Laboratory of Microbial Biotechnology, Biotechnology Research Center, The University of Tokyo

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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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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)