sbrc

KEK

about lab head

 Dr. Senda earned his master's degree from University of Tokyo (under the guidance of Prof. Yukio Mitsui). During the graduate student, he determined the crystal structure of interferon-beta [Senda, T., et al., EMBO J (1992)]. He received his Ph.D. from the Nagaoka University of Technology (under the guidance of Prof. Yukio Mitsui), where he determined the series of enzymes degrading persistent organic pollutants, such as PCB (polychlorobiphenyl). These studies provided a lot of information for the field of bioremediation. His career has included research at the national institute of Advanced Industrial Science and Technology (AIST), where he studied about epigenetics and chromatin based on the crystal structure of the complexes of chromatin factors [Natsume et al., Nature (2007); Muto et al., PNAS (2007); Akai et al., PNAS (2010)]. In 2013, Dr. Senda joined KEK as Professor and the director of SBRC.

CV

1988- Master's program of Pharmaceutical Science,
    Graduate School of Pharmaceutical Sciences,
    The University of Tokyo (under Prof. Yukio Mitsui)
1990- Researcher,
    Advanced Research Labolatory, Hitachi Ltd.
1992- Doctoral program of Integrated Bioscience and Technology,
    Nagaoka University of Technology (under Prof. Yukio Mitsui)
1995  Ph.D. in Engineering,
    Nagaoka University of Technology (under Prof. Yukio Mitsui)

1995- Assistant Professor,
    Integrated Bioscience and Technology, Nagaoka University of Technology
2001- Senior Researcher,
    BIRC, AIST
2013- Professor,
    IMSS, KEK
    Director of SBRC

Publication list

2014-

2013
Structural basis of the gamma-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
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. F68, 644-646 (2012).


2011
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. F67, 147-149 (2011).


2010
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. F66, 282-285 (2010).


2009
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. F65, 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
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. F64, 960-965 (2008).


2007
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. F63, 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. F63, 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. F63, 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. F63, 120-122 (2007).


2006
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. F62, 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. F62, 125-127 (2006).


2005
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
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 D60, 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 D60, 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
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 D59, 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
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
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
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
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
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
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
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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