
Pages: 50060-50068
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[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.
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Journal Title
Acta Crystallography D Biological Crystallography 60
Pages: 2098-2099
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[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.
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Journal Title
Genes to Cells 9
Pages: 865-875
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[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.
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Journal Title
Molecular Endocrinology 18
Pages: 2451-2462
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[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.
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Journal Title
Nucleic Acid Research 15
Pages: 3198-3211
Description
「研究成果報告書概要(和文)」より
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[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
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[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.
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Journal Title
Protein Engineering, Design & Selection 17
Pages: 305-314
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「研究成果報告書概要(和文)」より
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[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
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[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
Related Report
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
Related Report
-
[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
Related Report
-
[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
Related Report
-
[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
Related Report
-
[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
Related Report
-
[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
Related Report
-
[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
Related Report
-
[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
Related Report
-
[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
Related Report
-
[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
Related Report
-
[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
Related Report
-
[Journal Article] p53 suppresses c-Myb-induced trans-activation and transformation by recrulting the corepressor in Sin3 A2004
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
Related Report
-
[Journal Article] Structure of the N-terminal domain of PEX1 AAA-Atpase : characterization of a putative adaptor-binding domain2004
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
Related Report
-
[Journal Article] Structural basis for distinct roles of Lys63- and Lys48- linked polyubiquitin chains2004
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
Related Report
-
[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 Sox92004
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
Related Report
-
[Journal Article] Structure of human MTH1, a Nudix family hydrolase that selectively degrades oxidized purine nucleoside triphosphates2004
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
Related Report
-
[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
Related Report