原著論文 (査読あり)

Original Articles (peer-reviewed)

Anan, Y., Itakura, M., Shimoda, T., Yamaguchi, K., Lu, P., Nagata, K., Dong, J., Ueda, H. and Uchida, K. (2024). Molecular and structural basis of anti-DNA antibody specificity for pyrrolated proteins. Commun. Biol. 7, 149. doi: 10.1038/s42003-024-05851-0.

Zhang, C., Lu, P., Wei, S., Hu, C., Miyoshi, M., Okamoto, K., Itoh, H., Okuda, S., Suzuki, M., Kawakami, H. and Nagata, K. (2024). Refolding, crystallization, and crystal structure analysis of a scavenger receptor cysteine-rich domain of human salivary agglutinin expressed in Escherichia coli. Protein J.published online ahead of print. doi: 10.1007/s10930-023-10173-x.

Lu, P., Jiang, J., Liu, C., Okuda, S., Itoh, H., Okamoto, K., Suzuki, M. and Nagata, K.  (2024). Molecular mechanism of Fe³⁺ binding inhibition to Vibrio metschnikovii ferric ion-binding protein, FbpA, by rosmarinic acid and its hydrolysate, danshensu. Protein Sci. 33, e4881. doi: 10.1002/pro.4881.

Sano, K., Nakasato, S., Nagata, K. and Kobata, K. (2023). A single amino acid substitution alters the vanillylamine synthesis activity of Capsicum pAMT. Biochem. Biophys. Res. Commun. 680, 86-92. doi: 10.1016/j.bbrc.2023.09.011.

Lu, P., Zhou, J., Wei, S., Takada, K., Masutani, H., Okuda, S., Okamoto, K., Suzuki, M., Kitamura, T., Masujin, K., Kokuho, T., Itoh, H. and Nagata, K. (2023). Comparative genomic and transcriptomic analyses of African swine fever virus strains. Comput. Struct. Biotechnol. J. 21, 4322-4335. doi: 10.1016/j.csbj.2023.08.028.

Sekine, M., Okamoto, K., Pai, E. F., Nagata, K., Ichida, K., Hille, R. and Nishino, T. (2023). Allopurinol and oxypurinol differ in their strength and mechanisms of inhibition of xanthine oxidoreductase. J. Biol. Chem. 299, 105189. doi: 10.1016/j.jbc.2023.105189.

Tang, D., Kato, Y., Zhang, D., Negishi, L., Kurumizaka, H., Hirata, T., Nakakido, M., Tsumoto, K., Shuji, F., Tsuguyuki, S., Okumura, T., Nagata, K. and Suzuki, M. (2023). Dispersion function of a protein, DP-1, identified in Collimonas sp. D-25, for the synthesis of gold nanoparticles. ChemBioChem 24, e202300221. doi: 10.1002/cbic.202300221.

Watanabe, M., Kitamura, T., Nagata, K., Ikezawa, M., Kameyama, K., Masujin, K. and Kokuho, T. (2023). Development of a novel indirect ELISA for the serological diagnosis of African swine fever using p11.5 protein as a target antigen. Pathogens 12, 774. doi: 10.3390/pathogens12060774.

Yamashita, T., Matsuda, H., Koizumi, K., Thirumalaisamy, L., Kim, M., Negishi, L., Kurumizaka, H., Tominaga, Y., Takagi, Y., Takai, K., Okumura, T., Katayama, H., Horitani, M., Ahsan, N., Okada, Y., Nagata, K., Suzuki, Y. and Suzuki, M. (2023). Heme protein identified from scaly-foot gastropod can synthesize pyrite (FeS2) nanoparticles. Acta Biomater. 162, 110-119. doi: 10.1016/j.actbio.2023.03.005.

Zhu, L., Shimizu, K., Kintsu, H., Negishi, L., Zheng, Z., Kurumizaka, H., Sakuda, H., Kuriyama, I., Atsumi, T., Maeyama, K., Nagai, K., Kawabata, M., Kohtsuka, H., Miura, T., Oka, Y., Ifuku, S., Nagata, K. and Suzuki, M. (2023). Structural and functional analyses of chitinolytic enzymes in the nacreous layer of Pinctada fucata. Biochem. Eng. J. 191, 108780. doi: 10.1016/j.bej.2022.108780.

Morinaga, S., Nagata, K., Ihara, S., Yumita, T., Niimura, Y., Sato, K. and Touhara, K. (2022). Structural model for ligand binding and channel opening of an insect gustatory receptor. J. Biol. Chem. 298, 102573. doi: 10.1016/j.jbc.2022.102573.

Noguchi, M., Shimizu, M., Lu, P., Takahashi, Y., Yamauchi, Y., Sato, S., Kiyono, H., Kishino, S., Ogawa, J., Nagata, K. and Sato, R. (2022). Lactic acid bacteria-derived γ-linolenic acid metabolites are PPARδ ligands that reduce lipid accumulation in human intestinal organoids. J. Biol. Chem. 298, 102534. doi: 10.1016/j.jbc.2022.102534.

Lu, P., Takiguchi, S., Honda, Y., Lu, Y., Mitsui, T., Kato, S., Kodera, R., Furihata, K., Zhang, M., Okamoto, K., Itoh, H., Suzuki, M., Kono, H. and Nagata, K. (2022). NMR and HPLC profiling of bee pollen products from different countries. Food Chem. Mol. Sci. 5, 100119. doi: 10.1016/j.fochms.2022.100119.

Miyamoto, D., Sato, N., Nagata, K., Sakai, Y., Sugihara, H., Ohashi, Y., Stiburkova, B., Sebesta, I., Ichida, K. and Okamoto, K. (2022). Analysis of purine metabolism to elucidate the pathogenesis of acute kidney injury in renal hypouricemia. Biomedicines 10, 1584. doi: 10.3390/biomedicines10071584.

Abomosallam, M., Elalfy, M., Zheng, Z., Nagata, K. and Suzuki, M. (2022). Adsorption kinetics and thermodynamics of toxic metal ions onto chitosan nanoparticles extracted from shrimp shells. Nanotechnol. Environ. Eng. 7, 35–47. doi:10.1007/s41204-021-00179-0.

Lu, P., Sui, M., Zhang, M., Wang, M., Kamiya, T., Okamoto, K., Itoh, H., Okuda, S., Suzuki, M., Asakura, T., Fujiwara, T. and Nagata, K. (2021). Rosmarinic acid and sodium citrate have a synergistic bacteriostatic effect against Vibrio species by inhibiting iron uptake. Int. J. Mol. Sci. 22, 13010. doi: 10.3390/ijms222313010.

Hosaka, Y., Itoh, K., Matsutani, S., Kawate, S., Miura, A., Mizoura, Y., Yamada, S., Konno, H., Grave, E., Nagata, K., Wakui, H. and Itoh, H. (2021). Fermented food Tempeh induces interleukin 12 and enhances macrophage phagocytosis. J. Food Biochem. e13958. doi: 10.1111/jfbc.13958.

Yamaguchi, K., Itakura, M., Kitazawa, R., Lim, S. Y., Nagata, K., Shibata, T., Akagawa, M. and Uchida, K. (2021). Oxidative deamination of lysine residues by polyphenols generates an equilibrium of aldehyde and 2-piperidinol products. J. Biol. Chem. 297, 101035. doi: 10.1016/j.jbc.2021.101035.

Tanigawa, M., Yamamoto, K., Nagatoishi, S., Nagata, K., Noshiro, D., Noda, N. N., Tsumoto, K. and Maeda, T. (2021). A glutamine sensor that directly activates TORC1. Commun. Biol. 4, 1093. doi: 10.1038/s42003-021-02625-w.

Kintsu, H., Pérez-Huert, A., Ohtsuka, S., Okumura, T., Ifuku, S., Nagata, K., Kogure, T. and Suzuki M. (2021). Functional analyses of chitinolytic enzymes in the formation of calcite prisms in Pinctada fucata. Micron 145, 103063. doi: 10.1016/j.micron.2021.103063.

Therdtatha, P., Song, Y., Tanaka, M., Mariyatun, M., Almunifah, M., Manurung, N. E. P., Indriarsih, S., Lu, Y., Nagata, K., Fukami, K., Ikeda, T., Lee, Y. K., Rahayu, E. S. and Nakayama, J. (2021). Gut microbiome of indonesian adults associated with obesity and type 2 diabetes: A cross-sectional study in an asian city, Yogyakarta. Microorganisms 9, 897. doi: 10.3390/microorganisms9050897.

Zheng, Z., Kawakami, K., Zhang, D., Negishi, L., Abomosallam, M., Asakura, T., Nagata, K. and Suzuki, M. (2021). Identification and functional analysis of cadmium-binding protein in the visceral mass of Crassostrea gigas. Sci. Rep. 11, 11306. doi: 10.1038/s41598-021-90882-4.

Zhang, M., Lu, P., Terada, T., Sui, M., Furuta, H., Iida, K., Katayama, Y., Lu, Y., Okamoto, K., Suzuki, M., Asakura, T., Shimizu, K., Hakuno, F., Takahashi, S, Shimada, N., Yang, J., Ishikawa, T., Tatsuzaki, J. and Nagata, K. (2021). Quercetin 3,5,7,3’,4’-pentamethyl ether from Kaempferia parviflora directly and effectively activates human SIRT1. Commun. Biol. 4, 209. doi: 10.1038/s42003-021-01705-1.

Katayama, H. and Nagata, K. (2021). Application of 2,2′-dipyridyl disulfide-mediated thiazolidine ring-opening reaction to glycoprotein synthesis: Total chemical synthesis of evasin-3. J. Pept. Sci. 27, e3290. doi: 10.1002/psc.3290.

Zhu, L., Wang, L., Matsuura., A., Zhang, M., Lu, P., Iimura, K., Nagata, K. and Suzuki, M. (2021). Purification, crystallization and X-ray analysis of Pf-SCP (sarcoplasmic Ca-binding protein), related to storage and transport of calcium in mantle of Pinctada fucata. Protein Expr. Purif. 178, 105781. doi: 10.1016/j.pep.2020.105781.

Kintsu, H., Nishimura, R., Negishi, L., Kuriyama, I., Tsuchihashi, Y., Zhu, L., Nagata, K. and Suzuki, M. (2020). Identification of methionine-rich insoluble proteins in the shell of the pearl oyster, Pinctada fucata. Sci. Rep. 10, 18335. doi: 10.1038/s41598-020-75444-4.

Murase, K., Moriwaki, Y., Mori, T., Liu, X., Masaka, C., Takada, Y., Maesaki, R., Mishima, M., Fujii, S., Hirano, Y., Kawabe, Z., Nagata, K., Terada, T., Suzuki, G.,  Watanabe, M., Shimizu, K., Hakoshima, T. and Takayama, S. (2020). Mechanism of self/nonself-discrimination in Brassica self-incompatibility. Nat. Commun. 11, 4916. doi: 10.1038/s41467-020-18698-w.

Iwamoto, S., Shimizu, K., Negishi, L., Suzuki, N., Nagata, K. and Suzuki, M. (2020). Characterization of the chalky layer-derived EGF-like domain-containing protein (CgELC) in the pacific oyster, Crassostrea gigas. J. Struct. Biol. 212, 107594. doi: 10.1016/j.jsb.2020.107594.

Sebesta, I., Miyamoto, D., Stiburkova, B., Blahova, S., Sato, N., Nagata, K., Okamoto, K., Tsuruoka, S. and Ichida, K. (2020). Modified forearm ischemic test in hypouricemic patients. Nucleosides Nucleotides Nucleic Acids 39, 1432-1439. doi: 10.1080/15257770.2020.1750636.

Nagata, K., Okada, A., Ohtsuka, J., Ohkuri, T., Akama, Y., Sakiyama, Y., Miyazaki, E., Horita, S., Katayama, T., Ueda, T. and Tanokura, M. (2020). Crystal structure of the complex of the interaction domains of E. coli DnaB helicase and DnaC helicase loader: Structural basis implying a distortion-accumulation mechanism for the DnaB ring opening caused by DnaC binding. J. Biochem. 167, 1-14. doi: 10.1093/jb/mvz087.

Lu, P., Moriwaki, Y., Zhang, M., Katayama, Y., Lu, Y., Okamoto, K., Terada, T., Shimizu, K., Wang, M., Kamiya, T., Fujiwara, T., Asakura, T., Suzuki, M., Yoshimura, E. and Nagata, K. (2019). Functional characterisation of two ferric-ion coordination modes of TtFbpA, the periplasmic subunit of an ABC-type iron transporter from Thermus thermophilus HB8. Metallomics 11, 2078-2088. doi: 10.1039/c9mt00245f.

Hirose, S., Hioki, Y., Miyashita, H., Hirade, N., Yoshitake, J., Shibata, T., Kikuchi, R., Matsushita, T., Chikazawa, M., Itakura, M., Zhang, M., Nagata, K. and Uchida, K. (2019). Apolipoprotein E binds to and reduces serum levels of DNA-mimicking, pyrrolated proteins. J. Biol. Chem. 294, 11035-11045. doi: 10.1074/jbc.RA118.006629.

Horita, S., Kataoka, M., Kitamura, N., Miyakawa, T., Ohtsuka, J., Maejima, Y., Shimomura, K., Nagata, K., Shimizu, S. and Tanokura, M. (2019). Structural basis of different substrate preferences of two old yellow enzymes from yeasts in the asymmetric reduction of enone compounds. Biosci Biotechnol Biochem. 83, 456-462. doi: 10.1080/09168451.2018.1543014.

Gessesse, B., Nagaike, T., Nagata, K., Shimizu, Y. and Ueda, T. (2018). G-protein coupled receptor protein synthesis on a lipid bilayer using a reconstituted cell-free protein synthesis system. Life 8, E54. doi: 10.3390/life8040054.

Matsunaga, Y., Matsukawa, T., Iwasaki, T., Nagata, K. and Kawano, T. (2018). Comparison of physiological functions of antagonistic insulin-like peptides, INS-23 and INS-18, in Caenorhabditis elegans. Biosci. Biotechnol. Biochem. 82, 90-96. doi: 10.1080/09168451.2017.1415749.

Mizutani, H., Sugawara, H., Buckle, A. M., Sangawa, T., Miyazono, K., Ohtsuka, J., Nagata, K., Shojima, T., Nosaki, S., Xu, Y., Wang, D., Hu, X., Tanokura, M., Yura, K. (2017). REFOLDdb: a new and sustainable gateway to experimental protocols for protein refolding. BMC Struct. Biol. 217, 4. doi: 10.1186/s12900-017-0074-z.

Okai, M., Yamamura, A., Hayakawa, K., Tsutsui, S., Miyazono, K., Lee, W. C., Nagata, K., Inoue, Y., Tanokura, M. (2017). Insight into the transition between the open and closed conformations of Thermus thermophilus carboxypeptidase. Biochem. Biophys. Res. Commun. 484, 787-793. doi: 10.1016/j.bbrc.2017.01.167.

Nagata, K., Katayama, Y., Sato, T., Kwon, Y. and Kawabata, T. (2017). Toward the next step in G protein-coupled receptor research: a knowledge-driven analysis for the next potential targets in drug discovery. J. Struct. Funct. Genomics 17, 111-133. doi: 10.1007/s10969-016-9212-2.

Gojobori, T., Ikeo, K., Katayama, Y., Kawabata, T., Kinjo, A. R., Kinoshita, K., Kwon, Y., Migita, O., Mizutani, H., Muraoka, M., Nagata, K., Omori, S., Sugawara, H., Yamada, D. and Yura, K. (2016). VaProS: a database-integration approach for protein/genome information retrieval. J. Struct. Funct. Genomics 17, 69-81. doi: 10.1007/s10969-016-9211-3.

Tsutsui, N., Sakamoto, T., Arisaka, F., Tanokura, M., Nagasawa, H. and Nagata, K. (2016). Crystal structure of a crustacean hyperglycemic hormone (CHH) precursor suggests structural variety in the C-terminal regions of CHH superfamily members. FEBS J. 283, 4325-4339. doi: 10.1111/febs.13926.

Katayama, Y., Suzuki, T., Ebisawa, T., Ohtsuka, J., Wang, S., Natsume, R., Lo, Y.-H., Senda, S., Nagamine, T., Hull, J. J., Matsumoto, S., Nagasawa, H., Nagata, K. and Tanokura, M. (2016). A class-A GPCR solubilized under high hydrostatic pressure retains its ligand binding ability. Biochim. Biophys. Acta Biomembr. 1858, 2145-2151.

Nakamura, A., Ohtsuka, J., Kashiwagi, T., Numoto, N., Hirota, N., Ode, T., Okada, H., Nagata, K., Kiyohara, M., Suzuki, E., Kita, A., Wada, H. and Tanokura, M. (2016). In-situ and real-time growth observation of high-quality protein crystals under quasi-microgravity on earth. Sci. Rep. 6, 22127.

Horita, S., Kataoka, M., Kitamura, N., Nakagawa, T., Miyakawa, T., Ohtsuka, J., Nagata, K., Shimizu, S. and Tanokura, M. (2015). An engineered old yellow enzyme that enables efficient synthesis of (4R,6R)-actinol in a one-pot reduction system. ChemBioChem 16, 440-445.

Qin, H.-M., Imai, F. L., Miyakawa, T., Kataoka, M., Kitamura, N., Urano, N., Mori, K., Kawabata, H., Okai, M., Ohtsuka, J., Hou, F., Nagata, K., Shimizu, S. and Tanokura, M. (2014). L-allo-Threonine aldolase with an H128Y/S292R mutation from Aeromonas jandaei DK-39 reveals the structural basis of changes in substrate stereoselectivity. Acta Crystallogr. D70, 1695-1703.

Kawai, T., Katayama, Y., Guo, L., Liu, D., Suzuki, T., Hayakawa, K., Lee, J. M., Nagamine, T., Hull, J. J., Matsumoto, S., Nagasawa, H., Tanokura, M. and Nagata, K. (2014). Identification of functionally important residues of the silkmoth pheromone biosynthesis-activating neuropeptide receptor, an insect ortholog of the vertebrate neuromedin U receptor. J. Biol. Chem. 289, 19150-19163.

Tian, S., Ohtsuka, J., Wang, S., Nagata, K., Tanokura, M., Ohta, A., Horiuchi, H. and Fukuda, R. (2014). Human CTP:phosphoethanolamine cytidylyltransferase: Enzymatic properties and unequal catalytic roles of CTP-binding motifs in two cytidylyltransferase domains. Biochem. Biophys. Res. Commun. 449, 26-31.

Hou, F., Miyakawa, T., Kataoka, M., Takeshita, D., Kumashiro, S., Uzura, A., Urano, N., Nagata, K., Shimizu, S. and Tanokura, M. (2014). Structural basis for high substrate-binding affinity and enantioselectivity of 3-quinuclidinone reductase AtQR. Biochem. Biophys. Res. Commun. 446, 911-915.

Takeshita, D., Kataoka, M., Miyakawa, T., Miyazono, K., Kumashiro, S., Nagai, T., Urano, N., Uzura, A., Nagata, K., Shimizu, S. and Tanokura, M. (2014). Structural basis of stereospecific reduction by quinuclidinone reductase. AMB Express 4, 6, 1-10.

Wang, S., Ogata, M., Horita, S., Ohtsuka, J., Nagata, K. and Tanokura, M. (2014). A novel mode of ferric ion-coordination of the periplasmic ferric ion-binding subunit, FbpA, of an ABC-type iron transporter from Thermus thermophiles HB8. Acta Crystallogr. D70, 196-202.

Qin, H.-M., Yamamura, A., Miyakawa, T., Kataoka, M., Nagai, T., Kitamura, N., Urano, N., Maruoka, S., Ohtsuka, J., Nagata, K., Shimizu, S. and Tanokura, M. (2014). Structure of conjugated polyketone reductase from Candida parapsilosis IFO 0708 reveals conformational changes for substrate recognition upon NADPH binding. Appl. Microbiol. Biotechnol. 98, 243-249.

川上 浩, 早川 江, 永田 宏次, 田之倉 優 (2013). ラクトフェリンに夾雑する成分のプロテオーム解析. ミルクサイエンス 62, 29-37.

Yao, M. D., Ohtsuka, J., Nagata, K., Miyazono, K., Zhi, Y., Ohnishi, Y. and Tanokura, M. (2013). Complex structure of the DNA-binding domain of AdpA, the global transcription factor in Streptomyces griseus, and a target duplex DNA reveals the structural basis of its tolerant DNA sequence specificity. J. Biol. Chem. 288, 31019-31029.

Qin, H.-M., Yamamura, A., Miyakawa, T., Kataoka, M., Maruoka, S., Ohtsuka, J., Nagata, K., Shimizu, S. and Tanokura, M. (2013). Crystal structure of conjugated polyketone reductase (CPRC1) from Candida parapsilosis IFO 0708 complexed with NADPH. Proteins 81, 2059-2063.

Okai, M., Ohtsuka, J., Imai, F. L., Mase, T., Moriuchi, R., Tsuda, M., Nagata, K., Nagata, Y. and Tanokura, M. (2013). Crystal structure and site-directed mutagenesis analyses of haloalkane dehalogenase LinB from Sphingobium sp. MI1205. J. Bacteriol. 195, 2642-2651.

Suzuki, N., Imai, L. F., Kato, Y., Nagata, K., Ohashi, Y., Kuchitsu, K., Tanokura, M., Sakamoto, A., Nara, M., Nakano, M. and Yonezawa, N. (2013). Coordination structures of Mg²⁺ and Ca²⁺ in three types of tobacco calmodulins in solution: Fourier-transform infrared spectroscopic studies of side-chain COO^– groups. Biopolymers 99, 472-483.

Chiba, Y., Horita, S., Ohtsuka, J., Arai, H., Nagata, K., Igarashi, Y., Tanokura, M. and Ishii, M. (2013). Structural units important for activity of a novel-type phosphoserine phosphatase from Hydrogenobacter thermophilus TK-6 revealed by crystal structure analysis. J. Biol. Chem. 288, 11448-11458.

Nakayama, J., Yokohata, R., Sato, M., Suzuki, T., Matsufuji, T., Nishiguchi, K., Kawai, T., Yamanaka, Y., Nagata, K., Tanokura, M. and Sonomoto, K. (2013). Development of a peptide antagonist against fsr quorum sensing of Enterococcus faecalis. ACS Chem. Biol. 8, 804-811.

Nagata, K., Hongo, N., Kameda, Y., Yamamura, A., Sasaki, H., Lee, W. C., Ishikawa, K., Suzuki, E. I. and Tanokura, M. (2013). The structure of brazzein, a sweet-tasting protein from the wild African plant Pentadiplandra brazzeana. Acta Crystallogr. D69, 642-647.

Hou, F., Miyakawa, T., Takeshita, D., Kataoka, M., Uzura, A., Nagata, K., Shimizu, S. and Tanokura, M. (2012). Expression, purification, crystallization and X-ray analysis of 3-quinuclidinone reductase from Agrobacterium tumefaciens. Acta Crystallogr. F68, 1237-1239.

Guo, L., Okai, M., Mase, T., Imai, F. L., Miyakawa, T., Nagata, K., Yamanaka, H., Fujii, H., Hibi, M., Ogawa, J. and Tanokura, M. (2012). Expression, purification, crystallization and preliminary X-ray analysis of 4-hydroxy-3-methyl-2-keto-pentanoate aldolase (asHPAL) from Arthrobacter simplex strain AKU 626. Acta Crystallogr. F68, 958-961.

Yao, M., Miyazono, K, Ohtsuka, J., Hirano, S., Nagata, K., Horinouchi, S., Ohnishi, Y. and Tanokura, M. (2012). Purification, crystallization and preliminary X-ray analysis of the DNA-binding domain of AdpA, the central transcription factor in the A-factor regulatory cascade in the filamentous bacterium Streptomyces griseus, in complex with a duplex DNA. Acta Crystallogr. F68, 946-949.

Chiba, Y., Horita, S., Ohtsuka, J., Arai, H., Nagata, K., Igarashi, Y., Tanokura, M. and Ishii, M. (2012). Crystallization and preliminary X-ray diffraction analysis of a novel type of phosphoserine phosphatase from Hydrogenobacter thermophilus TK-6. Acta Crystallogr. F68, 911-913.

Okai, M., Ohtsuka, J., Asano, A., Guo, L., Miyakawa, T., Miyazono, K., Nakamura, A., Okada, A., Zheng, H., Kimura, K., Nagata, K. and Tanokura, M. (2012). High pressure refolding, purification, and crystallization of flavin reductase from Sulfolobus tokodaii strain 7. Protein Expr. Purif. 84, 214-218.

Lee, J. M., Hull, J. J., Kawai, T., Tsuneizumi, K., Kurihara, M., Tanokura, M., Nagata, K., Nagasawa, H. and Matsumoto, S. (2012). Establishment of Sf9 transformants constitutively expressing PBAN receptor (PBANR) variants: application to functional evaluation. Front. Endocrinol. 3, 56, 1-8.

Kawai, T., Lee, J. M., Nagata, K., Matsumoto, S. Tanokura, M. and Nagasawa, H. (2012). The arginine residue within the C-terminal active core of Bombyx mori pheromone biosynthesis-activating neuropeptide (PBAN) is essential for receptor binding and activation. Front. Endocrinol. 3, 42, 1-5.

Lee, J. M., Hull, J. J., Kawai, T., Goto, C., Kurihara, M., Tanokura, M., Nagata, K., Nagasawa, H. and Matsumoto, S. (2012). Re-evaluation of the PBAN receptor molecule: characterization of PBANR variants expressed in the pheromone glands of moths. Front. Endocrinol. 3, 6, 1-12.

Inoue, H., Tsutsui, N., Nagai, C., Nagata, K., Tanokura, M. and Nagasawa, H. (2011). Crystallization and preliminary X-ray analysis of crustacean hyperglycemic hormone from the kuruma prawn Marsupenaeus japonicus in its weakly-active precursor form. Acta Crystallogr. F67, 1586-1589.

Horita, S., Matsushita, N., Kawachi, T., Ayabe, R., Miyashita, M., Miyakawa, T., Nakagawa, Y., Nagata, K., Miyagawa, H. and Tanokura, M. (2011). Solution structure of a short-chain insecticidal toxin LaIT1 from the venom of scorpion Liocheles australasiae. Biochem. Biophys. Res. Commun. 411, 738-744.

Horita, S., Yamanaka, Y., Yamamura, A., Okada, A, Nakayama, J., Nagata, K. and and Tanokura, M. (2011). Crystallization and preliminary X-ray analysis of a putative sensor histidine kinase domain, the C-terminal domain of HksP4 from Aquifex aeolicus VF5. Acta Crystallogr. F67, 803-807.

Kubota, K., Nagata, K., Okai, M., Miyazono, K., Soemphol, W., Ohtsuka, J., Yamamura, A., Toyama, H., Matsushita, K. and Tanokura, M. (2011). The crystal structure of L-sorbose reductase from Gluconobacter frateurii complexed with NADPH and L-sorbose. J. Mol. Biol. 407, 543-555.

Kubota, K., Miyazono, K., Nagata, K., Toyama, H., Matsushita, K. and Tanokura, M. (2010). Crystallization and preliminary X-ray analysis of 5-keto-D-gluconate reductase from Gluconobacter suboxydans IFO12528 complexed with 5-keto-D-gluconate and NADPH. Acta Crystallogr. F66, 1680-1682.

Okai, M., Kubota, K., Fukuda, M., Nagata, Y., Nagata, K. and Tanokura, M. (2010). Crystal structure of γ-hexachlorocyclohexane dehydrochlorinase LinA from Sphingobium japonicum UT26. J. Mol. Biol. 403, 260-269.

Okada, A., Sano, K., Nagata, K., Yasumasu, S., Ohtsuka, J., Yamamura, A., Kubota, K., Iuchi, I. and Tanokura, M. (2010). Crystal structure of the hatching enzyme ZHE1 from the zebrafish Danio rerio. J. Mol. Biol. 402, 865-878.

Horita, S., Ishibashi, J., Nagata, K., Miyakawa, T., Yamakawa, M. and Tanokura, M. (2010). Isolation, cDNA cloning, and structure-based functional characterization of oryctin, a hemolymph protein from the coconut beetle, Oryctes rhinoceros, as a novel serine protease inhibitor. J. Biol. Chem. 285, 30150-30158.

Tadano, N., Du, C.-K., Yumoto, F., Morimoto, S., Ohta, M., Xie, M.-F., Nagata, K., Zhan, D.-Y., Lu, Q.-W., Miwa, Y., Takahashi-Yanaga, F., Tanokura, M., Ohtsuki, I. and Sasaguri, T. (2010). Biological actions of green tea catechins on cardiac troponin C. Brit. J. Pharmacol. 161, 1034-1043.

Miyazono, K., Zhi, Y., Takamura, Y., Nagata, K., Saigo, K., Kojima, T. and Tanokura, M. (2010). Cooperative DNA-binding and sequence-recognition mechanism of aristaless and clawless. EMBO J. 29, 1613-1623.

Jia, M. Z., Horita, S., Nagata, K. and Tanokura, M. (2010). An archaeal Dim2-like protein, aDim2p, forms a ternary complex with a/eIF2α and the 3’-end fragment of 16S rRNA. J. Mol. Biol. 398, 774-785.

Ebisawa, T., Yamamura, A., Kameda, Y., Hayakawa, K., Nagata, K. and and Tanokura, M. (2010). Structure of mAG, a monomeric mutant of the green fluorescent protein Azami-Green, reveals the structural basis of its stable green emission. Acta Crystallogr. F66, 485-489.

Maruoka, S., Horita, S., Lee, W. C., Nagata, K. and Tanokura, M. (2010). Crystal structure of the ATPPase subunit and its substrate-dependent association with the GATase subunit: A novel regulatory mechanism for a two-subunit-type GMP synthetase from Pyrococcus horikoshii OT3. J. Mol. Biol. 395, 417-429.

Ebisawa, T., Yamamura, A., Kameda, Y., Hayakawa, K., Nagata, K. and Tanokura, M. (2009). Crystallization and preliminary X-ray analysis of a monomeric mutant of Azami-Green (mAG), an Aequorea victoria green fluorescent protein (avGFP)-like green-emitting fluorescent protein from the stony coral Galaxea fascicularis. Acta Crystallogr. F65, 1292-1295.

Yamamura, A., Maruoka, S., Ohtsuka, J., Miyakawa, T., Nagata, K., Kataoka, M., Shimizu, S. and Tanokura, M. (2009). Expression, purification, crystallization, and preliminary X-ray analysis of conjugated polyketone reductase C2 (CPR-C2) from Candida parapsilosis IFO 0708. Acta Crystallogr. F65, 1145-1148.

Maher, M. J., Akimoto, S., Iwata, M., Nagata, K., Hori, Y., Yoshida, M., Yokoyama, S., Iwata, S. and Yokoyama, K. (2009). Crystal structure of A₃B₃ complex of V-ATPase from Thermus thermophilus. EMBO J. 28, 3771-3779.

Okada, A., Nagata, K., Sano, K., Yasumasu, S., Kubota, K., Ohtsuka, J., Iuchi, I. and Tanokura, M. (2009). Crystallization and preliminary X-ray analysis of ZHE1, a hatching enzyme of the zebrafish Danio rerio. Acta Crystallogr. F65, 1018-1020.

Okai, M., Kubota, K., Fukuda, M., Nagata, Y., Nagata, K. and Tanokura, M. (2009). Crystallization and preliminary X-ray analysis of γ-hexachlorocyclohexane dehydrochlorinase LinA from Sphingobium japonicum UT26. Acta Crystallogr. F65, 822-824.

Takeshita, D., Kataoka, M., Miyakawa, T., Miyazono, K., Uzura, A., Nagata, K., Shimizu, S. and Tanokura, M. (2009). Crystallization and preliminary X-ray analysis of the NADPH-dependent 3-quinuclidinone reductase from Rhodotorula rubra. Acta Crystallogr. F65, 645–647.

Kubota, K., Nagata, K., Miyazono, K., Toyama, H., Matsushita, K. and Tanokura, M. (2009). Purification, crystallization and preliminary X-ray analysis of L-sorbose reductase from Gluconobacter frateurii complexed with L-sorbose or NADPH. Acta Crystallogr. F65, 562–564.

Yamamura, A., Okada, A., Kameda, Y., Ohtsuka, J., Nakagawa, N., Ebihara, A., Nagata, K. and Tanokura, M. (2009). Crystal structure of TTHA1623, a novel metallo-β-lactamase superfamily protein from Thermus thermophilus HB8. Acta Crystallogr. F65, 455-459.

Yamamura, A., Ichimura, T., Kamekura, M., Mizuki, T., Usami, R., Makino, T.,  Ohtsuka, J., Miyazono, K., Okai, M., Nagata, K. and Tanokura, M. (2009). Molecular mechanism of the distinct salt-dependent enzyme activity of two halophilic nucleoside diphosphate kinases. Biophys. J. 96, 4692-4700.

Ohtsuka, J., Ichihara, Y., Ebihara, A., Nagata, K. and Tanokura, M. (2009). Crystal structure of TTHA1264, a putative M16-family zinc peptidase from Thermus thermophilus HB8 that is homologous to the β subunit of mitochondrial processing peptidase. Proteins 75, 774-780.

Nishiguchi, K., Nagata, K., Tanokura, M., Sonomoto, K. and Nakayama, J. (2009). Structure-activity relationship of gelatinase biosynthesis-activating pheromone of Enterococcus faecalis. J. Bacteriol. 191, 641-650.

Yamamura, A., Ohtsuka, J., Kubota, K., Agari, Y., Ebihara, A., Nakagawa, N., Nagata, K. and Tanokura, M. (2008). Crystal structure of TTHA1429, a novel metallo-β-lactamase superfamily protein from Thermus thermophilus HB8. Proteins 73, 1053-1057.

Ogasawara, Y., Kaya, H., Hiraoka, G., Yumoto, F., Kimura, S., Kadota, Y., Hishinuma, H., Senzaki, E., Yamagoe, S., Nagata, K., Nara, M., Suzuki, K., Tanokura, M. and Kuchitsu, K. (2008). Synergistic activation of Arabidopsis NADPH oxidase AtrbohD by Ca²⁺ and phosphorylation. J. Biol. Chem. 283, 8885-8892.

Yumoto, F., Tanaka, H., Nagata, K., Miyauchi, Y., Miyakawa, T., Ojima, T. and Tanokura, M. (2008). Spectroscopic and ITC study of the conformational change upon Ca²⁺-binding in TnC C-lobe and TnI peptide complex from Akazara scallop striated muscle. Biochem. Biophys. Res. Commun. 369, 109-114.

Okai, M., Miyauchi, Y., Lee, W. C., Yumoto, F., Nagata, K. and Tanokura, M. (2008). Crystal structure of the proline iminopeptidase-related protein TTHA1809 from Thermus thermophilus HB8. Proteins 70, 1646-1649.

Yamamura, A., Ichimura, T., Mimoto, F., Ohtsuka, J., Miyazono, K., Okai, M., Kamo, M., Lee, W.-C., Nagata, K. and Tanokura, M. (2008). A unique catalytic triad revealed by the crystal structure of APE0912, a short-chain dehydrogenase/reductase family protein from Aeropyrum pernix K1. Proteins 70, 1640-1645.

Imai, F. L., Nagata, K., Yonezawa, N., Nakano, M. and Tanokura, M. (2008). Crystal structure of calcium-bound human S100A13 at pH 7.5 at 1.8-Å resolution. Acta Crystallogr. F64, 70-76.

Nagata, K., Ohtsuka, J., Takahashi, M., Asano, A., Iino, H., Ebihara, A. and Tanokura, M. (2008). Crystal structure of TTHA0303 (TT2238), a four-helix bundle protein with an exposed histidine triad from Thermus thermophilus HB8 at 2.0 Å. Proteins 70, 1103-1107.

Takeshita, D., Zenno, S., Lee, W. C., Nagata, K., Saigo, K. and Tanokura, M. (2007). Homodimeric structure and double-stranded RNA cleavage activity of the C-terminal RNase III domain of human Dicer. J. Mol. Biol. 374, 106-120.

Makino, T., Morii, H., Shimizu, T., Arisaka, F., Kato, Y., Nagata, K. and Tanokura, M. (2007). Reversible and irreversible coiled coils in the stalk domain of ncd motor protein. Biochemistry 46, 9523-9532.

Jia, M. Z., Ohtsuka, J., Lee, W. C., Nagata, K. and Tanokura, M. (2007). Crystal structure of Dim2p, a pre-ribosomal RNA processing factor, from Pyrococcus horikoshii OT3 at 2.30 Å. Proteins 69, 428-432.

Yumoto, F., Nagata, K., Miyauchi, Y., Ojima, T., Tanaka, H., Nishita, K., Ohtsuki, I. and Tanokura, M. (2007). Crystallization and preliminary X-ray analysis of the Ca²⁺-bound C-terminal lobe of troponin C in complex with a troponin I-derived peptide fragment from Akazara scallop. Acta Crystallogr. F63, 535-537.

Shirokane, M., Sawano, Y., Miyazono, K., Nagata K. and Tanokura, M. (2007). Crystallization and preliminary X-ray analysis of PH1010 from Pyrococcus horikoshii OT3, a member of the archaeal DUF54 family of proteins. Acta Crystallogr. F63, 532-534.

Miyazono, K., Watanabe, M., Kosinski, J., Ishikawa, K., Kamo, M., Sawasaki, T., Nagata, K., Bujnicki, J. M., Endo, Y., Tanokura, M. and Kobayashi, I. (2007). Novel protein fold discovered in the PabI family of restriction enzymes. Nucl. Acids Res. 35, 1908-1918.

Ming, H., Kato, Y., Miyazono, K., Ito, K., Kamo, M., Nagata, K. and Tanokura, M. (2007). Crystal structure of thioredoxin domain of ST2123 from thermophilic archaea Sulfolobus tokodaii strain7. Proteins 69, 204-208.

Nakayama, J., Tanaka, E., Kariyama, R., Nagata, K., Nishiguchi, K., Mitsuhata, R., Uemura, Y., Tanokura, M., Kumon, H. and Sonomoto, K. (2007). Siamycin attenuates fsr quorum sensing mediated by gelatinase biosynthesis-activating pheromone in Enterococcus faecalis. J. Bacteriol. 189, 1358-1365.

Imai, F. L., Nagata, K., Yonezawa, N., Yu, J., Ito, E., Kanai, S., Tanokura, M. and Nakano. M. (2006). Crystallization and preliminary X-ray analysis of human S100A13. Acta Crystallogr. F62, 1144-1146.

Ohtsuka, J., Nagata, K., Lee, W. C., Ono, Y., Fukuda, R., Ohta, A. and Tanokura, M. (2006). Crystallization and preliminary X-ray analysis of CTP:phosphoethanolamine cytidylyltransferase (ECT) from Saccharomyces cerevisiae. Acta Crystallogr. F62, 1003-1005.

Okai, M., Kudo, N., Lee, W. C., Kamo, M., Nagata, K. and Tanokura, M. (2006). Crystal structures of the short-chain flavin reductase HpaC from Sulfolobus tokodaii strain 7 in its three states [NAD(P)⁺-free, NAD⁺-bound, and NADP⁺-bound]. Biochemistry 45, 5103-5110.

Takeshita, D., Zenno, S., Lee, W. C., Nagata, K., Saigo, K. and Tanokura, M. (2006). Crystallization and preliminary X-ray analysis of the C-terminal RNase III domain of human Dicer. Acta Crystallogr. F62, 402-404.

Nara, M., Yumoto, F., Nagata, K., Tanokura, M., Kagi, H., Ojima, T., Nishita, K. and Morii, H. (2006). Infrared spectroscopic study on Ca²⁺ binding to Akazara scallop troponin C in comparison with peptide analogues of its Ca²⁺-binding Site IV. Vibr. Spectr. 42, 188-191.

Kato, Y., Hino, Y., Nagata, K. and Tanokura, M. (2006). Solution structure and binding specificity of FBP11/HYPA WW domain as Group-II/III. Proteins 63, 227-234.

Jia, M. Z., Ohtsuka, J., Lee, W. C., Nagata, K. and Tanokura, M. (2006). Crystallization and preliminary X-ray analysis of PH1566, a putative ribosomal RNA processing factor from the hyperthermophilic archaeon Pyrococcus horikoshii OT3. Acta Crystallogr. F62, 47-48.

Miyakawa, T., Lee, W. C., Hatano, K., Kato, Y., Sawano, Y., Miyazono, K., Nagata, K. and Tanokura, M. (2006). Crystal Structure of the YjgF/YER057c/UK114 family protein from the hyperthermophilic archaeon Sulfolobus tokodaii strain 7. Proteins 62, 557-561.

Maruoka, S., Lee, W. C., Kamo, M., Kudo, N., Nagata, K. and Tanokura, M. (2005). Crystal structure of glutamine amidotransferase from Pyrococcus horikoshii OT3. Proc. Japan Acad. B81, 459-462.

Kawaguchi, M., Yasumasu, S., Shimizu, A., Hiroi, J., Yoshizaki, N., Nagata, K., Tanokura, M. and Iuchi, I. (2005). Purification and gene cloning of Fundulus heteroclitus hatching enzyme. A hatching enzyme system composed of high choriolytic enzyme and low choriolytic enzyme is conserved between two different teleosts, Fundulus heteroclitus and medaka Oryzias latipes. FEBS J. 272, 4315-4326.

Yumoto, F., Lu, Q. W., Morimoto, S., Tanaka, H., Kono, N., Nagata, K., Ojima, T., Takahashi-Yanaga, F., Miwa, Y., Sasaguri, T., Nishita, K., Tanokura, M. and Ohtsuki, I. (2005). Drastic Ca²⁺ sensitization of myofilament associated with a small structural change in troponin I in inherited restrictive cardiomyopathy. Biochem. Biophys. Res. Commun. 338, 1519-1526.

Miyakawa, T., Hatano, K., Lee, W. C., Kato, Y., Sawano, Y., Yumoto, F., Nagata, K. and Tanokura, M. (2005). Crystallization and preliminary X-ray analysis of the YjgF/YER057c/UK114-family protein ST0811 from Sulfolobus tokodaii strain7. Acta Crystallogr. F61, 828-830.

Okai, M., Kudo, N., Nagata, K., Lee, W. C., Kamo, M. and Tanokura, M. (2005). Crystal structure of the short-chain flavin reductase HpaC from Sulfolobus tokodaii strain 7. Proc. Japan Acad. B81, 229-232.

Nagata, K., Sasaki, H., Ohtsuka, J., Ming, H., Okai, M., Kubota, K., Kamo, M., Ito, K., Ichikawa, T., Koyama, Y. and Tanokura, M. (2005). Crystal structure of monomeric sarcosine oxidase from Bacillus sp. NS-129 reveals multiple conformations at the active-site loop. Proc. Japan Acad. B81, 220-224.

Kamo, M., Inouye, K., Nagata, K. and Tanokura, M. (2005). Preliminary X-ray crystallographic analysis of thermolysin in the presence of 4 M NaCl. Acta Crystallogr. D61, 710-712.

Nagata, K., Tsutsui, S., Lee, W.-C., Ito, K., Kamo, M., Inoue, Y. and Tanokura, M. (2004). Crystallization and preliminary X-ray analysis of carboxypeptidase 1 from Thermus thermophilus. Acta Crystallogr. D60, 1445-1446.

Ito, M., Nagata, K., Yumoto, F., Yamagoe, S., Suzuki, K., Adachi, K. and Tanokura, M. (2004). ¹H, ¹³C, ¹⁵N resonance assignments of the cytokine LECT2. J. Biomol. NMR 29, 543-544.

Kato, Y., Akai, A., Suzuki, R., Hosokawa, H., Ninomiya, H., Masaki, T., Nagata, K. and Tanokura, M. (2004). ¹H, ¹³C and ¹⁵N assignments of the tandem WW domains of human MAGI-1/BAP-1. J. Biomol. NMR 29, 539-540.

Nara, M., Yumoto, F., Nagata, K., Tanokura, M., Kagi, H., Ojima, T. and Nishita, K. (2004). Fourier transform infrared spectroscopic study on the binding of Mg²⁺ to a mutant Akazara scallop troponin C (E142Q). Biopolymers 74, 77-81.

Kato, Y., Nagata, K., Takahashi, M., Lian, L., Herrero, J. J., Sudol, M. and Tanokura, M. (2004). Common mechanism of ligand recognition by group II/III WW domains: redefining their functional classification. J. Biol. Chem. 279, 31833-31841.

Iwata, M., Imamura, H., Stambouli, E., Ikeda, C., Tamakoshi, M., Nagata, K., Makyio, H., Hankamer, B., Barber, J., Yoshida, M., Yokoyama, K. and Iwata, S. (2004). Crystal structure of a central stalk subunit C and reversible association/dissociation of V-ATPase. Proc. Natl Acad. Sci. USA 101, 59-64.

Yumoto, F., Nagata, K., Adachi, K., Nemoto, N., Ojima, T., Nishita, K., Ohtsuki, I. and Tanokura, M. (2003). NMR structural study of troponin C C-terminal domain complexed with troponin I fragment from Akazara scallop. Adv. Exp. Med. Biol. 538, 195-200.

Yokoyama, K., Nagata, K., Imamura, H., Ohkuma, S., Yoshida, M. and Tamakoshi, M. (2003). Subunit arrangement in V-ATPase from Thermus thermophilus. J. Biol. Chem. 278, 42686-42691.

Suzuki, R., Nagata, K., Yumoto, F., Kawakami, M., Nemoto, N., Furutani, M., Adachi, K., Maruyama, T. and Tanokura, M. (2003). Three-dimensional solution structure of an archaeal FKBP with a dual function of peptidyl prolyl cis–trans isomerase and chaperone-like activities. J. Mol. Biol. 328, 1149-1160.

Katayama, H., Nagata, K., Ohira, T., Yumoto, F., Tanokura, M. and Nagasawa, H. (2003). The solution structure of molt-inhibiting hormone from the kuruma prawn Marsupenaeus japonicus. J. Biol. Chem. 278, 9620-9623.

Ito, M., Nagata, K., Kato, Y. Oda, Y., Yamagoe, S., Suzuki, K. and Tanokura, M. (2003). Expression, oxidative refolding and characterization of six-histidine-tagged recombinant human LECT2, a 16-kDa chemotactic protein with three disulfide bonds. Protein Expr. Purif. 27, 272-278.

Sawano, Y., Muramatsu, T., Hatano, K., Nagata, K. and Tanokura, M. (2002). Characterization of genomic sequence coding for bromelain inhibitors in pineapple and expression of its recombinant isoform. J. Biol. Chem. 277, 28222-28227.

Kato, Y., Ito, M., Kawai, K., Nagata, K. and Tanokura, M. (2002). Determinants of ligand specificity in groups I and IV WW domains as studied by surface plasmon resonance and model building. J. Biol. Chem. 277, 10173-10177.

Ogura, K., Nagata, K., Horiuchi, M., Ebisui, E., Hasuda, T., Yuzawa, S., Nishida, M., Hatanaka, H. and Inagaki, F. (2002). Solution structure of N-terminal SH3 domain of Vav and the recognition site for Grb2 C-terminal SH3 domain. J. Biomol. NMR 22, 37-46.

Yumoto, F., Nara, M., Kagi, H., Iwasaki, W., Ojima, T., Nishita, K., Nagata, K. and Tanokura, M. (2001). Coordination structures of Ca²⁺ and Mg²⁺ in Akazara scallop troponin C in solution. FTIR spectroscopy of side-chain COO^– groups. Eur. J. Biochem. 268, 6284-6290.

Katayama, H., Ohira, T., Nagata, K. and Nagasawa, H. (2001). A recombinant molt-inhibiting hormone of the kuruma prawn has a similar secondary structure to a native hormone: determination of disulfide bond arrangements and measurement of circular dichroism spectra. Biosci. Biotechnol. Biochem. 65, 1832-1839.

Nishida, M., Nagata, K., Hachimori, Y., Horiuchi, M., Ogura, K., Mandiyan, V., Schlessinger, J. and Inagaki, F. (2001). Novel recognition mode between Vav and Grb2 SH3 domains. EMBO J. 20, 2995-3007.

Nagata, K., Kudo, N., Abe, K., Arai, S. and Tanokura, M. (2000). Three-dimensional solution structure of oryzacystatin-I, a cysteine proteinase inhibitor of the rice, Oryza sativa L. japonica. Biochemistry 39, 14753-14760.

Suzuki, R., Nagata, K., Kawakami, M., Nemoto, N., Furutani, M., Adachi, K., Maruyama, T. and Tanokura, M. (2000). Assignment of ¹H, ¹³C and ¹⁵N resonances of FKBP from Methanococcus thermolithotrophicus. J. Biomol. NMR 17, 183-184.

Murayama, K., Shindo, N., Suzuki, R., Kawakami, M., Mineki, R., Taka, H., Kazuno, S., Nagata, K., Maruyama, T. and Tanokura, M. (2000). Characterization of native and recombinant peptidyl prolyl cis-trans isomerases derived from Methanococcus thermolithotrophicus based on cDNA sequence. Electrophoresis 21, 1733-1739.

Satake, S., Nagata, K., Kataoka, H. and Mizoguchi, A. (1999). Bombyxin secretion in the adult silkmoth Bombyx mori: Sex-specificity and its correlation with metabolism. J. Insect Physiol. 45, 939-945.

Nagata, K., Maruyama, K., Kojima, K., Yamamoto, M., Tanaka, M., Kataoka, H., Nagasawa, H., Isogai, A., Ishizaki, H. and Suzuki, A. (1999). Prothoracicotropic activity of SBRPs, the insulin-like peptides of the saturniid silkworm Samia cynthia ricini. Biochem. Biophys. Res. Commun. 266, 575-578.

Tsuchiya, S., Ogura, K., Hatanaka, H., Nagata, K., Terasawa, H., Mandiyan, V., Schlessinger, J., Aimoto, S., Ohta, H. and Inagaki, F. (1999). Solution structure of the SH2 domain of Grb2/Ash complexed with EGF receptor-derived phosphotyrosine-containing peptide. J. Biochem. 125, 1151-1159.

Ogura, K., Nagata, K., Hatanaka, H., Habuchi, H., Kimata, K., Tate, S., Ravera, M. W., Jaye, M., Schlessinger, J. and Inagaki, F. (1999). Solution structure of human acidic fibroblast growth factor and interaction with heparin-derived hexasaccharide. J. Biomol. NMR 13, 11-24.

Satake, S., Masumura, M., Ishizaki, H., Nagata, K., Kataoka, H., Suzuki, A. and Mizoguchi, A. (1997). Bombyxin, an insulin-related peptide of insects, reduces the major storage carbohydrates in the silkworm Bombyx mori. Comp. Biochem. Physiol. B118, 349-357.

Iwasaki, W., Nagata, K., Hatanaka, H., Inui, T., Kimura, T., Muramatsu, T., Yoshida, K., Tasumi, M. and Inagaki, F. (1997). Solution structure of midkine, a new heparin-binding growth factor. EMBO J. 16, 6936-6946.

Nagata, K., Hatanaka, H., Kohda, D., Kataoka, H., Nagasawa, H., Isogai, A., Ishizaki, H., Suzuki, A. and Inagaki, F. (1995). Identification of the receptor-recognition surface of bombyxin-II, an insulin-like peptide of the silkmoth Bombyx mori: critical importance of the B-chain central part. J. Mol. Biol. 253, 759-770.

Nagata, K., Hatanaka, H., Kohda, D., Kataoka, H., Nagasawa, H., Isogai, A., Ishizaki, H., Suzuki, A. and Inagaki, F. (1995). Three-dimensional solution structure of bombyxin-II, an insulin-like peptide of the silkmoth Bombyx mori: structural comparison with insulin and relaxin. J. Mol. Biol. 253, 749-758.

Yagi, Y., Ishibashi, J., Nagata, K., Kataoka, H., Suzuki, A., Mizoguchi, A. and Ishizaki, H. (1995). The brain neurosecretory cells of the moth Samia cynthia ricini: immunohistochemical localization and developmental changes of the Samia homologues of the Bombyx prothoracicotropic hormone and bombyxin. Develop. Growth Differ. 37, 505-516.

Tanaka, M., Kataoka, H., Nagata, K., Nagasawa, H. and Suzuki, A. (1995). Morphological changes of BM-N4 cells induced by bombyxin, an insulin-related peptide of Bombyx mori. Regul. Pept. 57, 311-318.

Terasawa, H., Kohda, D., Hatanaka, H., Tsuchiya, S., Ogura, K., Nagata, K., Ishii, S., Mandiyan, V., Ullrich, A., Schlessinger, J. and Inagaki, F. (1994). Solution structure of N-terminal SH3 domain of GRB2 complexed with proline-rich peptide from the guanine nucleotide releasing factor Sos. Nature Struct. Biol. 1, 891-897.

Terasawa, H., Kohda, D., Hatanaka, H., Nagata, K., Higashihashi, N., Fujiwara, H., Sakano, K. and Inagaki, F. (1994). Solution structure of human insulin-like growth factor II; recognition sites for receptors and binding proteins. EMBO J. 13, 5590-5597.

Nagata, K., Kohda, D., Hatanaka, H., Ichikawa, S., Matsuda, S., Yamamoto, T., Suzuki, A. and Inagaki, F. (1994). Solution structure of the epidermal growth factor-like domain of heregulin-α, a ligand for p180erbB-4. EMBO J. 13, 3517-3523.

Nagata, K., Maruyama, K., Nagasawa, H., Urushibata, I., Isogai, A., Ishizaki, H. and Suzuki, A. (1992). Bombyxin-II and its disulfide bond isomers: synthesis and activity. Peptides 13, 653-662.

Maruyama, K., Nagata, K., Tanaka, M., Nagasawa, H., Isogai, A., Ishizaki, H. and Suzuki, A. (1992). Synthesis of bombyxin-IV, an insulin superfamily peptide from the silkworm, Bombyx mori, by stepwise and selective formation of three disulfide bonds. J. Prot. Chem. 11, 1-12.

 

学会プロシーディング (査読あり)

Proceedings (peer-reviewed)

Hasegawa, K., Zhang,. M., Lu, P., Hayakawa, K., Katayama, Y., Katayama, H., Nakayama, J., Sonomoto, J., Tanokura, M. and Nagata, K. (2019). Expression, purification, crystallization and preliminary X-ray crystallographic studies of FsrC, the cell surface receptor of the cyclic peptide quormone GBAP. In Peptide Science 2018 (Futaki, S. and Matsuzaki, K. eds.), p. 35, The Japanese Peptide Society, Osaka.

Matsunaga, Y., Matsukawa, T., Iwasaki, T., Nagata, K. and Kawano, T. (2017). Comparison of physiological functions of antagonistic insulin-like peptides, INS-23 and INS-18, in Caenorhabditis elegans. In Peptide Science 2016 (Akaji, K. ed.), pp. 45-46, The Japanese Peptide Society, Osaka.

Nagata, K., Kawai, T., Guo, L., Liu, D., Suzuki, T., Katayama, Y., Hayakawa, K., Lee, J. M., Nagamine, T., Hull, J. J., Matsumoto, S., Nagasawa, H. and Tanokura, M. (2014). Identification of functionally important residues of the silkmoth pheromone biosynthesis-activating neuropeptide by its receptor. In Peptide Science 2013 (Nishiuchi, Y. and Teshima, T. ed.), pp. 293-294, The Japanese Peptide Society, Osaka.

Nagata, K., Kawai, T., Ebisawa, T., Hayakawa, K., Lee, J. M., Hull, J. J., Matsumoto, S., Nagasawa, H. and Tanokura, M. (2012). Identification of the amino-acid residues important for the recognition of silkmoth pheromone biosynthesis-activating neuropeptide by its receptor. In Peptide Science 2011 (Sakaguchi, K. ed.), pp. 181-182, The Japanese Peptide Society, Osaka.

Kawai, T., Lee, J. M., Nagata, K., Hull, J. J., Matsumoto, S., Tanokura, M. and Nagasawa, H. (2012). Structure-activity relationship study of the C-terminal part of pheromone biosynthesis-activating neuropeptide. In Peptide Science 2011 (Sakaguchi, K. ed.), pp. 175-178, The Japanese Peptide Society, Osaka.

Miyashita, M., Horita, S., Miyakawa, T., Nakagawa, Y., Nagata, K., Miyagawa, H. and Tanokura, M. (2012). Solution structure and functional residues of a short-chain insecticidal toxin LaIT1 from the venom of scorpion Liocheles australasiae. In Peptide Science 2011 (Sakaguchi, K. ed.), pp. 169-170, The Japanese Peptide Society, Osaka.

Horita, S., Ishibashi, J., Nagata, K., Miyakawa, T., Yamakawa, M. and Tanokura, M. (2011). Structure-based functional characterization of oryctin, a hemolymph protein from the coconut rhinoceros beetle, Oryctes rhinoceros, as a novel serine protease inhibitor. In Peptide Science 2010: Proceedings of the Fifth International Peptide Symposium (Fujii, N. and Kiso, Y. eds.), p. 142, The Japanese Peptide Society, Osaka.

Kawai, T., Nagata. K., Okada, A., Hayakawa, K., Hull, J. J., Lee, J. M., Matsumoto, S., Tanokura, M. and Nagasawa, H. (2011). Structure-activity relationship studies of the pheromone biosynthesis activating neuropeptide of the silkmoth, Bombyx mori. In Peptide Science 2010: Proceedings of the Fifth International Peptide Symposium (Fujii, N. and Kiso, Y. eds.), p. 126, The Japanese Peptide Society, Osaka.

Kawai, T., Hull, J. J., Matsumoto, S., Nagata, K., Tanokura, M. and Nagasawa, H. (2010). Studies on the structure-activity relationship of pheromone-biosynthesis activating neuropeptide (PBAN). In Peptide Science 2009 (Okamoto, K. ed.), pp. 231-234, The Japanese Peptide Society, Osaka.

Yamanaka, Y., Hayakawa, K., Katayama, H., Nishiguchi, K., Sonomoto, K., Nakayama, J., Nagata, K. and Tanokura, M. (2010). Biosynthesis of the thiolactone derivative of Enterococcus faecalis gelatinase-biosynthesis activating pheromone by using the Mycobacterium xenopi GyrA mini-intein. In Peptide Science 2009 (Okamoto, K. ed.), pp. 171-172, The Japanese Peptide Society, Osaka.

Okada, A., Kawai, T., Sugisaka, A., Ohtsuka, J., Hull, J. J., Moto, K., Matsumoto, S., Nagasawa, H., Nagata, K. and Tanokura, M. (2009). Structural analysis of the active and inactive fragments of pheromone biosynthesis-activating neuropeptide (PBAN) from the silkmoth Bombyx mori. In Peptide Science 2008 (Nomizu, M. ed.), pp. 535-538, The Japanese Peptide Society, Osaka.

Kawai, T., Sugisaka, A., Hull, J. J., Matsumoto, S., Nagata, K., Tanokura, M. and Nagasawa, H. (2009). Development of a novel bioassay system for pheromone biosynthesis-activating neuropeptide (PBAN) using the Bombyx PBAN receptor expressed in insect cells. In Peptide Science 2008 (Nomizu, M. ed.), pp. 287-288, The Japanese Peptide Society, Osaka.

Nagata, K., Nishiguchi, K., Tanokura, M., Sonomoto, K. and Nakayama, J. (2009). Structure-activity relationship of gelatinase biosynthesis-activating pheromone from the Gram positive bacterium Enterococcus faecalis. In Peptide Science 2008 (Nomizu, M. ed.), pp. 91-94, The Japanese Peptide Society, Osaka.

Horita, S., Ishibashi, J., Yamakawa, M., Nagata, K. and Tanokura, M. (2009). NMR structure analysis of ORYCTIN from the coconut rhinoceros beetle, Oryctes rhinoceros, led to its functional characterization as a novel serine protease inhibitor. In Peptide Science 2008 (Nomizu, M. ed.), pp. 29-32, The Japanese Peptide Society, Osaka.

Nagata, K., Ohtsuka, J., Takahashi, M., Asano, A., Iino, H., Ebihara, A. and Tanokura, M. (2008). Crystal structure of TTHA0303 (TT2238), a four-helix bundle protein with an exposed histidine triad from Thermus thermophilus HB8. In Peptide Science 2007 (Aimoto, S. and Ono, S. eds.), pp. 299-302, The Japanese Peptide Society, Osaka.

Nagata, K., Tsutsui, S., Lee, W. C., Inoue, Y. and Tanokura, M. (2007). Crystal structure and substrate specificity of carboxypeptidase 1 from Thermus thermophilus. In Peptide Science 2006 (Ishida, H. and Mihara, H. eds.), pp. 181-182, The Japanese Peptide Society, Osaka.

Kato, Y., Ito, M., Kawai, K., Nagata, K. and Tanokura, M. (2003). Determinants of ligand specificity in group I and IV WW domains. In Peptide Science 2002 (Yamada, T. ed.), pp. 283-286, The Japanese Peptide Society, Osaka.

Katayama, H., Nagata, K., Ohira, T., Yumoto, F., Tanokura, M. and Nagasawa, H. (2003). Three-dimensional solution structure of a crustacean molt-inhibiting hormone. In Peptide Science 2002 (Yamada, T. ed.), pp. 89-92, The Japanese Peptide Society, Osaka.

Nagata, K., Irimoto, Y., Kudo, N., Abe, K., Arai, S., Yamane, H. and Tanokura, M. (2000). Structural and functional characterization of oryzacystatin-I monomer and dimer. In Peptide Science 1999 (Fujii, N. ed.), pp. 473-476, Protein Research Foundation, Osaka.

 

学会プロシーディング (査読なし)

Proceedings (not peer-reviewed)

Nagata, K., Yamanaka, Y., Horita, S., Katayama, H., Hayakawa, K., Yamamura, A., Sato, M., Nishiguchi, K., Sonomoto, K., Nakayama, J. and Tanokura, M. (2010). Synthesis of the thiolactone derivative of Enterococcus faecalis gelatinase biosynthesis-activating pheromone using the GyrA mini-intein. In Peptides 2010: Tales of Peptides: Proceedings of the 31st European Peptide Symposium (Lebl, M., Meldal, M., Jensen, K. J., Hoeg-Jensen, T. ed.), pp. 162-163, European Peptide Society, Prompt Scientific Publishing, San Diego.

Nagata, K., Okada, A., Kawai, T., Ohtsuka, J., Hull, J. J., Moto, K., Matsumoto, S., Nagasawa, H. and Tanokura, M. (2009). NMR solution structure analysis of the C-terminal linear and cyclic peptides of pheromone biosynthesis-activating neuropeptide (PBAN) from the silkmoth Bombyx mori. In Peptides: Breaking Away: Proceedings of the 21st American Peptide Symposium (Lebl, M. ed.), pp. 345-346, American Peptide Society, Prompt Scientific Publishing, San Diego.

Nagata, K., Okada, A., Ohtsuka, J., Takahashi, M., Kawai, T., Sugisaka, A., Hull, J. J., Moto, K., Matsumoto, S., Nagasawa, H. and Tanokura, M. (2009). NMR solution structure analysis of the active and inactive fragments of pheromone biosynthesis-activating neuropeptide (PBAN) from the silkmoth Bombyx mori. In Peptides 2008: Chemistry of Peptides in Life Science, Technology and Medicine: Proceedings of The Thirtieth European Peptide Symposium (Lankinen, H. ed.), pp. 578-579, The Finnish Peptide Society and The European Peptide Society, The Finnish Peptide Society, Helsinki.

Okai, M., Kudo, N., Nagata, K., Lee, W. C., Kamo, M. and Tanokura, M. (2005). Crystal structures of flavin reductase ST0723 from Sulfolobus tokodaii strain 7 and its complex with NAD⁺. In Flavins and Flavoproteins 2005 (Nishino, T, Miura, R., Tanokura, M., Fukui, K. ed.), pp. 271-274, ARchiTect inc., Tokyo.

Nagata, K., Sasaki, H., Ohtsuka, J., Ming, H., Okai, M., Kubota, K., Kamo, M., Ito, K., Ichikawa, T., Koyama, Y. and Tanokura, M. (2005). Crystal structure of monomeric sarcosine oxidase from Bacillus sp. NS-129. In Flavins and Flavoproteins 2005 (Nishino, T, Miura, R., Tanokura, M., Fukui, K. ed.), pp. 105-110, ARchiTect inc., Tokyo.

Nagata, K. and Tanokura, M. (2005). Cardioacceleratory peptide (CCAP) of the fruit fly Drosophila melanogaster: solution structure analysis and docking simulation to the receptor CG6111. In Peptide Science 2004 (Shimohigashi, Y. ed.), pp. 441-444, The Japanese Peptide Society, Osaka.

Katayama, H., Nagata, K., Ohira, T., Aida, K. and Nagasawa, H. (2002). NMR structural analysis of a molt-inhibiting hormone in the kuruma prawn Penaeus (Marsupenaeus) japonicus. In Proceedings of the 21st Conference of European Comparative Endocrinologists (Keller, R., Dircksen, H., Sedlmeier, D., Vaudry, H. ed.), pp.385-388, Monduzzi Editore S.p.A., Bologna (Italy).

Nagata, K., Kudo, N., Abe, K., Arai, S. and Tanokura, M. (1999). NMR structural studies of a rice cysteine proteinase inhibitor, oryzacystatin-I. In Peptide Science 1998 (Kondo, M. ed.), pp. 333-336, Protein Research Foundation, Osaka.

Nagata, K., Hatanaka, H., Kohda, D., Ishizaki, H., Momomura, K., Tamori, K., Kadowaki, T., Tanaka, M., Kataoka, H., Nagasawa, H., Isogai, A., Suzuki, A. and Inagaki, F. (1999). Three-dimensional structure and receptor-recognition sites of bombyxin-II, an insulin-like brain-secretory peptide of the silkmoth. In Peptide Science — Present and Future (Shimonishi, Y. ed.), pp. 245-248, Kluwer Academic Publishers, Dordrecht (The Netherlands).

Nagata, K., Hatanaka, H., Kohda, D., Ishizaki, H., Momomura, K., Tamori, K., Kadowaki, T., Tanaka, M., Kataoka, H., Nagasawa, H., Isogai, A., Suzuki, A. and Inagaki, F. (1997). Three-dimensional structure and receptor-recognition sites of bombyxin-II, an insulin-like brain-secretory peptide of the silkmoth. In Advances in Comparative Endocrinology (Kawashima, S., Kikuyama, S. ed.), pp. 121-124, Monduzzi Editore S.p.A., Bologna (Italy).

Nagata, K., Kataoka, H., Saido, T. C., Hatanaka, H., Ishizaki, H., Suzuki, A. and Inagaki, F. (1996). Identification of the receptor-recognition site of bombyxin-II, a silkmoth insulin-like peptide. In Peptide Chemistry 1995 (Nishi, N. ed.), pp. 257-260, Protein Research Foundation, Osaka.

Nagata, K., Hatanaka, H., Kohda, D., Kataoka, H., Nagasawa, H., Isogai, A., Ishizaki, H., Suzuki, A. and Inagaki, F. (1995). Three-dimensional structure and receptor-recognition site of bombyxin-II, an insulin-like brain-secretory peptide of the silkmoth Bombyx mori. In Molecular Mechanisms of Insect Metamorphosis and Diapause (Suzuki, A., Kataoka, H., Matsumoto, S. ed.), pp. 87-96, Industrial Publishing & Consulting, Inc., Tokyo.

Nagata, K., Hatanaka, H., Kohda, D., Kataoka, H., Nagasawa, H., Isogai, A., Ishizaki, H., Suzuki, A. and Inagaki, F. (1995). Three-dimensional structure and receptor-recognition surface of bombyxin-II, an insulin-related peptide of the silkmoth Bombyx mori. In Peptide Chemistry 1994 (Ohno, M. ed.), pp. 85-88, Protein Research Foundation, Osaka.

Nagata, K., Kohda, D., Hatanaka, H., Ichikawa, S., Matsuda, S., Yamamoto, T., Suzuki, A. and Inagaki, F. (1994). Synthesis and solution structure analysis of the EGF-like domain of heregulin-a, a ligand for p185erbB-2. In Peptide Chemistry 1993 (Okada, Y. ed.), pp. 421-424, Protein Research Foundation, Osaka.

Nagata, K., Momomura, K., Tamori, K., Kadowaki, T., Maruyama, K., Tanaka, M., Kojima, K., Nagasawa, H., Kataoka, H., Isogai, A., Ishizaki, H. and Suzuki, A. (1993). Insulin, bombyxin and their hybrids: synthesis and activity. In Peptide Chemistry 1992 (Yanaihara, N. ed.), pp. 416-419, ESCOM Science Publishers B. V., Leiden (The Netherlands).

Nagata, K., Maruyama, K., Nagasawa, H., Tanaka, M., Isogai, A., Ishizaki, H. and Suzuki, A. (1992). Synthesis of bombyxin-II, an insulin-like heterodimeric peptide of the silkmoth Bombyx mori, by regiospecific disulfide bond formation. In Peptide Chemistry 1991 (Suzuki, A. ed.), pp. 1-6, Protein Research Foundation, Osaka.

 

総説

Reviews

張迷敏, 立﨑仁, 永田宏次 (2021). 黒ウコンポリフェノールによる長寿遺伝子産物SIRT1の活性化機構. バイオサイエンスとインダストリー 79, 375-377.

石橋純, 逸見光, 永田宏次, 田之倉優 (2012). 構造生物学を利用した機能未知タンパク質の機能解明. 蚕糸・昆虫バイオテック 81, 125-129.

Nagata, K. (2010). Studies of the structure-activity relationships of peptides and proteins involved in growth and development based on their three-dimensional structures. Biosci. Biotechnol. Biochem. 74, 462-470.

田之倉 優, 永田宏次, 宮園健一, 宮川拓也, 岡井公彦 (2010). 近年の酵素・タンパク質結晶構造解析の進歩と展開. 日本結晶学会誌 52, 8-13.

田之倉 優, 永田宏次, 浅野敦子 (2008). 発生・分化とDNAの複製・修復. 蛋白質 核酸 酵素 53, 612-615.

田之倉優, 工藤紀雄, 永田宏次 (2003). 発生・分化とDNAの複製・修復の構造ゲノム科学. バイオイメージング 12, 146-150.

永田宏次, 鈴木昭憲, 稲垣冬彦 (1996). 昆虫のインスリン族ペプチドの分子構造と機能部位－インスリンとの比較. 蛋白質 核酸 酵素 41, 1485-1496.

 

著書 (分担)

Books (written jointly)

永田宏次, 木下滋晴 (2017). ミクロの世界を可視化する, In 科学の技法 東京大学「初年次ゼミナール理科」テキスト (東京大学教養教育高度化機構初年次教育部門, 増田建, 坂口菊恵編), pp. 126-129, 東京大学出版会 (東京).

永田宏次, 宮川拓也 (2013). NMR溶液構造解析法, In 21世紀のバイオサイエンス 実験農芸化学 (東京大学大学院農学生命科学研究科応用生命化学専攻・応用生命工学専攻編), pp. 150-151, 朝倉書店 (東京).

永田宏次 (2013). ゲル濾過クロマトグラフィー, In 21世紀のバイオサイエンス 実験農芸化学 (東京大学大学院農学生命科学研究科応用生命化学専攻・応用生命工学専攻編), pp. 136-138, 朝倉書店 (東京).

永田宏次, 田之倉優 (2005). タンパク質試料の定量, 純度検定, 一次構造確認. In タンパク質の結晶化－回折構造生物学のために (坂部知平監修，相原茂夫編著), pp. 58-68, 京都大学学術出版会 (京都).

永田宏次, 田之倉優 (2005). クロマトグラフィーによる試料の分離精製. In タンパク質の結晶化－回折構造生物学のために (坂部知平監修，相原茂夫編著), pp. 51-58, 京都大学学術出版会 (京都).

永田宏次, 田之倉優 (2004). タンパク質の発現. In ゲノミクス・プロテオミクスの新展開－生物情報の解析と応用－(今中忠行編), pp. 534-538, エヌ・ティー・エス (東京).

田之倉優, 永田宏次, 佐々木宏 (1999). X線およびNMRによる三次元構造解析. In 魚介類筋肉タンパク質－その構造と機能 (西田清義編), pp. 38-45, 恒星社厚生閣 (東京).

田之倉優, 永田宏次 (1999). タンパク質工学. In 分子生物学 (田沼靖一編), pp. 274-288, 丸善 (東京).

 

特許

Patents

出願人：国立大学法人東京大学. 発明者：永田宏次, 片山幸江, 川端真由. 全長ω－５グリアジンの製造方法. 特許出願2018-194188. 出願日2018年10月15日. 特許公開2020-061947. 公開日2020年4月23日.

出願人：国立大学法人東京大学, 株式会社テクノメデイカ. 発明者：鳥居徹, アル ハック ムハマッド イムラン, ルブラッスル エリック, 山崎浩樹, 永田宏次, 田之倉優. タンパク質結晶化方法. 特許出願2006-326813 (P2006-326813). 出願日2006年12月4日. 特許公開2008-137961 (P2008-137961A). 公開日2008年6月19日.

出願人：国立大学法人東京大学, 株式会社テクノメデイカ. 発明者：鳥居徹, アル ハック ムハマッド イムラン, ルブラッスル エリック, 山崎浩樹, 永田宏次, 田之倉優. タンパク質結晶化方法及び装置並びにタンパク質結晶化処理装置. 特許出願PCT/JP2006/323812. 出願日2006年11月29日. 特許公開WO2007/063898. 公開日2007年6月7日.

出願人：小濱一弘, 田之倉優. 発明者：小濱一弘, 中村彰男, 吉山伸司, 田之倉優, 永田宏次. 平滑筋弛緩剤とその有効成分の抽出方法. 特許出願2004-108238. 出願日2004年3月31日. 特許公開2005-289898. 公開日2005年10月20日.