研究業績

2021年

Charkraborty, J., Suzuki-Minakuchi, C., Tomita, T., Okada, K., Nojiri, H. A novel gene cluster is involved in the degradation of lignin-derived monoaromatics in Thermus oshimai JL-2. Appl. Environ. Microbiol., 87, e01589-20, (2021)

2020年

Suzuki, T., Tomita, T., Hirayama, K., Suzuki, M., Kuzuyama, T., Nishiyama, M. Involvement of subdomain II in the recognitionl of acetyl-CoA revealed by the crystal structure of homocitrate synthase from Sulfolobus acidocaldarius. FEBS J, Online ahead of print, (2020)
Kinugawa, H., Kondo, N., Komine-Abe, A., Tomita, T., Nishiyama, M., Kosono, S.In vitro reconstitution and characterization of pyruvate dehydrogenase and 2-oxoglutarate dehydrogenase hybrid complex from Corynebacterium glutamicum. Microbiologyopen., Aug 30:e1113, (2020)
Sakaki, K., Ohishi, K., Shimizu, T., Kobayashi, I., Mori, N., Matsuda, K., Tomita, T., Watanabe, H., Tanaka, K., Kuzuyama, T., Nishiyama, M. A suicide enzyme catalyzes multiple reactions for biotin biosynthesis in cyanobacteria. Nat. Chem. Biol., 16, 415-22, (2020)

2019年

Kobayashi, M., Tomita, T., Shin-ya, K., Nishiyama, M., and Kuzuyama, T., An unprecedented cyclization mechanism in the biosynthesis of carbazole alkaloids in Streptomyces. Angew. Chem. Int. Ed. Engl., 58, 13349-53, (2019)
Suzuki, T., Akiyama, N., Yoshida, A., Tomita, T., Lassak, K., Haurat, MF., Okada, T., Takahashi, K., Albers, SV., Kuzuyama, T., and Nishiyama, M., Biochemical characterization of archaeal homocitrate synthase from Sulfolobus acidocaldarius. FEBS Lett., 594, 126-34, (2019)
Tomita, T., Matsushita, H., Yoshida, A., Kosono, S., Yoshida, M., Kuzuyama, T., and Nishiyama, M., Glutamate dehydrogenase from Thermus thermophilus is activated by AMP and leucine as a complex with catalytically inactive adenine phosphoribosyltransferase homolog. J. Bacteriol., 201, e00710-18, (2019)
Chiba, Y., Yoshida, A., Shimamura, S., Kameya, M., Tomita, T., Nishiyama, M., and Takai, K., Discovery and analysis of a novel type of the serine biosynthetic enzyme phosphoserine phosphatase in Thermus thermophilus. FEBS J., 286, 726-36, (2019)

2018年

Matsuda, K., Tomita, T., Shin-Ya, K., Wakimoto, T., Kuzuyama, T., and Nishiyama, M., Discovery of unprecedented hydrazine-forming machinery in bacteria. J. Am. Chem. Soc., 140, 9083-6, (2018)
Sato, H., Narita, K., Minami, A., Yamazaki, M., Wang, C., Suemune, H., Nagano, S., Tomita, T., Oikawa, H., and Uchiyama, M. Theoretical study of sesterfisherol biosynthesis: computational prediction of key amino acid residue in terpene synthase. Sci. Rep., 8, 2473, (2018)

2017年

Tomita, T., Kobayashi, M., Karita, Y., Yasuno, Y., Shinada, T., Nishiyama, M., and Kuzuyama, T. Structure and mechanism of the monoterpene cyclolavandulyl diphosphate synthase that catalyzes consecutive condensation and cyclization. Angew. Chem. Int. Ed. Engl., 56, 14913-7, (2017)
Cho, SH., Kim, SY., Tomita, T., Shiraishi, T., Park, JS., Sato, S., Kudo, F., Eguchi, T., Funa, N., Nishiyama, M., and Kuzuyama, T. Fosfomycin biosynthesis via transient cytidylylation of 2-hydroxyethylphosphonate by the bifunctional fom1 enzyme. ACS Chem. Biol., 12, 2209-15, (2017)
Fujita, S., Cho, SH., Yoshida, A., Hasebe, F., Tomita, T., Kuzuyama, T., and Nishiyama, M. Crystal structure of LysK, an enzyme catalyzing the last step of lysine biosynthesis in Thermus thermophilus, in complex with lysine: Insight into the mechanism for recognition of the amino-group carrier protein, LysW. Biochem. Biophys. Res. Commun., 491, 409-415, (2017)
Tomita, T., Kim, SY., Teramoto, K., Meguro, A., Ozaki, T., Yoshida, A., Motoyoshi, Y., Mori, N., Ishigami, K., Watanabe, H., Nishiyama, M., and Kuzuyama, T. Structural insights into the cotb2-catalyzed cyclization of geranylgeranyl diphosphate to the diterpene cyclooctat-9-en-7-ol. ACS Chem. Biol., 12, 1621-8, (2017)
Tomita, T., Yin, L., Nakamura, S., Kosono, S., Kuzuyama, T., and Nishiyama, M. Crystal structure of the 2-iminoglutarate-bound complex of glutamate dehydrogenase from Corynebacterium glutamicum. FEBS Lett., 591, 1611-22, (2017)
Matsuda, K., Hasebe, F., Shiwa, Y., Kanesaki, Y., Tomita, T., Yoshikawa, H., Shin-Ya, K., Kuzuyama, T., and Nishiyama, M. Genome mining of amino group carrier protein-mediated machinery: discovery and biosynthetic characterization of a natural product with unique hydrazone unit. ACS Chem. Biol., 12, 124-31, (2017)
Shimizu, T., Yin, L., Yoshida, A., Yokooji, Y., Hachisuka, SI., Sato, T., Tomita, T., Nishida, H., Atomi, H., Kuzuyama, T., and Nishiyama, M. Structure and function of an ancestral-type β-decarboxylating dehydrogenase from Thermococcus kodakarensis. Biochem. J., 474, 105-22, (2017)
Kubota, T., Matsushita, H., Tomita, T., Kosono, S., Yoshida, M., Kuzuyama, T., and Nishiyama, M. Novel stand-alone RAM domain protein-mediated catalytic control of anthranilate phosphoribosyltransferase in tryptophan biosynthesis in Thermus thermophilus. Extremophiles, 21, 73-83, (2017)

2016年

Takahashi, K., Nakanishi, F., Tomita, T., Akiyama, N., Lassak, K., Albers, SV., Kuzuyama, T., and Nishiyama, M. Characterization of two β-decarboxylating dehydrogenases from Sulfolobus acidocaldarius. Extremophiles, 20, 843-53, (2016)
Hasebe, F., Matsuda, K., Shiraishi, T., Futamura, Y., Nakano, T., Tomita, T., Ishigami, K., Taka, H., Mineki, R., Fujimura, T., Osada, H., Kuzuyama, T., and Nishiyama, M. Amino-group carrier-protein-mediated secondary metabolite biosynthesis in Streptomyces. Nat. Chem. Biol., 12, 967-72, (2016)
Yoshida, A., Tomita, T., Atomi, H., Kuzuyama, T., and Nishiyama, M. Lysine biosynthesis of Thermococcus kodakarensis with the capacity to function as an ornithine biosynthetic system. J. Biol. Chem., 291, 21630-43, (2016)
Takahashi, K., Tomita, T., Kuzuyama, T., and Nishiyama M. Determinants of dual substrate specificity revealed by the crystal structure of homoisocitrate dehydrogenase from Thermus thermophilus in complex with homoisocitrate·Mg(2+)·NADH. Biochem. Biophys. Res. Commun., 478, 1688-93, (2016)
Tsujimoto, M., Yoshida, A., Shimizu, T., Tomita, T., Ohnishi, Y., Kuzuyama, T., and Nishiyama, M. Aspartate kinase involved in 4-hydroxy-3-nitrosobenzamide biosynthesis in Streptomyces murayamaensis. Biosci. Biotechnol. Biochem., 80, 2255-63, (2016)
Shimizu, T., Tomita, T., Kuzuyama, T., and Nishiyama, M. Crystal structure of the LysY・LysW complex from Thermus thermophilus. J. Biol. Chem., 291, 9948-59, (2016)

2015年

Meguro, A., Motoyoshi, Y., Teramoto, K., Ueda, S., Totsuka, Y., Ando, Y., Tomita, T., Kim, SY., Kimura, T., Igarashi, M., Sawa, R., Shinada, T., Nishiyama, M., and Kuzuyama, T. An unusual terpene cyclization mechanism involving a carbon-carbon bond rearrangement. Angew. Chem. Int. Ed. Engl., 54, 4353-6, (2015)
Yoshida, A., Tomita, T., Fujimura, T., Nishiyama, C., Kuzuyama, T., and Nishiyama, M. Structural insight into Amino Croup-carrier Protein-mediated Lysine biosynthesis: Crystal structure of the LysZ-LysY complex from Thermus thermophilus. J. Biol. Chem., 290, 435-47, (2015)

2014年

Tomita, T., Ozaki, T., Nishiyama, M., Matsuda, K., and Kuzuyama, T. Crystallization and preliminary X-ray diffraction analysis of cyclolavandulyl diphosphate synthase, a new member of the cis-isoprenyl diphosphate synthase superfamily. Acta Crystallogr. F. Struct. Biol. Commun., 70, 1410-3, (2014)
Iwanaga, N., Ide, K., Nagashima, T., Tomita, T., Agari, Y., Shinkai, A., Kuramitsu, S., Okada-Hatakeyama, M., Kuzuyama, T., and Nishiyama, M. Genome-wide comprehensive analysis of transcriptional regulation by ArgR in Thermus thermophilus. Extremophiles, 18, 995-1008, (2014)

2013年

Kanemaru, Y., Hasebe, F., Tomita, T., Kuzuyama, T., Nishiyama, M. ATP-binding cassette transporters involved in (S)-2-aminoethyl-cysteine uptake in Thermus thermophilus. J. Bacteriol., 195, 3845-53, (2013)
Ouchi, T., Tomita, T., Horie, A., Yoshida, A., Takahashi, K., Nishida, H., Lassak, K., Taka, H., Mineki, R., Fujimura, T., Kosono, S., Nishiyama, C., Masui, R., Kuramitsu, S., Albers, S.V., Kuzuyama, T., Nishiyama, M. Lysine and arginine biosyntheses mediated by a common carrier protein in Sulfolobus. Nat. Chem. Biol., 9, 277-83, (2013)
Meguro, A., Tomita, T., Nishiyama, M., Kuzuyama, T., Identification and characterization of bacterial diterpene cyclases that synthesize the cembrane skeleton. Chem. Biol., 9, 277-83, (2013)

2011年

Tomita, T., Kuzuyama, T., and Nishiyama, M. Structural basis for leucine-induced allosteric activation of glutamate dehydrogenase. J. Biol. Chem., 286, 37406-13, (2011)
Nishida, C., Tomita, T., Nishiyama, M., Suzuki, R., Hara, M., Itoh, Y., Ogawa, H., Okumura, K., Nishiyama, C. B-Transferase with a Pro234Ser Substitution Acquires AB-Transferase Activity. Biosci, Biotechnol. Biochem., 75, 1570-5, (2011)

2010年

Kumano, T., Tomita, T., Nishiyama, M., and Kuzuyama, T. Functional characterization of the promiscuous prenyltransferase responsible for furaquinocin biosynthesis: identification of a physiological polyketide substrate and its prenylated reaction products. J. Biol. Chem., 285, 39663-71, (2010)
Tomita, T., Miyazaki, T., Miyazaki, J., Kuzuyama, T., and Nishiyama, M. Hetero-oligomeric glutamate dehydrogenase from Thermus thermophilus. Microbiology, 156, 3801-13, (2010)
Matsue, Y. Mizuno, H., Tomita, T., Nishiyama, M., and Kuzuyama, T. The herbicide ketoclomazone inhibits 1-deoxy-D-xylulose 5-phosphate synthase in the 2-C-methyl-D-erithritol 4-phosphate pathway and shows arntibacterial activity against Haemophilus influenzae. J. Antibiot. (Tokyo), 63, 583-8, (2010)
Suzuki, Y., Asada, K., Miyazaki, J., Tomita, T., Kuzuyama, T., and Nishiyama, M. Enhancement of the latent 3-isopropylmalate dehydrogense activity of promiscuous homoisocitrate dehydrogenase by directed evolution. Biochem. J., 431, 401-10, (2010)
Yoshida, A., Tomita, T., Kuzuyama, T., Nishiyama, M. Mechanism of concerted inhibition of alpha2beta2-type hetero-oligomeric aspartate kinase from Corynebacterium glutamicum. J. Biol. Chem., 285, 27477-86, (2010)
Okamura, E., Tomita, T., Sawa, R., Nishiyama, M., and Kuzuyama, T. Unprecedented acetoacetyl-coenzyme A synthesizing enzyme of the thiolase superfamily involved in the mevalonate pathway. Proc. Natl. Acad. Sci. USA., 107, 11265-70, (2010)
Tomita, T., Okada, T., Wulandari, A.P., Kuzuyama, T., and Nishiyama, M. Mechanism of substrate recognition and insight into feedback inhibition of homocitrate synthase from Thermus thermophilus. J. Biol. Chem., 285, 4195-205, (2010)

2009年

Kim, S-Y., Zhao, P., Igrashi, M., Sawa, R., Tomita, T., Nishiyama, M., and Kuzuyama, T. Cloning and heterologous expression of the cyclooctatin biosynthetic gene cluster afford a diterpene cyclase and two P450 hydroxylases. Chem. Biol., 16, 736-43, (2009)
Ouchi, T., Tomita, T., Miyagawa, T., Kuzuyama, T., and Nishiyama, M. Dual roles of a conserved pair, Arg23 and Ser20, in recognition of multiple substrates in alpha-aminoadipate aminotransferase from Thermus thermophilus. Biochem. Biophys. Res. Commun., 388, 21-7, (2009)
Horie, A., Tomita, T., Saiki, A., Kono, H., Taka, H., Mineki, R., Fujimura, T., Nishiyama, C., Kuzuyama, T., and Nishiyama, M. Discovery of proteinaceous N-modification in lysine biosynthesis of Thermus thermophilus. Nat. Chem. Biol, 5, 673-9, (2009)
Yoshida, A., Tomita, T., Kono, H., Fushinobu, S., Kuzuyama, T., and Nishiyama, M. Crystal structure of the regulatory subunit of Thr-sensitive aspartate kinase from Thermus thermophilus FEBS J., 276, 3124-36, (2009)
Tomita, T., Miyagawa, T., Miyazaki, T., Fushinobu, S., Kuzuyama, T., and Nishiyama, M. Mechanism for multiple-substrates recognition of -aminoadipate aminotransferase from T. thermophilus. Proteins, 75, 348-59, (2009)

2007年

Yoshida, A., Tomita, T., Kurihara, T., Fushinobu, S., Kuzuyama, T., Nishiyama, M. Structural insight into concerted inhibition of alpha2 beta2-type aspartate kinase from Corynebacterium glutamicum. J. Mol. Biol., 368, 521-36, (2007)
Yoshida, A., Tomita, T., Kuzuyama, T., and Nishiyama, M. Purification, crystallization and preliminary X-ray analysis of the regulatory subunit of aspartate kinase from Thermus thermophilus. Acta Crystallogr., F63, 96-8, (2007)
Tomita, T. Structure, function, and regulation of enzymes involved in amino acid metabolism of bacteria and archaea. Biosci. Biotechnol. Biochem., 81, 2050-61, (2017)

2006年

Tomita, T., Kuzuyama, T., and Nishiyama, M. Alteration of Coenzyme Specificity of Lactate Dehydrogenase from Thermus thermophilus by Introducing the Loop Region of NADP(H)-Dependent Malate Dehydrogenase. Biosci. Biotech. Biochem., 70, 2230-5, (2006)
Tomita, T., Fushinobu, S., Kuzuyama, T., and Nishiyama, M. Structural basis for the alteration of coenzyme specificity in a malate dehydrogenase mutant. Biochem. Biophys. Res. Commun., 347, 502-8, (2006)
Jia, Y., Tomita, T., Yamauchi, K., Nishiyama, M., and Palmer, DR. Kinetics and product analysis of the reaction catalysed by recombinant homoaconitase from Thermus thermophilus. Biochem. J., 396, 479-85, (2006)

2005年

Tomita, T., Fushinobu, S., Kuzuyama, T., and Nishiyama, M. Crystal structure of NAD-dependent malate dehydrogenase complexed with NADP(H). Biochem. Biophys. Res. Commun., 334, 613-618, (2005)