Papers

2025

• Binding mode between peptidyl-tRNA hydrolase and the peptidyl-A76 moiety of the substrate.
  Uehara Y, Matsumoto A, Nakazawa T, Fukuta A, Ando K, Uchiumi T, Oka N, *Ito K. (*corresponding author)
  Journal of Biological Chemistry, 301(4), 108385, 2025
  

2024

• Novel archaeal ribosome dimerization factor facilitating unique 30S-30S dimerization.
  Hassan AH, Pinkas M, Yaeshima C, Ishino S, Uchiumi T, Ito K, Demo G.
  Nucleic Acids Research, 53(2), gkae1324, 2025
  

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. (*corresponding author)
  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. (*corresponding author)
  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. (*corresponding author)
  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 Research, 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. (*corresponding author)
  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.
  Biochemical 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. (*corresponding author)
  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. (*corresponding author)
  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. (*corresponding author)
  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. (*corresponding author)
  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. (*corresponding author)
  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.
  *Ito K, Qi H, Shimizu Y, Murakami R, Miura K, Ueda T, Uchiumi T. (*corresponding author)
  Acta Crystallographica 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.
  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