sbrc

KEK

センター長の紹介

センター長:千田 俊哉(物質構造科学研究所 教授)
研究分野:生物科学・構造生物化学・X線結晶構造解析

 大学院では三井幸雄先生のもとでインターフェロンβの結晶構造を決定しました [Senda, T., et al., EMBO J (1992)]。当時、インターフェロンの結晶構造解析は国際的に熾烈な競争となっていたため、その結晶構造解析は非常に大きなインパクトを持つ仕事として受け入れられました。

 その後、長岡技術科学大学では微生物による環境浄化技術(バイオレメディエーション)の開発を目的として、PCB(ポリ塩化ビフェニル)などの難分解性の環境汚染物質を分解可能な微生物が持つ、一連の代謝系酵素群の結晶構造解析を行いました。

 産業技術総合研究所ではエピジェネティクス分野の研究に着手し、細胞の機能や運命を決める情報がどのように利用されるのか、その仕組みをタンパク質の立体構造を使って解明しました [Natsume et al., Nature (2007); Muto et al., PNAS (2007); Akai et al., PNAS (2010)]。これらの研究は現在も継続し、さらなる発展を遂げています。

経歴

1988年〜 東京大学大学院 薬学系研究科・修士課程(指導教官:三井幸雄先生)
1990年〜 (株) 日立製作所 基礎研究所・研究員
1992年〜 長岡技術科学大学・博士後期課程(指導教官:三井幸雄先生)
1995年  長岡技術科学大学・博士(工学)(指導教官:三井幸雄先生)

1995年〜 長岡技術科学大学 生物系・助手
2001年〜 (独) 産業技術総合研究所 生物情報解析研究センター・主任研究員
2013年〜 高エネルギー加速器研究機構 物質構造科学研究所・教授
      構造生物学研究センター・センター長

文献リスト

2014年以降の文献はこちら

2013年
Structural basis of the γ-lactone-ring formation in ascorbic acid biosynthesis by the senescence marker protein-30/gluconolactonase.
Aizawa, S., Senda, M., Harada, A., Maruyama, N., Ishida, T., Aigaki, T., Ishigami, A. & Senda, T.
PLoS One 8, e53706 (2013).

Direct observation of protein microcrystals in crystallization buffer by atmospheric scanning electron microscopy.
Maruyama, Y., Ebihara, T., Nishiyama, H., Konyuba, Y., Senda, M., Numaga-Tomita, T., Senda, T., Suga, M. & Sato, C.
Int. J. Mol. Sci. 13, 10553-10567 (2013).


2012年
Tertiary structure-function analysis reveals the pathogenic signaling potentiation mechanism of Helicobacter pylori oncogenic effector CagA.
Hayashi, T., Senda, M., Morohashi, H., Higashi, H., Horio, M., Kashiba, Y., Nagase, L., Sasaya, D., Shimizu, T., Venugopalan, N., Kumeta, H., Noda, N.N., Inagaki, F., Senda, T. & Hatakeyama, M.
Cell Host Microbe. 12, 20-33 (2012).

Crystallization and preliminary crystallographic analysis of D-aspartate oxidase from porcine kidney.
Senda, M., Yamamoto, A., Tanaka, H., Ishida, T., Horiike, K. & Senda, T.
Acta Crystallogr. F Struct. Biol. Commun. 68, 644-646 (2012).


2011年
Roles of histone chaperone CIA/Asf1 in nascent DNA elongation during nucleosome replication.
Ishikawa, K., Ohsumi, T., Tada, S., Natsume, R., Kundu, L.R., Nozaki, N., Senda, T., Enomoto, T., Horikoshi, M. & Seki, M.
Genes Cells 16, 1050-1062 (2011).

Crystal structure of a zinc-dependent D-serine dehydratase from chicken kidney.
Tanaka, H., Senda, M., Venugopalan, N., Yamamoto, A., Senda, T., Ishida, T. & Horiike, K.
J. Biol. Chem. 286, 27548-27558 (2011).

Crystallization and preliminary crystallographic analysis of D-serine dehydratase from chicken kidney.
Senda, M., Tanaka, H., Ishida, T., Horiike, K. & Senda T.
Acta Crystallogr. F Struct. Biol. Commun. 67, 147-149 (2011).


2010年
Enantioselectivity of haloalkane dehalogenases and its modulation by surface loop engineering.
Prokop, Z., Sato, Y., Brezovsky, J., Mozga, T., Chaloupkova, R., Koudelakova, T., Jerabek, P., Stepankova, V., Natsume, R., van Leeuwen, J.G., Janssen, D.B., Florian, J., Nagata, Y., Senda, T. & Damborsky, J.
Angew. Chem. Int. Ed. Engl. 49, 6111-6115 (2010).

Regulatory system of the protocatechuate 4,5-cleavage pathway genes essential for lignin downstream catabolism.
Kamimura, N., Takamura, K., Hara, H., Kasai, D., Natsume, R., Senda, T., Katayama, Y., Fukuda, M. & Masai, E.
J. Bacteriol. 192, 3394-3405 (2010).

Structure of the histone chaperone CIA/ASF1-double bromodomain complex linking histone modifications and site-specific histone eviction.
Akai, Y., Adachi, N., Hayashi, Y., Eitoku, M., Sano, N., Natsume, R., Kudo, N., Tanokura, M., Senda, T. & Horikoshi M.
Proc. Natl. Acad. Sci. USA 107, 8153-8158 (2010).

Crystallization and preliminary crystallographic analysis of manganese(II)-dependent 2,3-dihydroxybiphenyl 1,2-dioxygenase from Bacillus sp. JF8.
Senda, M., Hatta, T., Kimbara, K. & Senda, T.
Acta Crystallogr. F Struct. Biol. Commun. 66, 282-285 (2010).


2009年
Crystallization and preliminary crystallographic analysis of gallate dioxygenase DesB from Sphingobium sp. SYK-6.
Sugimoto, K., Yamamoto, Y., Antoni, S., Senda, M., Kasai, D., Masai, E., Fukuda, M. & Senda, T.
Acta Crystallogr. F Struct. Biol. Commun. 65, 1171-1174 (2009).

Theoretical framework for the histone modification network: modifications in the unstructured histone tails form a robust scale-free network.
Hayashi, Y., Senda, T., Sano, N. & Horikoshi, M.
Genes Cells 14, 789-806 (2009).

Redox control of protein conformation in flavoproteins.
Senda, T., Senda, M., Kimura, S. & Ishida, T.
Antioxid Redox Signal 11, 1741-1766 (2009). Review


2008年
Crystal structure of Methanococcus jannaschii TATA box-binding protein.
Adachi, N., Senda, M., Natsume, R., Senda, T. & Horikoshi, M.
Genes Cells 13, 1127-1140 (2008).

Effect of leucine-to-methionine substitutions on the diffraction quality of histone chaperone SET/TAF-Ibeta/INHAT crystals.
Senda, M., Muto, S., Horikoshi, M. & Senda, T.
Acta Crystallogr. F Struct. Biol. Commun. 64, 960-965 (2008).


2007年
Molecular mechanism of the redox-dependent interaction between NADH-dependent ferredoxin reductase and Rieske-type [2Fe-2S] ferredoxin.
Senda, M., Kishigami, S., Kimura, S., Fukuda, M., Ishida, T. & Senda, T.
J. Mol. Biol. 373, 382-400 (2007).

Crystal structure of the radical SAM enzyme catalyzing tricyclic modified base formation in tRNA.
Suzuki, Y., Noma, A., Suzuki, T., Senda, M., Senda. T., Ishitani, R. & Nureki, O.
J. Mol. Biol. 372, 1204-1214 (2007).

Structural basis for recognition of cognate tRNA by tyrosyl-tRNA synthetase from these kingdoms.
Tsunoda, M., Kusakabe, Y., Tanaka, N., Ohno, S., Nakamura, M., Senda, T., Moriguchi, T., Asai, N., Sekine, M., Yokogawa, T., Nishikawa, K. & Nakamura, K.T.
Nucleic Acid Res. 35, 4289-4300 (2007).

Crystallization and preliminary X-ray analysis of the electron-transfer complex of Rieske-type [2Fe-2S] ferredoxin and NADH-dependent ferredoxin reductase derived from Acidovorax sp. strain KKS102.
Senda, M., Kishigami, S., Kimura, S. & Senda, T.
Acta Crystallogr. F Struct. Biol. Commun. 63, 520-523 (2007).

Crystallization and preliminary X-ray analysis of the reduced Rieske-type [2Fe-2S] ferredoxin derived from Pseudomonas sp. strain KKS102.
Senda, M., Kishigami, S., Kimura, S. & Senda, T.
Acta Crystallogr. F Struct. Biol. Commun. 63, 311-314 (2007).

Crystallization and preliminary crystallographic analysis of a haloalkane dehalogenase, DbjA, from Bradyrhizobium japonicum USDA110.
Sato, Y., Natsume, R., Tsuda, M., Damborsky, J., Nagata, Y. & Senda, T.
Acta Crystallogr. F Struct. Biol. Commun. 63, 294-296 (2007).

Relationship between the structure of SET/TAF-Ib/INHAT and its histone chaperone activity.
Muto, S., Senda, M., Akai, Y., Sato, L., Suzuki, T., Nagai, R., Senda, T. & Horikoshi, M.
Proc. Natl. Acad. Sci. USA 104, 4285-4290 (2007).

Structure and function of the histone chaperone CIA/ASF1 complexed with histones H3 and H4.
Natsume, R., Eitoku, M., Akai, Y., Sano, N., Horikoshi, M. & Senda, T.
Nature 446, 338-341 (2007).

Crystallization and preliminary crystallographic analysis of DtsR1, a carboxyltransferase subunit of acetyl-CoA carboxylase from Corynebacterium glutamicum.
Yamada, M., Natsume, R., Nakamatsu, T., Horinouchi, S., Kawasaki, H. & Senda, T.
Acta Crystallogr. F Struct. Biol. Commun. 63, 120-122 (2007).


2006年
Crystallization and preliminary X-ray analysis of the Rieske-type [2Fe-2S] ferredoxin component of biphenyl dioxygenase from Pseudomonas sp. strain KKS102.
Senda, M., Kimura, S., Kishigami, S. & Senda, T.
Acta Crystallogr. F Struct. Biol. Commun. 62, 590-592 (2006).

Crystallization and preliminary crystallographic analysis of a catechol 2,3-dioxygenase PheB from Bacillus stearothermophilus BR219.
Sugimoto, K., Matsufuzi, K., Ohnuma, H., Senda, M., Fukuda, M. & Senda, T.
Acta Crystallogr. F Struct. Biol. Commun. 62, 125-127 (2006).


2005年
Single-turnover kinetics of 2,3-dihydroxybiphenyl 1,2-dioxygenase reacting with 3-formylcatechol.
Ishida, T., Senda, T., Tanaka, H., Yamamoto, A. & Horiike, K.
Biochem. Biophys. Res. Commun. 338, 223-229 (2005).

Amino acids in positions 48, 52, and 73 differentiate the substrate specificities of the highly homologous chlorocatechol 1,2-dioxygenases CbnA and TcbC.
Liu, S., Ogawa, N., Senda, T., Hasebe, A. & Miyashita, K.
J. Bacteriol. 187, 5427-5436 (2005).

Tolerance of the Rieske-type [2Fe-2S] cluster in recombinant ferredoxin BphA3 from Pseudomonas sp. KKS102 to histidine ligand mutations.
Kimura, S., Kikuchi, A., Senda, T., Shiro, Y. & Fukuda, M.
Biochem. J. 388, 869-878 (2005).


2004年
Three-dimensional structure of the ternary complex of yeast tyrosyl-tRNA synthetase.
Tsunoda, M., Kusakabe, Y., Tanaka, N., Ohno, S., Nakamura, M., Senda, T., Sekine, M., Yokogawa, T., Nishikawa, K. & Nakamura, K.T.
Nucleic Acids Symp Ser (Oxf). 48, 155-156 (2004).

Purification, crystallization and preliminary X-ray analysis of Methanococcus jannaschii TATA box-binding protein (TBP).
Adachi, N., Natsume, R., Senda, M., Muto, S., Senda, T. & Horikoshi, M.
Acta Crystallogr. D Biol. Crystallogr. 60, 2328-2331 (2004).

Crystal structure of the terminal oxygenase component of biphenyl dioxygenase derived from Rhodococcus sp. strain RHA1.
Furusawa, Y., Nagarajan, V., Tanokura, M., Masai, E., Fukuda, M. & Senda, T.
J. Mol. Biol. 342, 1041-1052 (2004).

Purification, crystallization and preliminary X-ray diffraction analysis of human oncoprotein SET/TAF-1beta.
Muto, S., Senda, M., Adachi, N., Suzuki, T., Nagai, R., Senda, T. & Horikoshi, M.
Acta Crystallogr. D Biol. Crystallogr. 60, 712-714 (2004).

Crystal structure of a γ-butyrolactone autoregulator receptor protein in Streptomyces coelicolor A3(2).
Natsume, R., Ohnishi, Y., Senda, T. and Horinouchi, S.
J. Mol. Biol. 336, 409-419 (2004).


2003年
Crystallization of CprB, an autoregulator-receptor protein from Streptomyces coelicolor A3(2).
Natsume, R., Takeshita, R., Sugiyama, M., Ohnishi, Y., Senda, T. & Horinouchi, S.
Acta Crystallogr. D Biol. Crystallogr. 59, 2313-2315 (2003).

Crystallization of the terminal oxygenase component of biphenyl dioxygenase derived from Rhodococcus sp. strain RHA1.
Nagarajan, V., Sakurai, N., Kubota, M., Nonaka, T., Nagumo, H., Takeda, H., Nishizaki, T., Masai, E., Fukuda, M., Mitsui, Y. & Senda, T.
Protein Pept. Lett. 10, 412-417 (2003).

Purification and crystallization of a LysR-type transcriptional regulator CBNR from Ralstonia eutropha NH9.
Muraoka, S., Okumura, R., Uragami, Y., Nonaka, T., Ogawa, N., Miyashita, K., & Senda, T.
Protein Pept. Lett. 10, 325-329 (2003).

Crystal structure of a full-length LysR-type transcriptional regulator, CbnR: unusual combination of two subunit forms and molecular bases for causing and changing DNA bend.
Muraoka, S., Okumura, R., Ogawa, N., Nonaka, T., Miyashita, K. & Senda, T.
J. Mol. Biol. 328, 555-566 (2003).

Oxygen affinity of hemoglobin regulates O2 consumption, metabolism, and physical activity.
Shirasawa, T., Izumizaki, M., Suzuki, Y., Ishihara, A., Shimizu, T., Tamaki, M., Huang, F., Koizumi, K., Iwase, M., Sakai, H., Tsuchida, E., Ueshima, K., Inoue, H., Koseki, H., Senda, T., Kuriyama, T. & Homma, I.
J. Biol. Chem. 278, 5035-5043 (2003).


2002年
Crystal structures of the reaction intermediate and its homologue of an extradiol-cleaving catecholic dioxygenase.
Sato, N., Uragami, Y., Nishizaki, T., Takahashi, Y., Sazaki, G., Sugimoto, K., Nonaka, T., Masai, E., Fukuda, M. & Senda, T.
J. Mol. Biol. 321, 621-636 (2002).


2001年
Crystal structure of 2-hydroxyl-6-oxo-6-phenylhexa-2,4-dienoic acid (HPDA) hydrolase (BphD enzyme) from Rhodococcus sp. strain RHA1 of the PCB degradation pathway.
Nandhagopal, N., Yamda, A., Hatta, T., Masai, E., Fukuda, M., Mitsui, Y. & Senda, T.
J. Mol. Biol. 309, 1139-1151 (2001).


2000年
Crystal structure of NADH-dependent ferredoxin reductase component in biphenyl dioxygenase.
Senda, T., Ymada, T., Kubota, M., Nishizaki, T., Masai, E., Fukuda, M. & late Mitsui, Y.
J. Mol. Biol. 304, 397-410 (2000).


1999年
Crystal structure of an aromatic-ring-opening dioxygenase LigAB, a protocatechuate 4,5-dioxygenase, in aerobic condition.
Sugimoto, K., Senda, T., Aoshima, H., Masai, E., Fukuda, M. & Mitsui, Y.
Structure 7, 953-965 (1999).


1996年
Three-dimensional structures of free form and two substrate complexes of an extradiol ring-cleavage type dioxygenase, the BphC enzyme from Pseudomonas sp. strain KKS102.
Senda, T., Sugiyama, K., Narita, H., Yamamoto, T., Kimbara, K., Fukuda, M., Sato, M., Yano, K. & Mitsui, Y.
J. Mol. Biol. 255, 735-752 (1996).


1995年
Refined crystal structure of recombinant murine interferon-β at 2.15Å resolution.
Senda, T., Saitoh, S. & Mitsui, Y.
J. Mol. Biol. 253, 187-207 (1995).


1992年
Three-dimensional crystal structure of recombinant murine interferon-β.
Senda, T., Shimazu, T., Matsuda, S., Kawano, G., Shimizu, H., Nakamura, K.T. & Mitsui, Y.
EMBO J. 11, 3193-3201 (1992).


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