Achievement | Niigata University Ito Lab

Papers

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

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

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

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

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

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. (*corresponding author)
Molecular and Cellular Biology 38(16), e00067-18, 2018　 # Contributed equally

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

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

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

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

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

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

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. (*corresponding author)
Section F, Structural Biology and Crystallization Communications 67(Pt 12), 1566-1569, 2011

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

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

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

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

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