Achievement

Papers

2023

  • Dynamic action of an intrinsically disordered protein in DNA compaction that induces mycobacterial dormancy.
    Nishiyama A, Shimizu M, Narita T, Kodera N, Ozeki Y, Yokoyama A, Mayanagi K, Yamaguchi T, Hakamata M, Shaban AK, Tateishi Y, Ito K, Matsumoto S.
    Nucleic Acids Research, 52(2), 816-830, 2024

2022

  • The flexible N-terminal motif of uL11 unique to eukaryotic ribosomes interacts with P-complex and facilitates protein translation.
    Yang L, Lee KM, Yu CW, Imai H, Choi KA, Banfield DK, Ito K, Uchiumi T, Wong KB.
    Nucleic Acids Research, 50(9), 5335–5348, 2022
  • A novel ribosome-dimerization protein found in the hyperthermophilic archaeon Pyrococcus furiosus using ribosome-associated proteomics.
    Yaeshima C, Murata N, Ishino S, Sagawa I, Ito K, Uchiumi T.
    Biochemical and Biophysical Research Communications 593, 116-121, 2022

2021

  • Structural insights into the Switching Off of the Interaction between the Archaeal Ribosomal Stalk and aEF1A by Nucleotide Exchange Factor aEF1B. <Journal of molecular biology Featured article>
    Suzuki T, *Ito K, Miyoshi T, Murakami R, *Uchiumi T. (*責任著者)
    Journal of Molecular Biology 433(15), 167046, 2021

2020

  • Crystal structure of rice defensin OsAFP1 and molecular insight into lipid-binding.
    Ochiai A, Ogawa K, Fukuda M, Suzuki M, Ito K, Tanaka T, Sagehashi Y, Taniguchi M.
    Journal of Bioscience and Bioengineering 130(1), 6-13, 2020
  • Arabidopsis ROOT PHOTOTROPISM2 Is a Light-Dependent Dynamic Modulator of Phototropin1.
    Kimura T, Tsuchida-Mayama T, Imai H, Okajima K, Ito K, Sakai T.
    The Plant Cell 32(6), 2004-2019, 2020

2019

  • Switch of the interactions between the ribosomal stalk and EF1A in the GTP- and GDP-bound conformations.
    Maruyama K, Imai H, Kawamura M, Ishino S, Ishino Y, *Ito K, *Uchiumi T. (*責任著者)
    Scientific Reports 9(1), 14761, 2019
  • Structural and Mutagenesis Studies Evince the Role of the Extended Protuberant Domain of Ribosomal Protein uL10 in Protein Translation.
    Choi KA, Yang L, Lee KM, Yu CW, Banfield DK, Ito K, Uchiumi T, Wong KB.
    Biochemistry 58(36), 3744 - 3754, 2019
  • High-resolution crystal structure of peptidyl-tRNA hydrolase from Thermus thermophilus.
    Matsumoto A, Uehara Y, Shimizu Y, Ueda T, Uchiumi T, *Ito K. (*責任著者)
    Proteins 87(3), 226 - 235, 2019

2018

  • The ribosomal stalk protein is crucial for the action of the conserved ATPase ABCE1.
    Imai H, Abe T, Miyoshi T, Nishikawa S, Ito K, Uchiumi T.
    Nucleic Acids Res. 46(15), 7820-7830, 2018
  • The interaction between the ribosomal stalk proteins and translation initiation factor 5B promotes translation initiation.
    #Murakami R, #Singh CR, Morris J, Tang L, Harmon I, Takasu A, Miyoshi T, *Ito K, *Asano K, Uchiumi T. (*責任著者)
    Molecular and Cellular Biology 38(16), e00067-18, 2018  # Contributed equally

2017

  • Binding of translation elongation factors to individual copies of the archaeal ribosomal stalk protein aP1 assembled onto aP0.
    Honda T, Imai H, Suzuki T, Miyoshi T, Ito K, Uchiumi T.
    Biochem Biophysical Research Communications 483(1), 153-158, 2017

2016

  • Structural basis for the recognition of guide RNA and target DNA heteroduplex by Argonaute.
    *Miyoshi T,*Ito K, Murakami R, Uchiumi T. (*責任著者)
    Nature Communications. 7, 11846, 2016
  • Crystal structure of translation initiation factor 5B from the crenarchaeon Aeropyrum pernix.
    Murakami R, Miyoshi T,*Uchiumi T, *Ito K. (*責任著者)
    Proteins 84(5), 712-717, 2016

2015

  • Functional role of the C-terminal tail of the archaeal ribosomal stalk in recruitment of two elongation factors to the sarcin/ricin loop of 23S rRNA.
    Imai H, Miyoshi T, Murakami R, Ito K, Ishino Y, Uchiumi T.
    Genes to Cells 20(7), 613-624, 2015

2014

  • Molecular insights into the interaction of the ribosomal stalk protein with elongation factor 1α.
    *Ito K, Honda T, Suzuki T, Miyoshi T, Murakami R, Yao M, *Uchiumi T. (*責任著者)
    Nucleic Acids Research 42(22), 14042-14052, 2014
  • Crystal structure of α-amylase from Oryza sativa: molecular insights into enzyme activity and thermostability.
    Ochiai A, Sugai H, Harada K, Tanaka S, Ishiyama Y, Ito K, Tanaka T, Uchiumi T, Taniguchi M, Mitsui T.
    Bioscience, Biotechnology, and Biochemistry 78(6), 989-997, 2014

2013

  • Solution structure of human P1・P2 heterodimer provides insights into the role of eukaryotic stalk in recruiting the ribosome-inactivating protein trichosanthin to the ribosome.
    Lee KM, Yusa K, Chu LO, Yu CW, Oono M, Miyoshi T, Ito K, Shaw PC, Wong KB, Uchiumi T.
    Nucleic Acids Research 41(18), 8776-8787, 2013
  • Crystallization and preliminary X-ray analysis of peptidyl-tRNA hydrolase from Thermus thermophilus HB8.
    Matsumoto A, Shimizu Y, Takemoto C, Ueda T, Uchiumi T, *Ito K. (*責任著者)
    Acta Crystallographica Section F: Structural Biology and Crystallization Communications 69 (3), 332-335, 2013

2012

  • Structural basis for the substrate recognition and catalysis of peptidyl-tRNA hydrolase.
    *Ito K, Murakami R, Mochizuki M, Qi H, Shimizu Y, Miura K, Ueda T, Uchiumi T. (*責任著者)
    Nucleic Acids Research 40(20), 10521-10531, 2012
  • Analysis of Chimeric Ribosomal Stalk Complexes from Eukaryotic and Bacterial Sources: Structural Features Responsible for Specificity of Translation Factors.
    Mochizuki M, Kitamyo M, Miyoshi T, Ito K, *Uchiumi T.
    Genes to Cells 17(4), 273-284, 2012

2011

  • Crystallization and preliminary X-ray analysis of peptidyl-tRNA hydrolase from Escherichia coli in complex with the acceptor-TΨC domain of tRNA. Acta Crystallographica.
    *Ito K, Qi H, Shimizu Y, Murakami R, Miura K, Ueda T, Uchiumi T. (*責任著者)
    Section F, Structural Biology and Crystallization Communications 67(Pt 12), 1566-1569, 2011

2008

  • Expansion of substrate specificity and catalytic mechanism of azoreductase by X-ray crystallography and site-directed mutagenesis.
    Ito K, Nakanishi M, Lee WC, Zhi Y, Sasaki H, Zenno S, Saigo K, Kitade Y, Tanokura M.
    JOURNAL OF BIOLOGICAL CHEMISTRY 283(20), 13889 - 13896, 2008
  • The structure and reaction mechanism of azoreductase.
    Ito K, Tanokura M.
    Seikagaku 80(6), 550 - 559, 2008

2007

  • Crystal structure of thioredoxin domain of ST2123 from thermophilic archaea Sulfalabus tokodaii strain7.
    Ming H, Kato Y, Miyazono KI, Ito K, Kamo M, Nagata K, Tanokura M.
    Proteins 69(1), 204 - 208, 2007

2006

  • Three-dimensional structure of AzoR from Escherichia coli - An oxidereductase conserved in microorganisms.
    Ito K, Nakanishi M, Lee WC, Sasaki H, Zenno S, Saigo K, Kitade Y, Tanokura M.
    JOURNAL OF BIOLOGICAL CHEMISTRY 281(29), 20567 - 20576, 2006

2005

  • Crystal structure of monomeric sarcosine oxidase from Bacillus sp. NS-129 reveals multiple conformations at the active-site loop.
    Nagata K, Sasaki H, Ohtsuka J, Hua M, Okai M, Kubota K, Kamo M, Ito K, Ichikawa T, Koyama Y, Tanokura M.
    Proceedings of the Japan Academy Series B: Physical and Biological Sciences 81(6), 220 - 224, 2005
  • Crystal structure of azoreductase AzoR from Escherichia coli.
    Ito K, Nakanishi M, Lee WC, Sasaki H, Zenno S, Saigo K, Kitade Y, Tanokura M.
    Proceedings of the Japan Academy Series B: Physical and Biological Sciences 81(6), 225 - 228, 2005
  • Recombinant porcine zona pellucida glycoproteins expressed in Sf9 cells bind to bovine sperm but not to porcine sperm .
    Yonezawa N, Kudo K, Terauchi H, Kanai S, Yoda N, Tanokura M, Ito K, Miura KI, Katsumata T, Nakano M.
    The Journal of Biological Chemistry 280(21), 20189 - 20196, 2005
  • Crystallization and preliminary X-ray analysis of AzoR (azoreductase) from Escherichia coli .
    Ito K, Nakanishi M, Lee WC, Sasaki H, Zenno S, Saigo K, Kitade Y, Tanokura M.
    Acta crystallographica. Section F, Structural biology and crystallization communications 61(Pt 4), 399 - 402, 2005

2004

  • Crystallization and preliminary X-ray analysis of carboxypeptidase 1 from Thermus thermophilus.
    Nagata K, Tsutsui S, Lee WC, Ito K, Kamo M, Inoue Y, Tanokura M.
    Acta crystallographica. Section D, Biological crystallography 60(8), 1445 - 1446, 2004