KATO Ryuichi

Last updated: Jun 17, 2019 at 14:29

Name	KATO Ryuichi
Affiliation	High Energy Accelerator Research Organization
Section	Institute of Materials Structure Science

Research Interests

Structural biology(158) , Biochemistry(505)

Research Areas

Biological Science / Molecular biology /
Biological Science / Biophysics /
Biological Science / Functional biochemistry /
Biological Science / Structural biochemistry /

Published Papers

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キノコ由来ガレクチンACG の糖認識メカニズム

Trends in Glycoscience and Glycotechnology 30(172) SJ33-SJ46 2018 [Refereed][Invited]

Carbohydrate Recognition Mechanism of the Mushroom Galectin ACG

Jun Hirabayashi; Dan Hu; Hiroaki Tateno; Naoyuki Kuwabara; Ryuichi Kato; and Fumio Yagi

Trends in Glycoscience and Glycotechnology 30(172) SE75-SE88 2018 [Refereed][Invited]

Experimental phase determination with selenomethionine or mercury-derivatization in serial femtosecond crystallography

Yamashita, K., Kuwabara, N., Nakane, T., Murai, T., Mizohata, E., Sugahara, M., Pan, D., Masuda, T., Suzuki, M., Sato, T., Kodan, A., Yamaguchi, T., Nango, E., Tanaka, T., Tono, K., Joti, Y., Kameshima, T., Hatsui, T., Yabashi, M., Manya, H., Endo, T., Kato, R., Senda, T., Kato, H., Iwata, S., Ago, H., Yamamoto, M., Yumoto, F. & Nakatsu, T.

IUCr J. 4 639-647 2017 [Refereed]

X-ray structure of a protease-resistant mutant form of human galectin-9 having two carbohydrate recognition domains with a metal-binding site

Yoshida, H., Nishi, N., Wada, K., Nakamura, T., Hirashima, M., Kuwabara, N., Kato, R. & Kamitori, S.

Biochem. Biophys. Res. Commun. 490 1287-1293 2017 [Refereed]

Structural biology of muscular dystrophy by X-ray crystallography

N. Kuwabara, R. Kato

PF Highlights 46-47 2017 [Refereed]

Carbohydrate-binding domain of the POMGnT1 stem region modulates O-mannosylation sites of α-dystroglycan

Naoyuki Kuwabara, Hiroshi Manya, Takeyuki Yamada, Hiroaki Tateno, Motoi Kanagawa, Kazuhiro Kobayashi, Keiko Akasaka-Manya, Yuriko Hirose, Mamoru Mizuno, Mitsunori Ikeguchi, Tatsushi Toda, Jun Hirabayashi, Toshiya Send, Tamao Endo, and Ryuichi Kato

PNAS 113(33) 9280-9285 Aug 2016 [Refereed]

立体構造に基づいたフコースを結合するレクチンの比較と分類

Trends in Glycoscience and Glycotechnology 28(160) J25-J38 Mar 2016 [Refereed][Invited]

Classification and Comparison of Fucose-Binding Lectins Based on Their Structures

Hisayoshi Makyio; and Ryuichi Kato

Trends in Glycoscience and Glycotechnology 28(160) E25-E37 Mar 2016 [Refereed][Invited]

Six independent fucose-binding sites in the crystal structure of Aspergillus oryzae lectin

Hisayoshi Makyio, Junpei Shimabukuro, Tatsuya Suzuki, Akihiro Imamura, Hideharu Ishida, Makoto Kiso, Hiromune Ando, Ryuichi Kato

Biochemical and Biophysical Research Communications 477 477-482 2016 [Refereed]

Structure of a BAG6 (Bcl-2-associated Athanogene 6)-Ubl4a (Ubiquitin-like Protein 4a) Complex Reveals a Novel Binding Interface That Functions in Tail-anchored Protein Biogenesis

Naoyuki Kuwabara, Ryosuke Minami, Naoto Yokota, Hirofumi Matsumoto, Toshiya Senda, Hiroyuki Kawahara, and Ryuichi Kato

THE JOURNAL OF BIOLOGICAL CHEMISTRY 290(15) 9387-9398 Apr 2015 [Refereed]

POMGNT1 Is Glycosylated by Mucin-Type O-Glycans

Xin Xin, Keiko Akasaka-Manya, Hiroshi Manya, Jun-ichi Furukawa, Naoyuki Kuwahara, Kazue Okada, Hiroki Tsumoto, Nobuaki Higashi, Ryuichi Kato, Yasuro Shinohara, Tatsuro Irimura, and Tamao Endo

Biol. Pharm. Bull 38 1389-1394 2015 [Refereed]

Expanded potential of seleno-carbohydrates as a molecular tool for X-ray structural determination of a carbohydrate–protein complex with single/multi-wavelength anomalous dispersion phasing

Tatsuya Suzuki, Hisayoshi Makyio, Hiromune Ando, Naoko Komura, Masanori Menjo, Yusuke Yamada, Akihiro Imamura, Hideharu Ishida, Soichi Wakatsuki, Ryuichi Kato, Makoto Kiso

Bioorganic & Medicinal Chemistry 22 2090-2101 2014 [Refereed]

Conformational change of a unique sequence in a fungal galectin from Agrocybe cylindracea controls glycan ligand-binding specificity.

Kuwabara N, Hu D, Tateno H, Makyio H, Hirabayashi J, Kato R

FEBS letters Sep 2013 [Refereed]

Structural basis of preferential binding of fucose-containing saccharide by the Caenorhabditis elegans galectin LEC-6.

Makyio H, Takeuchi T, Tamura M, Nishiyama K, Takahashi H, Natsugari H, Arata Y, Kasai K, Yamada Y, Wakatsuki S, Kato R

Glycobiology 23 797-805 Jul 2013 [Refereed]

Structural basis for phosphorylation-triggered autophagic clearance of Salmonella.

Rogov VV, Suzuki H, Fiskin E, Wild P, Kniss A, Rozenknop A, Kato R, Kawasaki M, McEwan DG, Löhr F, Güntert P, Dikic I, Wakatsuki S, Dötsch V

The Biochemical journal Jun 2013 [Refereed]

Direct metal recognition by guanine nucleotide-exchange factor in the initial step of the exchange reaction.

Uejima T, Ihara K, Sunada M, Kawasaki M, Ueda T, Kato R, Nakano A, Wakatsuki S

Acta crystallographica. Section D, Biological crystallography 69 345-351 Mar 2013 [Refereed]

Structural basis for membrane binding specificity of the Bin/Amphiphysin/Rvs (BAR) domain of Arfaptin-2 determined by Arl1 GTPase.

Nakamura K, Man Z, Xie Y, Hanai A, Makyio H, Kawasaki M, Kato R, Shin HW, Nakayama K, Wakatsuki S

The Journal of biological chemistry 287 25478-25489 Jul 2012 [Refereed]

Structural basis for Arf6-MKLP1 complex formation on the Flemming body responsible for cytokinesis.

Makyio H, Ohgi M, Takei T, Takahashi S, Takatsu H, Katoh Y, Hanai A, Ueda T, Kanaho Y, Xie Y, Shin HW, Kamikubo H, Kataoka M, Kawasaki M, Kato R, Wakatsuki S, Nakayama K

The EMBO journal 31 2590-2603 May 2012 [Refereed]

Structure of a compact conformation of linear diubiquitin.

Rohaim A, Kawasaki M, Kato R, Dikic I, Wakatsuki S

Acta crystallographica. Section D, Biological crystallography 68 102-108 Feb 2012 [Refereed]

Structural basis of the strict phospholipid binding specificity of the pleckstrin homology domain of human evectin-2.

Okazaki S, Kato R, Uchida Y, Taguchi T, Arai H, Wakatsuki S

Acta crystallographica. Section D, Biological crystallography 68 117-123 Feb 2012 [Refereed]

Intracellular phosphatidylserine is essential for retrograde membrane traffic through endosomes.

Uchida Y, Hasegawa J, Chinnapen D, Inoue T, Okazaki S, Kato R, Wakatsuki S, Misaki R, Koike M, Uchiyama Y, Iemura S, Natsume T, Kuwahara R, Nakagawa T, Nishikawa K, Mukai K, Miyoshi E, Taniguchi N, Sheff D, Lencer WI, Taguchi T, Arai H

Proceedings of the National Academy of Sciences of the United States of America 108 15846-15851 Sep 2011 [Refereed]

Crystallization of small proteins assisted by green fluorescent protein.

Suzuki N, Hiraki M, Yamada Y, Matsugaki N, Igarashi N, Kato R, Dikic I, Drew D, Iwata S, Wakatsuki S, Kawasaki M

Acta crystallographica. Section D, Biological crystallography 66 1059-1066 Oct 2010 [Refereed]

[Advancement of synchrotron radiation protein crystallography in the targeted protein research program: beamline developments at the photon factory].

Wakatsuki S, Yamada Y, Chavas LM, Igarashi N, Kawasaki M, Kato R, Hiraki M, Matsugaki N

Yakugaku zasshi : Journal of the Pharmaceutical Society of Japan 130 631-640 May 2010 [Refereed]

Complexity in influenza virus targeted drug design: interaction with human sialidases.

Chavas LM, Kato R, Suzuki N, von Itzstein M, Mann MC, Thomson RJ, Dyason JC, McKimm-Breschkin J, Fusi P, Tringali C, Venerando B, Tettamanti G, Monti E, Wakatsuki S

Journal of medicinal chemistry 53 2998-3002 Apr 2010 [Refereed]

Crystal structures of the CERT START domain with inhibitors provide insights into the mechanism of ceramide transfer.

Kudo N, Kumagai K, Matsubara R, Kobayashi S, Hanada K, Wakatsuki S, Kato R

Journal of molecular biology 396 245-251 Feb 2010 [Refereed]

Specific recognition of linear ubiquitin chains by NEMO is important for NF-kappaB activation.

Rahighi S, Ikeda F, Kawasaki M, Akutsu M, Suzuki N, Kato R, Kensche T, Uejima T, Bloor S, Komander D, Randow F, Wakatsuki S, Dikic I

Cell 136 1098-1109 Mar 2009 [Refereed]

Structural analysis of the recognition mechanism of poly-N-acetyllactosamine by the human galectin-9 N-terminal carbohydrate recognition domain.

Nagae M, Nishi N, Murata T, Usui T, Nakamura T, Wakatsuki S, Kato R

Glycobiology 19 112-117 Feb 2009 [Refereed]

Nucleotide-dependent conformational changes and assembly of the AAA ATPase SKD1/VPS4B.

Inoue M, Kamikubo H, Kataoka M, Kato R, Yoshimori T, Wakatsuki S, Kawasaki M

Traffic (Copenhagen, Denmark) 9 2180-2189 Dec 2008 [Refereed]

1,2-alpha-l-Fucosynthase: a glycosynthase derived from an inverting alpha-glycosidase with an unusual reaction mechanism.

Wada J, Honda Y, Nagae M, Kato R, Wakatsuki S, Katayama T, Taniguchi H, Kumagai H, Kitaoka M, Yamamoto K

FEBS letters 582 3739-3743 Nov 2008 [Refereed]

Elucidation of Rab27 recruitment by its effectors: structure of Rab27a bound to Exophilin4/Slp2-a.

Chavas LM, Ihara K, Kawasaki M, Torii S, Uejima T, Kato R, Izumi T, Wakatsuki S

Structure (London, England : 1993) 16 1468-1477 Oct 2008 [Refereed]

[Molecular basis of sugar-protein interaction].

Kato R, Nagae M, Wakatsuki S

Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme 53 1670-1675 Sep 2008 [Refereed]

Purification, crystallization and preliminary X-ray crystallographic analysis of Rab27a GTPase in complex with exophilin4/Slp2-a effector.

Chavas LM, Ihara K, Kawasaki M, Kato R, Izumi T, Wakatsuki S

Acta crystallographica. Section F, Structural biology and crystallization communications 64 599-601 Jul 2008 [Refereed]

Miranda cargo-binding domain forms an elongated coiled-coil homodimer in solution: implications for asymmetric cell division in Drosophila.

Yousef MS, Kamikubo H, Kataoka M, Kato R, Wakatsuki S

Protein science : a publication of the Protein Society 17 908-917 May 2008 [Refereed]

[Structural and functional biology for post translational modification and transport in eukaryotes].

Wakatsuki S, Kato R, Kawasaki M, Igarashi N, Masahiko H

Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme 53 628-631 Apr 2008 [Refereed]

Structural analysis of the human galectin-9 N-terminal carbohydrate recognition domain reveals unexpected properties that differ from the mouse orthologue.

Nagae M, Nishi N, Nakamura-Tsuruta S, Hirabayashi J, Wakatsuki S, Kato R

Journal of molecular biology 375 119-135 Jan 2008 [Refereed]

Structural basis for specific lipid recognition by CERT responsible for nonvesicular trafficking of ceramide.

Kudo N, Kumagai K, Tomishige N, Yamaji T, Wakatsuki S, Nishijima M, Hanada K, Kato R

Proceedings of the National Academy of Sciences of the United States of America 105 488-493 Jan 2008 [Refereed]

Design of disulfide-linked thioredoxin dimers and multimers through analysis of crystal contacts.

Das M, Kobayashi M, Yamada Y, Sreeramulu S, Ramakrishnan C, Wakatsuki S, Kato R, Varadarajan R

Journal of molecular biology 372 1278-1292 Oct 2007 [Refereed]

Structural basis for recognition of high mannose type glycoproteins by mammalian transport lectin VIP36.

Satoh T, Cowieson NP, Hakamata W, Ideo H, Fukushima K, Kurihara M, Kato R, Yamashita K, Wakatsuki S

The Journal of biological chemistry 282 28246-28255 Sep 2007 [Refereed]

Molecular basis for autoregulatory interaction between GAE domain and hinge region of GGA1.

Inoue M, Shiba T, Ihara K, Yamada Y, Hirano S, Kamikubo H, Kataoka M, Kawasaki M, Kato R, Nakayama K, Wakatsuki S

Traffic (Copenhagen, Denmark) 8 904-913 Jul 2007 [Refereed]

Structure of the small GTPase Rab27b shows an unexpected swapped dimer.

Chavas LM, Torii S, Kamikubo H, Kawasaki M, Ihara K, Kato R, Kataoka M, Izumi T, Wakatsuki S

Acta crystallographica. Section D, Biological crystallography 63 769-779 Jul 2007 [Refereed]

Structural basis of the catalytic reaction mechanism of novel 1,2-alpha-L-fucosidase from Bifidobacterium bifidum.

Nagae M, Tsuchiya A, Katayama T, Yamamoto K, Wakatsuki S, Kato R

The Journal of biological chemistry 282 18497-18509 Jun 2007 [Refereed]

Crystal structure of GlcAT-S, a human glucuronyltransferase, involved in the biosynthesis of the HNK-1 carbohydrate epitope.

Shiba T, Kakuda S, Ishiguro M, Morita I, Oka S, Kawasaki T, Wakatsuki S, Kato R

Proteins 65 499-508 Nov 2006 [Refereed]

Crystal structure of the galectin-9 N-terminal carbohydrate recognition domain from Mus musculus reveals the basic mechanism of carbohydrate recognition.

Nagae M, Nishi N, Murata T, Usui T, Nakamura T, Wakatsuki S, Kato R

The Journal of biological chemistry 281 35884-35893 Nov 2006 [Refereed]

Structural basis of ubiquitin recognition by mammalian Eap45 GLUE domain.

Hirano S, Suzuki N, Slagsvold T, Kawasaki M, Trambaiolo D, Kato R, Stenmark H, Wakatsuki S

Nature structural & molecular biology 13 1031-1032 Nov 2006 [Refereed]

Structural basis for Rab11-dependent membrane recruitment of a family of Rab11-interacting protein 3 (FIP3)/Arfophilin-1.

Shiba T, Koga H, Shin HW, Kawasaki M, Kato R, Nakayama K, Wakatsuki S

Proceedings of the National Academy of Sciences of the United States of America 103 15416-15421 Oct 2006 [Refereed]

Development of an automated large-scale protein-crystallization and monitoring system for high-throughput protein-structure analyses.

Hiraki M, Kato R, Nagai M, Satoh T, Hirano S, Ihara K, Kudo N, Nagae M, Kobayashi M, Inoue M, Uejima T, Oda S, Chavas LM, Akutsu M, Yamada Y, Kawasaki M, Matsugaki N, Igarashi N, Suzuki M, Wakatsuki S

Acta crystallographica. Section D, Biological crystallography 62 1058-1065 Sep 2006 [Refereed]

Structures of the carbohydrate recognition domain of Ca2+-independent cargo receptors Emp46p and Emp47p.

Satoh T, Sato K, Kanoh A, Yamashita K, Yamada Y, Igarashi N, Kato R, Nakano A, Wakatsuki S

The Journal of biological chemistry 281 10410-10419 Apr 2006 [Refereed]

Double-sided ubiquitin binding of Hrs-UIM in endosomal protein sorting.

Hirano S, Kawasaki M, Ura H, Kato R, Raiborg C, Stenmark H, Wakatsuki S

Nature structural & molecular biology 13 272-277 Mar 2006 [Refereed]

Structural basis for recognition of ubiquitinated cargo by Tom1-GAT domain.

Akutsu M, Kawasaki M, Katoh Y, Shiba T, Yamaguchi Y, Kato R, Kato K, Nakayama K, Wakatsuki S

FEBS letters 579 5385-5391 Oct 2005 [Refereed]

Molecular mechanism of ubiquitin recognition by GGA3 GAT domain.

Kawasaki M, Shiba T, Shiba Y, Yamaguchi Y, Matsugaki N, Igarashi N, Suzuki M, Kato R, Kato K, Nakayama K, Wakatsuki S

Genes to cells : devoted to molecular & cellular mechanisms 10 639-654 Jul 2005 [Refereed]

Structure determination of GGA-GAE and gamma1-ear in complex with peptides: crystallization of low-affinity complexes in membrane traffic.

Yamada Y, Inoue M, Shiba T, Kawasaki M, Kato R, Nakayama K, Wakatsuki S

Acta crystallographica. Section D, Biological crystallography 61 731-736 Jun 2005 [Refereed]

[Progress and maturation of protein crystallographic experiments].

Wakatsuki S, Kato R, Igarashi N, Kawasaki M, Matsugaki N, Hiraki M, Yamada Y

Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme 50 846-852 Jun 2005 [Refereed]

[Molecular mechanisms in acceptor substrate recognition of a human glucuronyltransferase, GlcAT-P, an enzyme critical in the biosynthesis of the carbohydrate epitope HNK-1].

Shiba T, Kakuda S, Oka S, Ishiguro M, Kawasaki T, Wakatsuki S, Kato R

Seikagaku. The Journal of Japanese Biochemical Society 77 153-158 Feb 2005 [Refereed]

Crystal structure of the human cytosolic sialidase Neu2. Evidence for the dynamic nature of substrate recognition.

Chavas LM, Tringali C, Fusi P, Venerando B, Tettamanti G, Kato R, Monti E, Wakatsuki S

The Journal of biological chemistry 280 469-475 Jan 2005 [Refereed]

Structural basis for acceptor substrate recognition of a human glucuronyltransferase, GlcAT-P, an enzyme critical in the biosynthesis of the carbohydrate epitope HNK-1.

Kakuda S, Shiba T, Ishiguro M, Tagawa H, Oka S, Kajihara Y, Kawasaki T, Wakatsuki S, Kato R

The Journal of biological chemistry 279 22693-22703 May 2004 [Refereed]

Molecular mechanism of membrane recruitment of GGA by ARF in lysosomal protein transport.

Shiba T, Kawasaki M, Takatsu H, Nogi T, Matsugaki N, Igarashi N, Suzuki M, Kato R, Nakayama K, Wakatsuki S

Nature structural biology 10 386-393 May 2003 [Refereed]

Structural basis for the accessory protein recruitment by the gamma-adaptin ear domain.

Nogi T, Shiba Y, Kawasaki M, Shiba T, Matsugaki N, Igarashi N, Suzuki M, Kato R, Takatsu H, Nakayama K, Wakatsuki S

Nature structural biology 9 527-531 Jul 2002 [Refereed]

Structural basis for recognition of acidic-cluster dileucine sequence by GGA1.

Shiba T, Takatsu H, Nogi T, Matsugaki N, Kawasaki M, Igarashi N, Suzuki M, Kato R, Earnest T, Nakayama K, Wakatsuki S

Nature 415 937-941 Feb 2002 [Refereed]

Association Memberships

PROTEIN SCIENCE SOCIETY OF JAPAN(279) , THE MOLECULAR BIOLOGY SOCIETY OF JAPAN(2576) , THE JAPANESE BIOCHEMICAL SOCIETY(1715) , THE CRYSTALLOGRAPHIC SOCIETY OF JAPAN(214)

Research Grants & Projects

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Structural and functional study of enzymes which are related to central nervous system disorders with muscle deficiency

Ministry of Education, Culture, Sports, Science and Technology: Grants-in-Aid for Scientific Research(基盤研究(B))

Project Year: 2008 - 2010 Investigator(s): Ryuichi KATO

We elucidated PomT1 and T2 require sugar modification on their proteins for the activity. We also showed that mechanism of PomT1-T2 complex formation is different between human and yeast but similar between human and zebra-fish. Over expression an...

Basic study of drug development for anti-influenza virus based on structural analysis of sialidase

Ministry of Education, Culture, Sports, Science and Technology: Grants-in-Aid for Scientific Research(基盤研究(C))

Project Year: 2004 - 2005 Investigator(s): Ryuichi KATO

Neuraminidases, or sialidases, are glycohydrolytic enzymes broadly present among species. They are found in viruses, bacteria and mammals, where they catalyze the removal of sialic acid on the non-reducing termini of complex carbohydrates, and act...