Yutaka Ito : Publications
Papers
2010
Inoue, J., Nagae, T., Mishima, M., Ito, Y., Shibata, T. & Mikawa, T.
“A mechanism for SSB displacement from single-stranded DNA upon SSB-RecO interaction.”
J. Biol. Chem. in press (2011).
Sato, A., Mishima, M., Nagai, A., Kim, S.-Y., Ito, Y., Hakoshima, T., Jee, J.-G. & Kitano, K.
“Solution structure of the HRDC domain of human Bloom syndrome protein BLM.”
J. Biochem. 148, 517-525 (2010).
Ikeya,
T., Sasaki, A., Sakakibara, D., Shigemitsu, Y., Hamatsu, J., Hanashima,
T., Mishima, M., Yoshimasu, M., Hayashi, N., Mikawa, T., Nietlispach,
D., Wälchli, M., Smith, B. O., Shirakawa, M., Güntert, P.
& Ito, Y.
“NMR protein structure determination in living E. coli cells” Nat. Protoc. 5, 1051-1060 (2010)
Isogai, S., Kanno, S., Ariyoshi, M., Tochio, H., Ito, Y., Yasui, A. & Shirakawa M.
“Solution structure of a zinc-finger domain that binds to poly-ADP-ribose.”
Genes Cells 15, 101-110 (2010)
2009
Masuda, T., Ito, Y., Terada, T., Shibata, T. & Mikawa, T.
“A non-canonical DNA structure enables homologous recombination in various genetic systems.”
J. Biol. Chem. 284, 30230-30239 (2009)
Sato, A., Watanabe, T., Maki, Y., Ueta, M., Yoshida, H., Ito, Y., Wada, A. & Mishima, M.
“Solution structure of the E. coli ribosome hibernation promoting factor HPF: Implications for the relationship between structure and function.”
Biochem. Biophys. Res. Commun., in press (2009)
Sakakibara,
D., Sasaki, A., Ikeya, T., Hamatsu, J., Hanashima, T., Mishima, M.,
Yoshimasu, M., Hayashi, N., Mikawa, T., Wälchli, M., Smith, B. O.,
Shirakawa, M., Güntert, P., & Ito, Y.
“Protein structure determination in living cells by in-cell NMR spectroscopy.”
Nature 458, 102-105 (2009)
Inomata,
K., Ohno, A., Tochio, H., Isogai, S., Tenno, T., Nakase, I., Takeuchi,
T., Futaki, S., Ito, Y., Hiroaki, H. & Shirakawa, M.
“High-resolution multi-dimensional NMR spectroscopy of proteins in human cells.”
Nature 458, 106-109 (2009)
2008
Terada, T., Satoh, D., Mikawa, T., Ito, Y. & Shimizu, K.
“Understanding
the roles of amino acid residues in tertiary structure formation of
chignolin by using molecular dynamics simulation.”
Proteins 73, 621-631 (2008)
2007
Kurashima-Ito, K., Moromisato, K., Nishimura, K., Wälchli, M., Tame, J. R. H. & Ito, Y.
“Backbone 1H, 13C and 15N assignments of a 59 kDa Salmonella typhimurium periplasmic oligopeptide binding protein OppA.”
Biomol. NMR Assignments 1, 37-39 (2007)
2006
Sakai, T., Tochio, H., Tenno, T. Ito, Y., Kokubo, T., Hiroaki, H. & Shirakawa, M.
“In-Cell NMR Spectroscopy of Proteins inside Xenopus laevis Oocytes.”
J. Biomol. NMR 36, 179-188 (2006)
Kurashima-Ito, K., Ikeya, T., Senbongi, H., Tochio, H., Mikawa, T., Shibata, T. & Ito, Y.
“Heteronuclear
multidimensional NMR and homology modelling studies of the C-terminal
nucleotide-binding domain of the human mitochondrial ABC transporter
ABCB6.”
J. Biomol. NMR 35, 53-71, (2006)
Honda, M., Inoue, J., Yoshimasu, M., Ito, Y., Shibata, T. & Mikawa, T.
“Identification
of the RecR Toprim domain as the binding site for both RecF and RecO. A
role of RecR in RecFOR assembly at double-stranded DNA-single-stranded
DNA junctions.”
J. Biol. Chem. 281, 18549-18559, (2006)
2005
Isogai, Y., Ito, Y., Ikeya, T., Shiro, Y. & Ota, M.
“Design of lambda Cro fold: solution structure of a monomeric variant of the de novo protein.”
J. Mol. Biol. 354, 801-814 (2005)
Kurashima-Ito, K., Kasai, Y., Hosono, K., Tamura, K., Oue, S., Isogai, M., Ito, Y., Nakamura, H & Shiro, Y.
“Solution structure of the C-terminal transcriptional activator domain of FixJ from Sinorhizobium meliloti and its recognition of the fixK promoter.”
Biochemistry 44, 14835-14844 (2005)
Rajesh, S., Heddle, J. G., Kurashima-Ito, K., Nietlispach, D., Shirakawa, M., Tame, J. R. & Ito Y.
“Backbone 1H, 13C, and 15N assignments of a 56 kDa E. coli nickel binding protein NikA.”
J. Biomol. NMR 32, 177 (2005)
2004
Hayashi,
N., Nakagawa, C., Ito, Y., Takasaki, A., Jinbo, Y., Yamakawa, Y.,
Titani, K., Hashimoto, K., Izumi, Y. & Matsushima, N.
“Myristoylation-regulated direct interaction between calcium-bound calmodulin and N-terminal region of pp60v-src.”
J. Mol. Biol. 338, 169-180 (2004)
Honda, M., Rajesh, S., Nietlispach, D., Mikawa, T., Shibata, T. & Ito, Y.
“Backbone 1H, 13C, and 15N assignments of a 42 kDa RecR Homodimer.”
J. Biomol. NMR 28, 199-200 (2004)
Kiyoshi,
T., Maeda, H., Kikuchi, J., Ito, Y., Hirota, H., Yokoyama, S., Ito, S.,
Miki, T., Hamada, M., Ozaki, O., Hayashi, S., Kurihara, N., Suematsu,
H., Yoshikawa, M., Matsumoto, S., Sato, A. & Wada, H.
“Present status of 920 MHz high-resolution NMR spectrometers.”
IEEE Trans. Appl. Supercond. 14, 1608-1612 (2004)
2003
Rajesh, S., Nietlispach, D., Nakayama, H., Takio, K., Laue, E. D., Shibata, T. & Ito, Y.
“A
novel method for the biosynthesis of deuterated proteins with selective
protonation at the aromatic rings of Phe, Tyr and Trp.”
J. Biomol. NMR 27, 81-86 (2003)
Yoshimasu, M., Aihara, H., Ito, Y., Rajesh, S., Ishibe, S., Mikawa, T., Yokoyama, S., & Shibata, T.
“An NMR study on the interaction of Escherichia coli DinI with RecA-ssDNA complexes.”
Nucleic Acids Res. 31, 1735-1743 (2003)
2002
Nietlispach, D., Ito, Y. & Laue, E.D.
“A novel approach for the sequential backbone assignment of larger proteins: selective intra-HNCA and DQ-HNCA.”
J. Am. Chem. Soc. 124, 11199-11207 (2002)
2001
Terada, T., Shirouzu, M., Fukumori, Y., Fujimori, F., Ito, Y., Kigawa, T., Yokoyama, S. & Uchida, T.
“Solution structure of the human parvulin-like peptidyl prolyl cis/trans isomerase, hPar14.”
J. Mol. Biol. 305, 917-926 (2001)
2000
Tanaka, T., Sugai, M., Ito, Y., Inokuchi, K. & Kohno, T.
“Assignments of the 1H, 13C, and 15N resonances of the 21 kDa Vesl/Homer family protein, Vesl-1S.”
J. Biomol. NMR 18, 181-182 (2000)
Mishima, M., Hatanaka, M., Yokoyama, S., Ikegami, T., Wälchli, M., Ito, Y. & Shirakawa, M.
“Intermolecular 31P-15N and 31P-1H scalar couplings across hydrogen bonds formed between a protein and a nucleotide.”
J. Am. Chem. Soc. 122; 5883-5884 (2000)
1999
Sakamoto, T., Tanaka, T., Ito, Y., Rajesh, S., Iwamoto-Sugai, M., Kodera, Y., Tsuchida, N., Shibata, T. & Kohno T.
“An
NMR analysis of ubiquitin recognition by yeast ubiquitin hydrolase:
evidence for novel substrate recognition by a cysteine protease.”
Biochemistry 38, 11634-11642 (1999)
Rajesh, S., Sakamoto, T., Iwamoto-Sugai, M.,
Shibata, T., Kohno, T. & Ito, Y.
“Ubiquitin binding interface
mapping on yeast ubiquitin hydrolase by NMR chemical shift
perturbation.”
Biochemistry 38, 9242-9253 (1999)
Aihara, H., Ito, Y., Kurumizaka, H., Yokoyama, S.
& Shibata, T.
“The N-terminal domain of the human Rad51 protein
binds DNA: structure and a DNA binding surface as revealed by NMR.”
J.
Mol. Biol. 290, 495-504 (1999)
Terada, T., Ito, Y., Shirouzu, M., Tateno, M.,
Hashimoto, K., Kigawa, T., Ebisuzaki, T., Takio, K., Shibata, T.,
Yokoyama, S., Smith, B. O., Laue, E. D. & Cooper, J. A.
“Nuclear
magnetic resonance and molecular dynamics studies on the interactions
of the Ras-binding domain of Raf-1 with wild-type and mutant Ras
proteins.”
J. Mol. Biol. 286, 219-232 (1999)
Kigawa, T., Yabuki, T., Yoshida, Y., Tsutsui, M.,
Ito, Y., Shibata, T. & Yokoyama, S.
“Cell-free production and
stable-isotope labeling of milligram quantities of proteins.”
FEBS
Lett. 442, 15-19 (1999)
1998
Kigawa, T., Endo, M., Ito, Y., Shirouzu, M.,
Kikuchi, A. & Yokoyama, S.
“Solution structure of the Ras-binding
domain of RGL.”
FEBS Lett. 441, 413-418 (1998)
Nishinaka. T., Shinohara, A., Ito, Y., Yokoyama, S.
& Shibata, T.
“Base pair switching by interconversion of sugar
puckers in DNA extended by proteins of RecA-family: A model for
homology search in homologous genetic recombination.”
Proc. Natl. Acad.
Sci. U.S.A. 95, 11071-11076 (1998)
Yabuki, T., Kigawa, T., Dohmae, N., Takio, K.,
Terada, T., Ito, Y., Laue, E. D., Cooper, J. A., Kainosho, M. &
Yokoyama, S.
“Dual amino acid-selective and site-directed
stable-isotope labeling of the human c-Ha-Ras protein by cell-free
synthesis.”
J. Biomol. NMR 11, 295-306 (1998)
1997
Ito, Y., Yamasaki, K., Iwahara, J., Terada, T.,
Kamiya, A., Shirouzu, M., Muto, Y., Kawai, G., Yokoyama, S., Laue, E.
D., Wälchli, M., Shibata, T., Nishimura, S. & Miyazawa, T.
“Regional polysterism in the GTP-bound form of the human c-Ha-Ras
protein.”
Biochemistry 36, 9109-9119 (1997)
Aihara, H., Ito, Y., Kurumizaka, H., Terada, T.,
Yokoyama, S. & Shibata, T.
“An interaction between a specified
surface of the C-terminal domain of RecA protein and double-stranded
DNA for homologous pairing,”
J. Mol. Biol. 274, 213-221 (1997)
Akashi, S., Shirouzu, M., Terada, T., Ito, Y.,
Yokoyama, S. & Takio, K.
“Characterization of the structural
difference between active and inactive forms of the Ras protein by
chemical modification followed by mass spectrometric peptide mapping.”
Anal. Biochem. 248, 15-25 (1997)
Nishinaka, T., Ito, Y., Yokoyama, S. & Shibata,
T.
“An extended DNA structure through deoxyribose-base stacking induced
by RecA protein.”
Proc. Natl. Acad. Sci. U.S.A. 94, 6623-6628 (1997)
1996
Smith, B. O., Ito, Y., Raine, A., Teichmann, S.,
Ben-Tovim, L., Nietlispach, D., Broadhurst, R. W., Terada, T., Kelly,
M., Oschkinat, H., Shibata, T., Yokoyama, S., & Laue, E. D. (the
first two authors contributed equally to this work)
“An approach to
global fold determination using limited NMR data from larger proteins
selectively protonated at specific residue types.”
J. Biomol. NMR 8,
360-368 (1996)
Nietlispach, D., Clowes, R. T., Broadhurst, R. W.,
Ito, Y., Keeler, J., Kelly, M., Ashurst, J., Oschkinat, H., Domaille,
P. J., & Laue, E. D.
“An approach to the structure determination of
larger proteins using triple-resonance NMR experiments in conjugation
with random fractional deuteration.”
J. Am. Chem. Soc. 118, 407-415
(1996)
1995
Fujita-Yoshigaki, J., Shirouzu, M., Ito, Y.,
Hattori, S., Furuyama, S., Nishimura, S., & Yokoyama, S.
“A
constitutive effector region on the C-terminal side of switch I of the
Ras protein.”
J. Biol. Chem. 270, 4661-4667 (1995)
1994
Yamasaki, K., Shirouzu, M., Muto, Y.,
Fujita-Yoshigaki, J., Koide, H., Ito, Y., Kawai, G., Hattori, S.,
Yokoyama, S., Nishimura, S. & Miyazawa, T.
“Site-directed
mutagenesis, fluorescence, and two-dimensional NMR studies on
microenvironments of effector region aromatic residues of human
c-Ha-Ras protein.”
Biochemistry 33, 65-73 (1994)
1993
Muto, Y., Yamasaki, K., Ito, Y., Yajima, S., Masaki,
H., Uozumi, T., Wälchli, M., Nishimura, S., Miyazawa T., &
Yokoyama, S.
“Sequence-specific 1H and 15N resonance assignments and
secondary structure of GDP-bound human c-Ha-Ras protein in solution.”
J. Biomol. NMR 3, 165-184 (1993)
1992
Fujita-Yoshigaki, J., Ito, Y., Yamasaki, K., Muto,
Y., Miyazawa, T., Nishimura, S. & Yokoyama, S.
“Guanine-nucleotide
binding activity, interaction with GTPase-activating protein and
solution conformation of the human c-Ha-Ras protein catalytic domain
are retained upon deletion of C-terminal 18 amino acid residues.”
J.
Protein Chem. 11: 731-739 (1992)
Yamasaki, K., Muto, Y., Ito, Y., Wälchli, M.,
Miyazawa, T., Nishimura, S. & Yokoyama, S.
“A 1H-15N NMR study of
human c-Ha-ras protein: biosynthetic incorporation of 15N-labeled amino
acids.”
J. Biomol. NMR 2, 71-82 (1992)
Shirouzu, M., Fujita-Yoshigaki, J., Ito, Y., Koide,
H., Nishimura, S., & Yokoyama, S.
“A glutamic acid residue at
position 31 of Ras protein is essential to the signal transduction for
neurite outgrowth of PC12 cells and the stimulation of GTPase activity
by GAPRas.”
Oncogene 7, 475-480 (1992)
1989
Hata-Tanaka, A., Kawai, G., Yamasaki, K., Ito, Y.,
Kajiura, H., Ha, J.-M., Miyazawa, T., Yokoyama, S. & Nishimura, S.
“Spin-labeling proton NMR study on aromatic amino acid residues in the
guanine nucleotide binding site of human c-Ha-ras(1-171) protein.”
Biochemistry 28: 9550-9556 (1989)
Ha, J.-M., Ito, Y., Kawai, G., Miyazawa, T., Miura,
K., Ohtsuka, E., Noguchi, S., Nishimura, S. & Yokoyama, S.
“Conformation of guanosine 5'-diphosphate as bound to a human c-Ha-ras
mutant protein: a nuclear Overhauser effect study.”
Biochemistry 28,
8411-8416 (1989)
Yamasaki, K., Kawai, G., Ito, Y., Muto, Y., Fujita,
J., Miyazawa, T., Nishimura, S. & Yokoyama, S.
“Conformation change
of effector-region residues in antiparallel beta-sheet of human c-Ha-ras
protein on GDP->GTP-gamma-S exchange: a two-dimensional NMR study.”
Biochem.
Biophys. Res. Commun. 162, 1054-1062 (1989)
Reviews, Books, Proceedings etc.
2010
Ito, Y. & Selenko, P.
“Cellular structural biology.”
Curr. Opin. Struct. Biol. 20, 640-648 (2010)
2009
Güntert, P. & Ito, Y.
“Seeing
Proteins inside Living Cells: Structures and Dynamics of Proteins by In-cell
NMR.”
BIOforum Europe 5/2009, 25-27 (2009)
2002
Yoshimasu, M., Honda, M., Mikawa, T.,
Shibata, T. & Ito, Y.
“NMR approaches to investigate protein-protein
and protein-nucleic acid complexes”
RIKEN Review 46, 32-35 (2002)
Rajesh, S. & Ito, Y.
“Molecular
insights into the surface regions of ubiquitin recognised by interacting
proteins”
RIKEN Review 46, 36-38 (2002)
2001
Shibata,
T., Nishinaka, T., Mikawa, T., Aihara, H., Kurumizaka, H., Yokoyama, S. & Ito,
Y.
“Homologous genetic recombination as an intrinsic dynamic property of a
DNA structure induced by RecA/Rad51-family proteins: a possible advantage of
DNA over RNA as genomic material.”
Proc. Natl. Acad. Sci. U.S.A. 98,
8425-8432 (2001)
2000
Yokoyama, S., Hirota, H., Kigawa, T., Yabuki,
T., Shirouzu, M., Terada, T., Ito, Y., Matsuo, Y., Kuroda, Y., Nishimura,
Y., Kyogoku, Y., Miki, K., Masui, R. & Kuramitsu, S.,
“Structural genomics
projects in Japan.”
Nat Struct Biol 7 Suppl,943-945 (2000)
Yokoyama, S., Matsuo, Y., Hirota, H., Kigawa,
T., Shirouzu, M., Kuroda, Y., Kurumizaka, H., Kawaguchi, S., Ito, Y., Shibata,
T., Kainosho, M., Nishimura, Y., Inoue, Y. & Kuramitsu, S.
“Structural
genomics projects in japan”
Prog. Biophys. Mol. Biol. 73, 363-376 (2000)
1997
Nishinaka, T., Ito, Y., Yokoyama, S.
& Shibata, T.
“Conformational distortion of sugar moieties in the
RecA-bound DNA structure determined by a simulated annealing method.” Nucleic Acids Symposium Series 37, 269-270 (1997)
1996
Nishinaka, T., Ito, Y., Yokoyama, S.
& Shibata, T.
“Molecular models for the structure of DNA in recombination
protein filaments.”
Nucleic Acids
Symposium Series 33, 217-218
(1996)
Ito, Y., Terada, T. & Yokoyama, S.
"New techniques for NMR
structural Biology"
J. Pesticide
Science 21, 450-459 (1996)