Voltage sensors of a Na+ channel dissociate from the pore domain and form inter-channel dimers in the resting state

Ayumi Sumino, Takashi Sumikama, Mikihiro Shibata &,, Katsumasa Irie ,,
Nature Communications volume 14, Article number: 7835 (2023)

DOI:https://doi.org/10.1038/s41467-023-43347-3

Recognition mechanism of a novel gabapentinoid drug, mirogabalin, for recombinant human a2d1 a voltage-gated calcium channel subunit

Daisuke Kozai, Nobutaka Numoto, Kouki Nishikawa, Akiko Kamegawa, Shohei Kawasaki, Yoko Hiroaki, Katsumasa Irie, Atsunori Oshima, Hiroyuki Hanzawa, Kousei Shimada, Yutaka Kitano, Yoshinori Fujiyoshi

Journal of Molecular Biology 168049-168049 2023年3月

The structural basis of divalent cation block in a tetrameric prokaryotic sodium channel

Katsumasa Irie, Yoshinori Oda, Takashi Sumikama, Atsunori Oshima, Yoshinori Fujiyoshi

Nature Communications. 2023 Jul 15,14(1):4236. doi: 10.1038/s41467-023-39987-0.

Gastric proton pump with two occluded K+ engineered with sodium pump-mimetic mutations.
Kazuhiro Abe, Kenta Yamamoto, Katsumasa Irie, Tomohiro Nishizawa, Atsunori Oshima
Nature communications 12(1) 5709-5709

The crystal structure of the CmABCB1 G132V mutant, which favors the outward-facing state, reveals the mechanism of the pivotal joint between TM1 and TM3
Matsuoka, K., Nakatsu, T. and Kato, H.
PROTEIN SCIENCE 30, 1064-1071

Development of Novel AKR1C3 Inhibitors as New Potential Treatment for Castration-Resistant Prostate Cancer.
Satoshi Endo, Hiroaki Oguri, Jin Segawa, Mina Kawai, Dawei Hu, Shuang Xia, Takuya Okada, Katsumasa Irie, Shinya Fujii, Hiroaki Gouda, Kazuhiro Iguchi, Takuo Matsukawa, Naohiro Fujimoto, Toshiyuki Nakayama, Naoki Toyooka, Toshiyuki Matsunaga, Akira Ikari
Journal of medicinal chemistry 63(18) 10396-10411

Crystal structure of a human plasma membrane phospholipid flippase.
Hanayo Nakanishi, Katsumasa Irie, Katsumori Segawa, Kazuya Hasegawa, Yoshinori Fujiyoshi, Shigekazu Nagata, Kazuhiro Abe
The Journal of biological chemistry 295(30) 10180-10194

X-ray dose-dependent structural changes of the [2Fe-2S] ferredoxin from Chlamydomonas reinhardtii

Yusuke Ohnishi, Norifumi Muraki, Daiki Kiyota, Hideo Okumura, Seiki Baba, Yoshiaki Kawano, ,, Takashi Kumasaka, Hideaki Tanaka, Genji Kurisu
The Journal of Biochemistry, 167(6) 549-555

ABCB1/MDR1/P-gp employs an ATP-dependent twist-and-squeeze mechanism to export hydrophobic drugs
Kodan, A., Futamata, R., Kimura, Y., Kioka, N., Nakatsu, T., Kato, H. and Ueda, K.
FEBS Letters 595, 707-716

A native prokaryotic voltage-dependent calcium channel with a novel selectivity filter sequence
Takushi Shimomura, Yoshiki Yonekawa, Hitoshi Nagura, Michihiro Tateyama, Yoshinori Fujiyoshi, Katsumasa Irie
eLife 9

Improvement of Production and Isolation of Human Neuraminidase-1 in Cellulo Crystals.
Koiwai, K., Tsukimoto, J., Higashi, T., Mafuné,,, F., Miyajima, K., Nakane, T., Matsugaki, N., Kato, R., Sirigu, S., Jakobi, A., Wilmanns, M., Sugahara, M., Tanaka, T., Tono, K., Joti, Y., Yabashi, M., Nureki, O., Mizohata, E., Nakatsu, T., Nango, E., Iwata, S., Chavas, L., Senda, T., Itoh, K. and Yumoto, F.
ACS Applied Bio Materials 2, 4941-4952

Genetic manipulation of autonomic nerve fiber innervation and activity and its effect on breast cancer progression.
Kamiya A, Hayama Y, Kato S, Shimomura A, Shimomura T, Irie K, Kaneko R, Yanagawa Y, Kobayashi K, Ochiya T
Nature neuroscience 22(8) 1289-1305

A single K+-binding site in the crystal structure of the gastric proton pump.
Yamamoto K, Dubey V, Irie K, Nakanishi H, Khandelia H, Fujiyoshi Y, Abe K
eLife 8

Morphologic determinant of tight junctions revealed by claudin-3 structures.
Shun Nakamura, Katsumasa Irie, Hiroo Tanaka, Kouki Nishikawa, Hiroshi Suzuki, Yasunori Saitoh, Atsushi Tamura, Sachiko Tsukita, Yoshinori Fujiyoshi
Nature communications 10(1) 816-816

Inward- and outward-facing X-ray crystal structures of homodimeric P-glycoprotein CmABCB1.,
A. Kodan, T. Yamaguchi, T. Nakatsu, K. Matsuoka, Y. Kimura, K. Ueda, H. Kato
Nat. Commun. 10, 88

Experimental phase determination with selenome¬,thionine or mercury-derivatization in serial femtosecond crystallography.,
K. Yamashita, N. Kuwabara, T. Nakane, T. Murai, E. Mizohata, M. Sugahara, D. Pan, T. Masuda, M. Suzuki, T. Sato, A. Kodan, T. Yamaguchi, E. Nango, T. Tanaka, K. Tono, Y. Joti, T. Kameshima, T. Hatsui, M. Yabashi, H. Manya, T. Endo, R. Kato, T. Senda, H. Kato, S. Iwata, H. Ago, M. Yamamoto, F. Yumoto, T. Nakatsu,
IUCrJ, 4, 639&ndash,647

Development of a dose-limiting data collection strategy for serial synchrotron rotation crystallography.
K. Hasegawa, K. Yamashita, T. Murai, N. Nuemket, K. Hirata, G. Ueno, H. Ago, T. Nakatsu, T. Kumasaka, M. Yamamoto,
Journal of Synchrotron Radiation, 24, 29-41

Hydroxyethyl cellulose matrix applied to serial crystallography.
M. Sugahara, T. Nakane, T. Masuda, M. Suzuki, S. Inoue, C. Song, R. Tanaka, T. Nakatsu, E. Mizohata, F. Yumoto, K. Tono, Y. Joti, T. Kameshima, T. Hatsui, M. Yabashi, O. Nureki, K. Numata, E. Nango, S. Iwata,
Sci Rep, 7, 703

Redox-coupled proton transfer mechanism in nitrite reductase revealed by femtosecond crystallography.,
Y. Fukuda, K. M. Tse, T. Nakane, T. Nakatsu, M. Suzuki, M. Sugahara, S. Inoue, T. Masuda, F. Yumoto, N. Matsugaki, E. Nango, K. Tono, Y. Joti, T. Kameshima, C. Song, T. Hatsui, M. Yabashi, O. Nureki, M. E. Murphy, T. Inoue, S. Iwata, E. Mizohata,
Pro. Nat. Acad. Sci. USA, 113, 2928&ndash,2933

Synthesis and inhibitory activity of substrate-analog fructosyl peptide oxidase inhibitors.,
B. Watanabe, A. Ichiyanagi, K. Hirokawa, K. Gomi, T. Nakatsu, H. Kato, N. Kajiyama,
Bioorg Med Chem Lett., 25(18), 3910-3

An isomorphous replacement method for efficient de novo phasing for serial femtosecond crystallography.,
K. Yamashita, D. Pan, T. Okuda, M. Sugahara, A. Kodan, T. Yamaguchi, T. Murai, K. Gomi, N. Kajiyama, E. Mizohata, M. Suzuki, E. Nango, K. Tono, Y. Joti, T. Kameshima, J. Park, C. Song, T. Hatsui, M. Yabashi, S. Iwata, H. Kato, H. Ago, M. Yamamoto, T. Nakatsu,
Scientific Reports, 5, Article number: 14017

Native sulfur/chlorine SAD phasing for serial femtosecond crystallography.,
T. Nakane, C. Song, M. Suzuki, E. Nango, J. Kobayashi, T. Masuda, S. Inoue, E. Mizohata, T. Nakatsu, T. Tanaka, R. Tanaka, T. Shimamura, K. Tono, Y. Joti, T. Kameshima, T. Hatsui, M. Yabashi, O. Nureki, S. Iwata, M. Sugahara,
Acta Cryst., D, 71, 2519-25

Crystal structures of beta-primeverosidase in complex with disaccharide amidine inhibitors.,
H. Saino, T. Shimizu, J. Hiratake, T. Nakatsu, H. Kato, K. Sakata, M. Mizutani,
J. Biol. Chem., 289, 16826&ndash,16834

Structural basis for gating mechanisms of a eukaryoticP-glycoprotein homolog.,
A. Kodan, T. Yamaguchi, T. Nakatsu, K. Sakiyama, C. J. Hipolito, A.Fujioka, R. Hirokane, K. Ikeguchi, B. Watanabe, J. Hiratake, Y. Kimura, H. Suga, K. Ueda, H. Kato,
Proc Natl Acad Sci U S A., epub ahead of print

Crystal structure of peroxisomal targeting signal-2 bound to its
receptor complex Pex7p-Pex21p., D. Pan, T. Nakatsu, H. Kato, Nat
Struct Mol Biol., 20, 987-993

Impact of site-directed mutant luciferase on quantitative green and orange/red emission intensities in firefly bioluminescence.
Y. Wang, H. Akiyama, K. Terakado, T. Nakatsu>,,
Sci Rep, 3, 2490

String like Assembly of Aligned Single-Wall Carbon Nanotubes in a Single-Chiral State.
H. Kawai, K. Hasegawa, T. Nakatsu, Y. Naitoh, Y. Takagi, Y. Wada, T. Takenobu, K. Yanagi,
Applied Physics Express, 6, 065103

Crystallization and preliminary crystallographic analysis of two eukaryotic fructosyl peptide oxidases.
Ichiyanagi, A., Hirokawa, K., Gomi, K., Nakatsu, T., Kato, H. and Kajiyama, N.
Acta Crystallogr Sect F Struct Biol Cryst Commun 69, 130-133

Crystallization and preliminary X-ray crystallographic analysis of Pz peptidase B from Geobacillus collagenovorans MO-1.
H. Nakano, A. Hosokawa, R. Tagawa, K. Inaka, K. Ohta, K. Nakatsu, H. Kato, K. Watanabe,
Acta Crystallogr Sect F Struct Biol Cryst Commun, 68, 757-759

Structural basis for docking of peroxisomal membrane protein
carrier Pex19p onto its receptor Pex3p., Y. Sato,
H. Shibata, T. Nakatsu, H.
Nakano, Y. Kashiwayama, T. Imanaka, H. Kato,
Embo J., 29, 4083-4093

Deleting two C-terminal alpha-helices is effective to crystallize
the bacterial ABC transporter Escherichia coli MsbA complexed with
AMP-PNP., K. Terakado, A.
Kodan, N. Nakano,Y. Kimura, K. Ueda, T. Nakatsu, H. Kato, Acta
Cryst., D66, 319-323

Functional role of the linker region in purified human
P-glycoprotein., T. Sato, A.
Kodan, Y. Kimura, K. Ueda, T. Nakatsu, H. Kato, FEBS J., 276, 3504-16

X-ray crystallographic study of an HIV-1 fusion inhibitor with the gp41 S138A substitution.
T. Watabe, Y. Terakawa, K. Watanabe, H. Ohno, H. Nakano, T. Nakatsu, H. Kato, K. Izumi, E. Kodama, M. Matsuoka, K. Kitaura, S. Oishi, N. Fujii,
J Mol Biol, 392, 657-665

Mechanism of efficient firefly bioluminescence via adiabatic
transition state and seam of sloped conical intersection. L.W.Chung, S.
Hayashi, M. Lundberg, T. Nakatsu, H. Kato, K. Morokuma, J Am Chem Soc., 13012880-1

Structural basis for gibberellin recognition by its receptor GID1.A. Shimada, M. Ueguchi-Tanaka, T.
Nakatsu, M. Nakajima, Y. Naoe, H. Ohmiya, H. Kato, M. Matsuoka, Nature., 456, 520-3

Crystallization and preliminary X-ray crystallographic studies of
Pz peptidase A from Geobacillus collagenovorans MO-1., Kawasaki, A., Nakano, H., Tsujimoto, Y., Matsui, H., Shimizu, T.,
Nakatsu, T., Kato, H.,
Watanabe, K., Acta Crystallogr., F63, 142-144

Structural Basis for Spectral Difference in
Luciferase Bioluminescence., Nakatsu, T.,
Ichiyama, S., Hiratake, J., Saldanha, A., Kobashi, N., Sakata, K. and Kato, H.: Nature, 440, 372-376

Overexpression, purification, crystallization and preliminary
X-ray crystallographic studies of a proline-specific aminopeptidase
from Aneurinibacillussp. Strain AM-1., Akioka, M., Nakano,
H., Horikiri, A., Tsujimoto, Y., Matsui, H., Shimizu, T., Nakatsu, T., Kato, H., and
Watanabe, K., Acta Crystallogr., F62, 1266-1268

Structure and function of the PsbP protein of Photosystem II from
higher plants. K. Ifuku, T. Nakatsu, R. Shimamoto, Y. Yamamoto, S.
Ishihara, H. Kato and F. Sato, Photosynth Res 84, 251-255

Crystallization and preliminary crystallographic analysis of
bacterial fructosyl amino acid oxidase. R. Sakaue, T. Nakatsu, Y.
Yamaguchi, H. Kato and N. Kajiyama, Acta Crystallogr. F 61, 196-198

Crystal structures of pyruvate phosphate dikinase from maize
revealed an altrnative conformation in the swiveling-domain motion T.
Nakanishi, T. Nakatsu, M. Matsuoka, K. Sakata and H. Kato, Biochemistry
44, 1136-1144

Expression, purification, and crystallization of
endopolygalacturonase from a pathogenic fungus, Stereum purpureum, in
Escherichia coli T. Shimizu, H. Shibata, T. Araya, T. Nakatsu, K.
Miyairi, T. Okuno and H. Kato, Protein Expr Purif 44, 130-135

Crystal structure of gamma-glutamylcysteine synthetase: insights
into the mechanism of catalysis by a key enzyme for glutathione
homeostasis T. Hibi, H. Nii, T. Nakatsu, A. Kimura, H. Kato, J.
Hiratake and J. Oda, Proc Natl Acad Sci U S A 101, 15052-15057

Reaction Mechanism on X-ray Crystallography at Atomic Resolution
of Endopolygaracturonase I from Fungus Stereum purpureum. T. Shimizu,
T. Nakatsu, K. Miyairi, T. Okuno and H, Kato. J. Applied Glycoscience
51, 161-167

Crystal structure of the PsbP protein of photosystem II from
Nicotiana tabacum K. Ifuku, T. Nakatsu, H. Kato and F. Sato, EMBO Rep
5, 362-367

Crystal structure of a myristoylated CAP-23/NAP-22 N-terminal
domain complexed with Ca2+/calmodulin M. Matsubara, T. Nakatsu, H. Kato
and H. Taniguchi, Embo J 23, 712-718

Crystal structure of the C-terminal clock-oscillator
domain of the cyanobacterial KaiA protein T. Uzumaki, M. Fujita, T.
Nakatsu, F. Hayashi, H. Shibata, N. Itoh, H. Kato and M. Ishiura, Nat
Struct Mol Biol 11, 623-631

Crystallization and preliminary crystallographic studies on the
extrinsic 23 kDa protein in the oxygen-evolving complex of photosystem
II K. Ifuku, T. Nakatsu, H. Kato and F. Sato, Acta Crystallogr D Biol
Crystallogr 59, 1462-1463

Capturing enzyme structure prior to reaction initiation:
tropinone reductase-II-substrate complexes A. Yamashita, M. Endo, T.
Higashi, T. Nakatsu, Y. Yamada, J. Oda and H. Kato, Biochemistry 42,
5566-5573

Crystal structure of a MARCKS peptide containing the
calmodulin-binding domain in complex with Ca2+-calmodulin E. Yamauchi,
T. Nakatsu, M. Matsubara, H. Kato and H. Taniguchi, Nat Struct Biol 10,
226-231

Crystal structure of the Homer 1 family conserved region reveals
the interaction between the EVH1 domain and own proline-rich motif K.
Irie, T. Nakatsu, K. Mitsuoka, A. Miyazawa, K. Sobue, Y. Hiroaki, T.
Doi, Y. Fujiyoshi and H. Kato, J Mol Biol 318, 1117-1126

Active-site architecture of endopolygalacturonase I from Stereum
purpureum revealed by crystal structures in native and ligand-bound
forms at atomic resolution T. Shimizu, T. Nakatsu, K. Miyairi, T. Okuno
and H. Kato, Biochemistry 41, 6651-6659

Escherichia coli B gamma-glutamylcysteine synthetase:
modification, purification, crystallization and preliminary
crystallographic analysis T. Hibi, H. Hisada, T. Nakatsu, H. Kato and
J. Oda, Acta Crystallogr D Biol Crystallogr 58, 316-318

Characterization of inhibitors acting at the synthetase site of Escherichia coli asparagine synthetase B S. K. Boehlein, T. Nakatsu, J. Hiratake, R. Thirumoorthy, J. D. Stewart, N. G. Richards and S. M. Schuster, Biochemistry 40, 11168-11175

Crystallization and preliminary X-ray study of endopolygalacturonase from the pathogenic fungus Stereum purpureum T. Shimizu, T. Nakatsu, K. Miyairi, T. Okuno and H. Kato, Acta Crystallogr D Biol Crystallogr 57, 1171-1173

Crystal structure of tobacco PR-5d protein at 1.8 A resolution reveals a conserved acidic cleft structure in antifungal thaumatin-like proteins H. Koiwa, H. Kato, T. Nakatsu, J. Oda, Y. Yamada and F. Sato, J Mol Biol 286, 1137-1145

Structure of tropinone reductase-II complexed with NADP+ and pseudotropine at 1.9 A resolution: implication for stereospecific substrate binding and catalysis A. Yamashita, H. Kato, S. Wakatsuki, T. Tomizaki, T. Nakatsu, K. Nakajima, T. Hashimoto, Y. Yamada and J. Oda, Biochemistry 38, 7630-7637