2021/09/28 更新

写真a

カトウ コウジ
加藤 公児
KATOU Kouji
所属
異分野基礎科学研究所 准教授(特任)
職名
准教授(特任)
外部リンク

学位

  • 博士(理学) ( 大阪大学 )

研究キーワード

  • X線結晶構造解析

  • vault

  • 核酸-タンパク質複合体

  • 生体超分子複合体

  • タンパク質-核酸複合体

  • ボルト

研究分野

  • ライフサイエンス / 構造生物化学

学歴

  • 大阪大学    

    2003年4月 - 2006年3月

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経歴

  • 岡山大学   異分野基礎科学研究所   特任准教授

    2018年4月 - 現在

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  • 北海道大学   大学院先端生命科学研究院   助教

    2013年4月 - 2018年3月

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  • 兵庫県立大学   大学院・生命理学研究科   特任講師

    2012年7月 - 2013年3月

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  • カリフォルニア工科大学   博士研究員

    2011年1月 - 2012年6月

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  • 兵庫県立大学   大学院・生命理学研究科   特任助教

    2009年10月 - 2011年1月

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  • 大阪大学   蛋白質研究所   特任研究員

    2007年4月 - 2009年9月

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  • 大阪大学   蛋白質研究所   技術補佐員

    2006年4月 - 2007年3月

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▼全件表示

 

論文

  • Cryo-EM structure of monomeric photosystem II at 2.78 Å resolution reveals factors important for the formation of dimer. 国際誌

    Huaxin Yu, Tasuku Hamaguchi, Yoshiki Nakajima, Koji Kato, Keisuke Kawakami, Fusamichi Akita, Koji Yonekura, Jian-Ren Shen

    Biochimica et biophysica acta. Bioenergetics   1862 ( 10 )   148471 - 148471   2021年10月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    Photosystem II (PSII) functions mainly as a dimer to catalyze the light energy conversion and water oxidation reactions. However, monomeric PSII also exists and functions in vivo in some cases. The crystal structure of monomeric PSII has been solved at 3.6 Å resolution, but it is still not clear which factors contribute to the formation of the dimer. Here, we solved the structure of PSII monomer at a resolution of 2.78 Å using cryo-electron microscopy (cryo-EM). From our cryo-EM density map, we observed apparent differences in pigments and lipids in the monomer-monomer interface between the PSII monomer and dimer. One β-carotene and two sulfoquinovosyl diacylglycerol (SQDG) molecules are found in the monomer-monomer interface of the dimer structure but not in the present monomer structure, although some SQDG and other lipid molecules are found in the analogous region of the low-resolution crystal structure of the monomer, or cryo-EM structure of an apo-PSII monomer lacking the extrinsic proteins from Synechocystis sp. PCC 6803. In the current monomer structure, a large part of the PsbO subunit was also found to be disordered. These results indicate the importance of the β-carotene, SQDG and PsbO in formation of the PSII dimer.

    DOI: 10.1016/j.bbabio.2021.148471

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  • High-resolution cryo-EM structure of photosystem II reveals damage from high-dose electron beams. 査読 国際誌

    Koji Kato, Naoyuki Miyazaki, Tasuku Hamaguchi, Yoshiki Nakajima, Fusamichi Akita, Koji Yonekura, Jian-Ren Shen

    Communications biology   4 ( 1 )   382 - 382   2021年3月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    Photosystem II (PSII) plays a key role in water-splitting and oxygen evolution. X-ray crystallography has revealed its atomic structure and some intermediate structures. However, these structures are in the crystalline state and its final state structure has not been solved. Here we analyzed the structure of PSII in solution at 1.95 Å resolution by single-particle cryo-electron microscopy (cryo-EM). The structure obtained is similar to the crystal structure, but a PsbY subunit was visible in the cryo-EM structure, indicating that it represents its physiological state more closely. Electron beam damage was observed at a high-dose in the regions that were easily affected by redox states, and reducing the beam dosage by reducing frames from 50 to 2 yielded a similar resolution but reduced the damage remarkably. This study will serve as a good indicator for determining damage-free cryo-EM structures of not only PSII but also all biological samples, especially redox-active metalloproteins.

    DOI: 10.1038/s42003-021-01919-3

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  • Molecular organizations and function of iron-stress-induced-A protein family in Anabaena sp. PCC 7120. 査読 国際誌

    Ryo Nagao, Makio Yokono, Yoshifumi Ueno, Takehiro Suzuki, Koji Kato, Ka-Ho Kato, Naoki Tsuboshita, Tian-Yi Jiang, Naoshi Dohmae, Jian-Ren Shen, Shigeki Ehira, Seiji Akimoto

    Biochimica et biophysica acta. Bioenergetics   1862 ( 1 )   148327 - 148327   2021年1月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    Iron-stress-induced-A proteins (IsiAs) are expressed in cyanobacteria under iron-deficient conditions, and surround photosystem I (PSI) trimer with a ring formation. A cyanobacterium Anabaena sp. PCC 7120 has four isiA genes; however, it is unknown how the IsiAs are associated with PSI. Here we report on molecular organizations and function of the IsiAs in this cyanobacterium. A deletion mutant of the isiA1 gene was constructed, and the four types of thylakoids were prepared from the wild-type (WT) and ΔisiA1 cells under iron-replete (+Fe) and iron-deficient (-Fe) conditions. Immunoblotting analysis exhibits a clear expression of the IsiA1 in the WT-Fe. The PSI-IsiA1 supercomplex is found in the WT-Fe, and excitation-energy transfer from IsiA1 to PSI is verified by time-resolved fluorescence analyses. Instead of the IsiA1, both IsiA2 and IsiA3 are bound to PSI monomer in the ΔisiA1-Fe. These findings provide insights into multiple-expression system of the IsiA family in this cyanobacterium.

    DOI: 10.1016/j.bbabio.2020.148327

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  • A solution-free crystal-mounting platform for native SAD. 査読 国際誌

    Jian Yu, Akira Shinoda, Koji Kato, Isao Tanaka, Min Yao

    Acta crystallographica. Section D, Structural biology   76 ( Pt 10 )   938 - 945   2020年10月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    The native SAD phasing method uses the anomalous scattering signals from the S atoms contained in most proteins, the P atoms in nucleic acids or other light atoms derived from the solution used for crystallization. These signals are very weak and careful data collection is required, which makes this method very difficult. One way to enhance the anomalous signal is to use long-wavelength X-rays; however, these wavelengths are more strongly absorbed by the materials in the pathway. Therefore, a crystal-mounting platform for native SAD data collection that removes solution around the crystals has been developed. This platform includes a novel solution-free mounting tool and an automatic robot, which extracts the surrounding solution, flash-cools the crystal and inserts the loop into a UniPuck cassette for use in the synchrotron. Eight protein structures (including two new structures) have been successfully solved by the native SAD method from crystals prepared using this platform.

    DOI: 10.1107/S2059798320011584

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  • A straightforward approach to antibodies recognising cancer specific glycopeptidic neoepitopes 査読

    Hajime Wakui, Yoshikazu Tanaka, Toyoyuki Ose, Isamu Matsumoto, Koji Kato, Yao Min, Taro Tachibana, Masaharu Sato, Kentaro Naruchi, Fayna Garcia Martin, Hiroshi Hinou, Shin Ichiro Nishimura

    Chemical Science   11 ( 19 )   4999 - 5006   2020年5月

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    掲載種別:研究論文(学術雑誌)   出版者・発行元:Royal Society of Chemistry (RSC)  

    © The Royal Society of Chemistry 2020. Aberrantly truncated immatureO-glycosylation in proteins occurs in essentially all types of epithelial cancer cells, which was demonstrated to be a common feature of most adenocarcinomas and strongly associated with cancer proliferation and metastasis. Although extensive efforts have been made toward the development of anticancer antibodies targeting MUC1, one of the most studied mucins having cancer-relevant immatureO-glycans, no anti-MUC1 antibody recognises carbohydrates and the proximal MUC1 peptide region, concurrently. Here we present a general strategy that allows for the creation of antibodies interacting specifically with glycopeptidic neoepitopes by using homogeneous synthetic MUC1 glycopeptides designed for the streamlined process of immunization, antibody screening, three-dimensional structure analysis, epitope mapping and biochemical analysis. The X-ray crystal structure of the anti-MUC1 monoclonal antibody SN-101 complexed with the antigenic glycopeptide provides for the first time evidence that SN-101 recognises specifically the essential epitope by forming multiple hydrogen bonds both with the proximal peptide and GalNAc linked to the threonine residue, concurrently. Remarkably, the structure of the MUC1 glycopeptide in complex with SN-101 is identical to its solution NMR structure, an extended conformation induced by site-specific glycosylation. We demonstrate that this method accelerates dramatically the development of a new class of designated antibodies targeting a variety of “dynamic neoepitopes” elaborated by disease-specificO-glycosylation in the immunodominant mucin domains and mucin-like sequences found in intrinsically disordered regions of many proteins.

    DOI: 10.1039/d0sc00317d

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  • Structural basis for assembly and function of a diatom photosystem I-light-harvesting supercomplex. 査読 国際誌

    Ryo Nagao, Koji Kato, Kentaro Ifuku, Takehiro Suzuki, Minoru Kumazawa, Ikuo Uchiyama, Yasuhiro Kashino, Naoshi Dohmae, Seiji Akimoto, Jian-Ren Shen, Naoyuki Miyazaki, Fusamichi Akita

    Nature communications   11 ( 1 )   2481 - 2481   2020年5月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    Photosynthetic light-harvesting complexes (LHCs) play a pivotal role in collecting solar energy for photochemical reactions in photosynthesis. One of the major LHCs are fucoxanthin chlorophyll a/c-binding proteins (FCPs) present in diatoms, a group of organisms having important contribution to the global carbon cycle. Here, we report a 2.40-Å resolution structure of the diatom photosystem I (PSI)-FCPI supercomplex by cryo-electron microscopy. The supercomplex is composed of 16 different FCPI subunits surrounding a monomeric PSI core. Each FCPI subunit showed different protein structures with different pigment contents and binding sites, and they form a complicated pigment-protein network together with the PSI core to harvest and transfer the light energy efficiently. In addition, two unique, previously unidentified subunits were found in the PSI core. The structure provides numerous insights into not only the light-harvesting strategy in diatom PSI-FCPI but also evolutionary dynamics of light harvesters among oxyphototrophs.

    DOI: 10.1038/s41467-020-16324-3

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  • Structure of a cyanobacterial photosystem I surrounded by octadecameric IsiA antenna proteins. 査読 国際誌

    Fusamichi Akita, Ryo Nagao, Koji Kato, Yoshiki Nakajima, Makio Yokono, Yoshifumi Ueno, Takehiro Suzuki, Naoshi Dohmae, Jian-Ren Shen, Seiji Akimoto, Naoyuki Miyazaki

    Communications biology   3 ( 1 )   232 - 232   2020年5月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    Iron-stress induced protein A (IsiA) is a chlorophyll-binding membrane-spanning protein in photosynthetic prokaryote cyanobacteria, and is associated with photosystem I (PSI) trimer cores, but its structural and functional significance in light harvesting remains unclear. Here we report a 2.7-Å resolution cryo-electron microscopic structure of a supercomplex between PSI core trimer and IsiA from a thermophilic cyanobacterium Thermosynechococcus vulcanus. The structure showed that 18 IsiA subunits form a closed ring surrounding a PSI trimer core. Detailed arrangement of pigments within the supercomplex, as well as molecular interactions between PSI and IsiA and among IsiAs, were resolved. Time-resolved fluorescence spectra of the PSI-IsiA supercomplex showed clear excitation-energy transfer from IsiA to PSI, strongly indicating that IsiA functions as an energy donor, but not an energy quencher, in the supercomplex. These structural and spectroscopic findings provide important insights into the excitation-energy-transfer and subunit assembly mechanisms in the PSI-IsiA supercomplex.

    DOI: 10.1038/s42003-020-0949-6

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  • Crystal structures clarify cofactor binding of plant tyrosine decarboxylase. 査読 国際誌

    Hang Wang, Jian Yu, Yasuharu Satoh, Yusuke Nakagawa, Ryusuke Tanaka, Koji Kato, Min Yao

    Biochemical and biophysical research communications   523 ( 2 )   500 - 505   2020年3月

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    記述言語:英語  

    Plant tyrosine decarboxylase (TyrDC) is a group II pyridoxal 5'-phosphate (PLP)-dependent decarboxylase that mainly catalyzes the decarboxylation of tyrosine to tyramine. This is biologically important for diverting essential primary metabolites into secondary metabolic pathways. Intensive studies have characterized the effective of PLP-binding and the substrate specificity of mammalian 3,4-dihydroxyphenyl-l-alanine (Dopa) decarboxylases, a member of group II PLP-dependent decarboxylase. However, the characteristics of PLP binding and substrate specificity of plant TyrDCs remain unknown. In this study, we focus on the PLP binding manner, and determined the crystal structures of the apo and PLP binding form of type II TyrDC from Papaver somniferum (PsTyrDCII and PsTyrDCII-PLP). The structures showed that, unlike mammalian Dopa decarboxylase, the binding of PLP does not induce distinct conformational changes of PsTyrDCII regarding the overall structure, but the PLP binding pocket displays conformational changes at Phe124, His203 and Thr262. Combining structural comparation and the obtained biochemical findings, it is demonstrated that PsTyrDCII does not binds PLP tightly. Such characteristics of PLP binding may be required by its catalytic reaction and substrate binding. The activity of TyrDC probably regulated by the concentration of PLP in cells.

    DOI: 10.1016/j.bbrc.2019.12.077

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  • Structural basis for the adaptation and function of chlorophyll f in photosystem I. 査読 国際誌

    Koji Kato, Toshiyuki Shinoda, Ryo Nagao, Seiji Akimoto, Takehiro Suzuki, Naoshi Dohmae, Min Chen, Suleyman I Allakhverdiev, Jian-Ren Shen, Fusamichi Akita, Naoyuki Miyazaki, Tatsuya Tomo

    Nature communications   11 ( 1 )   238 - 238   2020年1月

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    記述言語:英語  

    Chlorophylls (Chl) play pivotal roles in energy capture, transfer and charge separation in photosynthesis. Among Chls functioning in oxygenic photosynthesis, Chl f is the most red-shifted type first found in a cyanobacterium Halomicronema hongdechloris. The location and function of Chl f in photosystems are not clear. Here we analyzed the high-resolution structures of photosystem I (PSI) core from H. hongdechloris grown under white or far-red light by cryo-electron microscopy. The structure showed that, far-red PSI binds 83 Chl a and 7 Chl f, and Chl f are associated at the periphery of PSI but not in the electron transfer chain. The appearance of Chl f is well correlated with the expression of PSI genes induced under far-red light. These results indicate that Chl f functions to harvest the far-red light and enhance uphill energy transfer, and changes in the gene sequences are essential for the binding of Chl f.

    DOI: 10.1038/s41467-019-13898-5

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  • Crystallographic analysis of Eisenia hydrolysis-enhancing protein using a long wavelength for native-SAD phasing. 査読 国際誌

    Xiaomei Sun, Yuxin Ye, Naofumi Sakurai, Koji Kato, Keizo Yuasa, Akihiko Tsuji, Min Yao

    Acta crystallographica. Section F, Structural biology communications   76 ( Pt 1 )   20 - 24   2020年1月

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    記述言語:英語  

    Eisenia hydrolysis-enhancing protein (EHEP), which is a novel protein that has been identified in Aplysia kurodai, protects β-glucosidases from phlorotannin inhibition to facilitate the production of glucose from the laminarin abundant in brown algae. Hence, EHEP has attracted attention for its potential applications in producing biofuel from brown algae. In this study, EHEP was purified from the natural digestive fluid of A. kurodai and was crystallized using the sitting-drop vapor-diffusion method. Native and SAD (single-wavelength anomalous diffraction) data sets were successfully collected at resolutions of 1.20 and 2.48 Å using wavelengths of 1.0 and 2.1 Å, respectively, from crystals obtained in initial screening. The crystals belonged to space group P212121 and contained one EHEP molecule in the asymmetric unit. All 20 S-atom sites in EHEP were located and the phases were determined by the SAD method using the S atoms in the natural protein as anomalous scatterers (native-SAD). After phase improvement, interpretable electron densities were obtained and 58% of the model was automatically built.

    DOI: 10.1107/S2053230X19016716

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  • Structure of a cyanobacterial photosystem I tetramer revealed by cryo-electron microscopy. 査読 国際誌

    Koji Kato, Ryo Nagao, Tian-Yi Jiang, Yoshifumi Ueno, Makio Yokono, Siu Kit Chan, Mai Watanabe, Masahiko Ikeuchi, Jian-Ren Shen, Seiji Akimoto, Naoyuki Miyazaki, Fusamichi Akita

    Nature communications   10 ( 1 )   4929 - 4929   2019年10月

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    記述言語:英語  

    Photosystem I (PSI) functions to harvest light energy for conversion into chemical energy. The organisation of PSI is variable depending on the species of organism. Here we report the structure of a tetrameric PSI core isolated from a cyanobacterium, Anabaena sp. PCC 7120, analysed by single-particle cryo-electron microscopy (cryo-EM) at 3.3 Å resolution. The PSI tetramer has a C2 symmetry and is organised in a dimer of dimers form. The structure reveals interactions at the dimer-dimer interface and the existence of characteristic pigment orientations and inter-pigment distances within the dimer units that are important for unique excitation energy transfer. In particular, characteristic residues of PsaL are identified to be responsible for the formation of the tetramer. Time-resolved fluorescence analyses showed that the PSI tetramer has an enhanced excitation-energy quenching. These structural and spectroscopic findings provide insights into the physiological significance of the PSI tetramer and evolutionary changes of the PSI organisations.

    DOI: 10.1038/s41467-019-12942-8

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  • The pH-dependent conformational change of eukaryotic translation initiation factor 5: Insights into partner-binding manner. 査読

    Ye Y, Chen M, Kato K, Yao M

    Biochemical and biophysical research communications   519 ( 1 )   186 - 191   2019年10月

  • Structural basis for energy harvesting and dissipation in a diatom PSII–FCPII supercomplex 査読

    Ryo Nagao, Koji Kato, Takehiro Suzuki, Kentaro Ifuku, Ikuo Uchiyama, Yasuhiro Kashino, Naoshi Dohmae, Seiji Akimoto, Jian-Ren Shen, Naoyuki Miyazaki, Fusamichi Akita

    Nature Plants   5 ( 8 )   890 - 901   2019年8月

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    掲載種別:研究論文(学術雑誌)   出版者・発行元:Springer Science and Business Media LLC  

    DOI: 10.1038/s41477-019-0477-x

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    その他リンク: http://www.nature.com/articles/s41477-019-0477-x

  • Neutron crystallographic study of heterotrimeric glutamine amidotransferase CAB. 査読

    Li L, Adachi M, Yu J, Kato K, Shinoda A, Ostermann A, Schrader TE, Ose T, Yao M

    Acta crystallographica. Section F, Structural biology communications   75 ( Pt 3 )   193 - 196   2019年3月

  • Function and structure of GH13_31 α-glucosidase with high α-(1→4)-glucosidic linkage specificity and transglucosylation activity. 査読

    Auiewiriyanukul W, Saburi W, Kato K, Yao M, Mori H

    FEBS letters   2018年6月

  • The C-terminal helix of ribosomal P stalk recognizes a hydrophobic groove of elongation factor 2 in a novel fashion. 査読

    Tanzawa T, Kato K, Girodat D, Ose T, Kumakura Y, Wieden HJ, Uchiumi T, Tanaka I, Yao M

    Nucleic acids research   46 ( 6 )   3232 - 3244   2018年4月

  • Biochemical and structural characterization of Marinomonas mediterranea D-mannose isomerase Marme_2490 phylogenetically distant from known enzymes 査読

    Wataru Saburi, Nongluck Jaito, Koji Kato, Yuka Tanaka, Min Yao, Haruhide Mori

    Biochimie   144   63 - 73   2018年1月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Elsevier B.V.  

    D-Mannose isomerase (MI) reversibly isomerizes D-mannose to D-fructose, and is attractive for producing D-mannose from inexpensive D-fructose. It belongs to the N-acylglucosamine 2-epimerase (AGE) superfamily along with AGE, cellobiose 2-epimerase (CE), and aldose-ketose isomerase (AKI). In this study, Marinomonas mediterranea Marme_2490, showing low sequence identity with any known enzymes, was found to isomerize D-mannose as its primary substrate. Marme_2490 also isomerized D-lyxose and 4-OH D-mannose derivatives (D-talose and 4-O-monosaccharyl-D-mannose). Its activity for D-lyxose is known in other D-mannose isomerizing enzymes, such as MI and AKI, but we identified, for the first time, its activity for 4-OH D-mannose derivatives. Marme_2490 did not isomerize D-glucose, as known MIs do not, while AKI isomerizes both D-mannose and D-glucose. Thus, Marme_2490 was concluded to be an MI. The initial and equilibrium reaction products were analyzed by NMR to illuminate mechanistic information regarding the Marme_2490 reaction. The analysis of the initial reaction product revealed that β-D-mannose was formed. In the analysis of the equilibrated reaction products in D2O, signals of 2-H of D-mannose and 1-H of D-fructose were clearly detected. This indicates that these protons are not substituted with deuterium from D2O and Marme_2490 catalyzes the intramolecular proton transfer between 1-C and 2-C. The crystal structure of Marme_2490 in a ligand-free form was determined and found that Marme_2490 is formed by an (α/α)6-barrel, which is commonly observed in AGE superfamily enzymes. Despite diverse reaction specificities, the orientations of residues involved in catalysis and substrate binding by Marme_2490 were similar to those in both AKI (Salmonella enterica AKI) and epimerase (Rhodothermus marinus CE). The Marme_2490 structure suggested that the α7→α8 and α11→α12 loops of the catalytic domain participated in the formation of an open substrate-binding site to provide sufficient space to bind 4-OH D-mannose derivatives.

    DOI: 10.1016/j.biochi.2017.10.016

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  • Structural basis for tRNA-dependent cysteine biosynthesis 査読

    Meirong Chen, Koji Kato, Yume Kubo, Yoshikazu Tanaka, Yuchen Liu, Feng Long, William B. Whitman, Pascal Lill, Christos Gatsogiannis, Stefan Raunser, Nobutaka Shimizu, Akira Shinoda, Akiyoshi Nakamura, Isao Tanaka, Min Yao

    NATURE COMMUNICATIONS   8 ( 1 )   1521   2017年11月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:NATURE PUBLISHING GROUP  

    Cysteine can be synthesized by tRNA-dependent mechanism using a two-step indirect pathway, where O-phosphoseryl-tRNA synthetase (SepRS) catalyzes the ligation of a mismatching O-phosphoserine (Sep) to tRNA(Cys) followed by the conversion of tRNA-bounded Sep into cysteine by Sep-tRNA:Cys-tRNA synthase (SepCysS). In ancestral methanogens, a third protein SepCysE forms a bridge between the two enzymes to create a ternary complex named the transsulfursome. By combination of X-ray crystallography, SAXS and EM, together with biochemical evidences, here we show that the three domains of SepCysE each bind SepRS, SepCysS, and tRNA(Cys), respectively, which mediates the dynamic architecture of the transsulfursome and thus enables a global long-range channeling of tRNA(Cys) between SepRS and SepCysS distant active sites. This channeling mechanism could facilitate the consecutive reactions of the two-step indirect pathway of Cys-tRNA(Cys) synthesis (tRNA-dependent cysteine biosynthesis) to prevent challenge of translational fidelity, and may reflect the mechanism that cysteine was originally added into genetic code.

    DOI: 10.1038/s41467-017-01543-y

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  • A novel glycoside hydrolase family 97 enzyme: Bifunctional β-l-arabinopyranosidase/α-galactosidase from Bacteroides thetaiotaomicron. 査読

    Kikuchi A, Okuyama M, Kato K, Osaki S, Ma M, Kumagai Y, Matsunaga K, Klahan P, Tagami T, Yao M, Kimura A

    Biochimie   142   41 - 50   2017年11月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    DOI: 10.1016/j.biochi.2017.08.003

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  • Crystal structure of the flexible tandem repeat domain of bacterial cellulose synthesis subunit C 査読

    Shingo Nojima, Ayumi Fujishima, Koji Kato, Kayoko Ohuchi, Nobutaka Shimizu, Kento Yonezawa, Kenji Tajima, Min Yao

    SCIENTIFIC REPORTS   7 ( 1 )   13018   2017年10月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:NATURE PUBLISHING GROUP  

    Bacterial cellulose (BC) is synthesized and exported through the cell membrane via a large protein complex (terminal complex) that consists of three or four subunits. BcsC is a little-studied subunit considered to export BC to the extracellular matrix. It is predicted to have two domains: a tetratrico peptide repeat (TPR) domain and a beta-barrelled outer membrane domain. Here we report the crystal structure of the N-terminal part of BcsC-TPR domain (Asp24-Arg272) derived from Enterobacter CJF-002. Unlike most TPR-containing proteins which have continuous TPR motifs, this structure has an extra a-helix between two clusters of TPR motifs. Five independent molecules in the crystal had three different conformations that varied at the hinge of the inserted a-helix. Such structural feature indicates that the inserted a-helix confers flexibility to the chain and changes the direction of the TPR super-helix, which was also suggested by structural analysis of BcsC-TPR (Asp24-Leu664) in solution by size exclusion chromatography-small-angle X-ray scattering. The flexibility at the a-helical hinge may play important role for exporting glucan chains.

    DOI: 10.1038/s41598-017-12530-0

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  • Crystallographic analysis of a subcomplex of the transsulfursome with tRNA for Cys-tRNA(Cys) synthesis 査読

    Meirong Chen, Yuto Nakazawa, Yume Kubo, Nozomi Asano, Koji Kato, Isao Tanaka, Min Yao

    ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS   72 ( Pt 7 )   569 - 572   2016年7月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:INT UNION CRYSTALLOGRAPHY  

    In most organisms, Cys-tRNA(Cys) is directly synthesized by cysteinyl-tRNA synthetase (CysRS). Many methanogenic archaea, however, use a two-step, indirect pathway to synthesize Cys-tRNA(Cys) owing to a lack of CysRS and cysteine-biosynthesis systems. This reaction is catalyzed by O-phosphoseryl-tRNA synthetase (SepRS), Sep-tRNA:Cys-tRNA synthase (SepCysS) and SepRS/ SepCysS pathway enhancer (SepCysE) as the transsulfursome, in which SepCysE connects both SepRS and SepCysS. On the transsulfursome, SepRS first ligates an O-phosphoserine to tRNA(Cys), and the mischarged intermediate Sep-tRNA(Cys) is then transferred to SepCysS, where it is further modified to Cys-tRNA(Cys). In this study, a subcomplex of the transsulfursome with tRNA(Cys) (SepCysS-SepCysE-tRNA(Cys)), which is involved in the second reaction step of the indirect pathway, was constructed and then crystallized. The crystals diffracted X-rays to a resolution of 2.6 angstrom and belonged to space group P6(5)22, with unit-cell parameters a = b = 107.2, c = 551.1 angstrom. The structure determined by molecular replacement showed that the complex consists of a SepCysS dimer, a SepCysE dimer and one tRNA(Cys) in the asymmetric unit.

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  • Template-dependent nucleotide addition in the reverse (3'-5') direction by Thg1-like protein 査読

    Shoko Kimura, Tateki Suzuki, Meirong Chen, Koji Kato, Jian Yu, Akiyoshi Nakamura, Isao Tanaka, Min Yao

    SCIENCE ADVANCES   2 ( 3 )   e1501397   2016年3月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER ASSOC ADVANCEMENT SCIENCE  

    Thg1-like protein (TLP) catalyzes the addition of a nucleotide to the 5'-end of truncated transfer RNA(tRNA) species in a Watson-Crick template-dependent manner. The reaction proceeds in two steps: the activation of the 5'-end by adenosine 5'-triphosphate (ATP)/guanosine 5'-triphosphate (GTP), followed by nucleotide addition. Structural analyses of the TLP and its reaction intermediates have revealed the atomic detail of the template-dependent elongation reaction in the 3'-5' direction. The enzyme creates two substrate binding sites for the first-and second-step reactions in the vicinity of one reaction center consisting of two Mg2+ ions, and the two reactions are executed at the same reaction center in a stepwise fashion. When the incoming nucleotide is bound to the second binding site with Watson-Crick hydrogen bonds, the 3'-OH of the incoming nucleotide and the 5'-triphosphate of the tRNA are moved to the reaction center where the first reaction has occurred. That the 3'-5' elongation enzyme performs this elaborate two-step reaction in one catalytic center suggests that these two reactions have been inseparable throughout the process of protein evolution. Although TLP and Thg1 have similar tetrameric organization, the tRNA binding mode of TLP is different from that of Thg1, a tRNA(His)-specific G(-1) addition enzyme. Each tRNA(His) binds to three of the four Thg1 tetramer subunits, whereas in TLP, tRNA only binds to a dimer interface and the elongation reaction is terminated by measuring the accepter stem length through the flexible beta-hairpin. Furthermore, mutational analyses show that tRNA(His) is bound to TLP in a similar manner as Thg1, thus indicating that TLP has a dual binding mode.

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  • Structural insights into the difference in substrate recognition of two mannoside phosphorylases from two GH130 subfamilies 査読

    Yuxin Ye, Wataru Saburi, Rei Odaka, Koji Kato, Naofumi Sakurai, Keisuke Komoda, Mamoru Nishimoto, Motomitsu Kitaoka, Haruhide Mori, Min Yao

    FEBS LETTERS   590 ( 6 )   828 - 837   2016年3月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:WILEY-BLACKWELL  

    In Ruminococcus albus, 4-Omicron-beta-D-mannosyl-D-glucose phosphorylase (RaMP1) and beta-(1,4)-mannooligosaccharide phosphorylase (RaMP2) belong to two subfamilies of glycoside hydrolase family 130. The two enzymes phosphorolyze beta-mannosidic linkages at the nonreducing ends of their substrates, and have substantially diverse substrate specificity. The differences in their mechanism of substrate binding have not yet been fully clarified. In the present study, we report the crystal structures of RaMP1 with/without 4-Omicron-beta-D-mannosyl-D-glucose and RaMP2 with/without beta-(1 -> 4)-mannobiose. The structures of the two enzymes differ at the +1 subsite of the substrate-binding pocket. Three loops are proposed to determine the different substrate specificities. One of these loops is contributed from the adjacent molecule of the oligomer structure. In RaMP1, His245 of loop 3 forms a hydrogen-bond network with the substrate through a water molecule, and is indispensible for substrate binding.

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  • Crystal Structure of the 3.8-MDa Respiratory Supermolecule Hemocyanin at 3.0 Å Resolution. 査読

    Gai Z, Matsuno A, Kato K, Kato S, Khan MR, Shimizu T, Yoshioka T, Kato Y, Kishimura H, Kanno G, Miyabe Y, Terada T, Tanaka Y, Yao M

    Structure (London, England : 1993)   23 ( 12 )   2204 - 2212   2015年12月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)  

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  • Structural basis for pore-forming mechanism of staphylococcal α-hemolysin. 査読

    Sugawara T, Yamashita D, Kato K, Peng Z, Ueda J, Kaneko J, Kamio Y, Tanaka Y, Yao M

    Toxicon : official journal of the International Society on Toxinology   108   226 - 231   2015年12月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    DOI: 10.1016/j.toxicon.2015.09.033

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  • Structural analysis of the α-glucosidase HaG provides new insights into substrate specificity and catalytic mechanism. 査読

    Shen X, Saburi W, Gai Z, Kato K, Ojima-Kato T, Yu J, Komoda K, Kido Y, Matsui H, Mori H, Yao M

    Acta crystallographica. Section D, Biological crystallography   71 ( Pt 6 )   1382 - 1391   2015年6月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)  

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  • Crystallization and preliminary X-ray crystallographic study of a 3.8-MDa respiratory supermolecule hemocyanin 査読

    Asuka Matsuno, Zuoqi Gai, Miyuki Tanaka, Koji Kato, Sanae Kato, Tsuyoshi Katoh, Takeshi Shimizu, Takeya Yoshioka, Hideki Kishimura, Yoshikazu Tanaka, Min Yao

    JOURNAL OF STRUCTURAL BIOLOGY   190 ( 3 )   379 - 382   2015年6月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ACADEMIC PRESS INC ELSEVIER SCIENCE  

    Many molluscs transport oxygen using a very large cylindrical multimeric copper-containing protein named hemocyanin. The molluscan hemocyanin forms a decamer (cephalopods) or multidecamer (gastropods) of approximately 330-450 kDa subunits, resulting in a molecular mass >3.3 MDa. Therefore, molluscan hemocyanin is one of the largest proteins. The reason why these organisms use such a large supermolecule for oxygen transport remains unclear. Atomic-resolution X-ray crystallographic analysis is necessary to unveil the detailed molecular structure of this mysterious large molecule. However, its propensity to dissociate in solution has hampered the crystallization of its intact form. In the present study, we successfully obtained the first crystals of an intact decameric molluscan hemocyanin. The diffraction dataset at 3.0-angstrom resolution was collected by merging the datasets of two isomorphic crystals. Electron microscopy analysis of the dissolved crystals revealed cylindrical particles. Furthermore, self-rotation function analysis clearly showed the presence of a fivefold symmetry with several twofold symmetries perpendicular to the fivefold axis. The absorption spectrum of the crystals showed an absorption peak around 345 nm. These results indicated that the crystals contain intact hemocyanin decamers in the oxygen-bound form. (C) 2015 Elsevier Inc. All rights reserved.

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  • Structural and functional analysis of the Rpf2-Rrs1 complex in ribosome biogenesis 査読

    Nozomi Asano, Koji Kato, Akiyoshi Nakamura, Keisuke Komoda, Isao Tanaka, Min Yao

    NUCLEIC ACIDS RESEARCH   43 ( 9 )   4746 - 4757   2015年5月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:OXFORD UNIV PRESS  

    Proteins Rpf2 and Rrs1 are required for 60S ribosomal subunit maturation. These proteins are necessary for the recruitment of three ribosomal components (5S ribosomal RNA [rRNA], RpL5 and RpL11) to the 90S ribosome precursor and subsequent 27SB pre-rRNA processing. Here we present the crystal structure of the Aspergillus nidulans (An) Rpf2-Rrs1 core complex. The core complex contains the tightly interlocked N-terminal domains of Rpf2 and Rrs1. The Rpf2 N-terminal domain includes a Brix domain characterized by similar N-and C-terminal architecture. The long alpha-helix of Rrs1 joins the C-terminal half of the Brix domain as if it were part of a single molecule. The conserved proline-rich linker connecting the N- and C-terminal domains of Rrs1 wrap around the side of Rpf2 and anchor the C-terminal domain of Rrs1 to a specific site on Rpf2. In addition, gel shift analysis revealed that the Rpf2-Rrs1 complex binds directly to 5S rRNA. Further analysis of Rpf2-Rrs1 mutants demonstrated that Saccha-romyces cerevisiae Rpf2 R236 (corresponds to R238 of AnRpf2) plays a significant role in this binding. Based on these studies and previous reports, we have proposed a model for ribosomal component recruitment to the 90S ribosome precursor.

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  • Structural insights into the catalytic reaction that is involved in the reorientation of Trp238 at the substrate-binding site in GH13 dextran glucosidase 査読

    Momoko Kobayashi, Wataru Saburi, Daichi Nakatsuka, Hironori Hondoh, Koji Kato, Masayuki Okuyama, Haruhide Mori, Atsuo Kimura, Min Yao

    FEBS LETTERS   589 ( 4 )   484 - 489   2015年2月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

    Streptococcus mutans dextran glucosidase (SmDG) belongs to glycoside hydrolase family 13, and catalyzes both the hydrolysis of substrates such as isomaltooligosaccharides and subsequent transglucosylation to form alpha-(1 -> 6)-glucosidic linkage at the substrate non-reducing ends. Here, we report the 2.4 angstrom resolution crystal structure of glucosyl-enzyme intermediate of SmDG. In the obtained structure, the Trp238 side-chain that constitutes the substrate-binding site turned away from the active pocket, concurrently with conformational changes of the nucleophile and the acid/base residues. Different conformations of Trp238 in each reaction stage indicated its flexibility. Considering the results of kinetic analyses, such flexibility may reflect a requirement for the reaction mechanism of SmDG. (C) 2015 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

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  • Structure of the Pseudomonas aeruginosa transamidosome reveals unique aspects of bacterial tRNA-dependent asparagine biosynthesis 査読

    Tateki Suzuki, Akiyoshi Nakamura, Koji Kato, Dieter Soell, Isao Tanaka, Kelly Sheppard, Min Yao

    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA   112 ( 2 )   382 - 387   2015年1月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:NATL ACAD SCIENCES  

    Many prokaryotes lack a tRNA synthetase to attach asparagine to its cognate tRNA(Asn), and instead synthesize asparagine from tRNA(Asn)-bound aspartate. This conversion involves two enzymes: a nondiscriminating aspartyl-tRNA synthetase (ND-AspRS) that forms Asp-tRNA(Asn), and a heterotrimeric amidotransferase GatCAB that amidates Asp-tRNA(Asn) to form Asn-tRNA(Asn) for use in protein synthesis. ND-AspRS, GatCAB, and tRNAAsn may assemble in an similar to 400-kDa complex, known as the Asn-transamidosome, which couples the two steps of asparagine biosynthesis in space and time to yield Asn-tRNA(Asn). We report the 3.7-angstrom resolution crystal structure of the Pseudomonas aeruginosa A-transamidosome, which represents the most common machinery for asparagine biosynthesis in bacteria. We show that, in contrast to a previously described archaeal-type transamidosome, a bacteria-specific GAD domain of ND-AspRS provokes a principally new architecture of the complex. Both tRNA(Asn) molecules in the transamidosome simultaneously serve as substrates and scaffolds for the complex assembly. This architecture rationalizes an elevated dynamic and a greater turnover of ND-AspRS within bacterial-type transamidosomes, and possibly may explain a different evolutionary pathway of GatCAB in organisms with bacterial-type vs. archaeal-type Asn-transamidosomes. Importantly, because the two-step pathway for Asn-tRNA(Asn) formation evolutionarily preceded the direct attachment of Asn to tRNA(Asn), our structure also may reflect the mechanism by which asparagine was initially added to the genetic code.

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  • Crystallization and preliminary X-ray crystallographic analysis of ribosome assembly factors: The Rpf2-Rrs1 complex 査読

    Nozomi Asano, Akiyoshi Nakamura, Keisuke Komoda, Koji Kato, Isao Tanaka, Min Yao

    Acta Crystallographica Section F:Structural Biology Communications   70   1649 - 1652   2014年12月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:International Union of Crystallography  

    Rpf2 and Rrs1 are essential proteins for ribosome biogenesis. These proteins form a complex (the Rpf2-subcomplex) with 5S rRNA and two ribosomal proteins (L5 and L11). This complex is recruited to the ribosome precursor (the 90S pre-ribosome). This recruitment is necessary for the maturation of 25S rRNA. Genetic depletion of Rpf2 and Rrs1 results in accumulation of the 25S rRNA precursor. In this study, Rpf2 and Rrs1 from Aspergillus nidulans were co-overexpressed in Escherichia coli, purified and crystallized. Subsequent analysis revealed that these crystals contained the central core region of the complex consisting of both N-terminal domains. X-ray diffraction data were collected to 2.35Å resolution. Preliminary analysis revealed that the crystals belonged to space group P212121, with unit-cell parameters a = 54.1, b = 123.3, c = 133.8Å. There are two complexes in the asymmetric unit. Structure determination using selenomethionine-labelled protein is in progress.

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  • Crystallization and preliminary X-ray crystallographic analysis of ribosome assembly factors: the Rpf2-Rrs1 complex 査読

    Nozomi Asano, Akiyoshi Nakamura, Keisuke Komoda, Koji Kato, Isao Tanaka, Min Yao

    ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS   70 ( Pt 12 )   1649 - 1652   2014年12月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:WILEY-BLACKWELL  

    Rpf2 and Rrs1 are essential proteins for ribosome biogenesis. These proteins form a complex (the Rpf2-subcomplex) with 5S rRNA and two ribosomal proteins (L5 and L11). This complex is recruited to the ribosome precursor (the 90S pre-ribosome). This recruitment is necessary for the maturation of 25S rRNA. Genetic depletion of Rpf2 and Rrs1 results in accumulation of the 25S rRNA precursor. In this study, Rpf2 and Rrs1 from Aspergillus nidulans were co-overexpressed in Escherichia coli, purified and crystallized. Subsequent analysis revealed that these crystals contained the central core region of the complex consisting of both N-terminal domains. X-ray diffraction data were collected to 2.35 angstrom resolution. Preliminary analysis revealed that the crystals belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 54.1, b = 123.3, c = 133.8 angstrom. There are two complexes in the asymmetric unit. Structure determination using selenomethionine-labelled protein is in progress.

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  • Determination of damage-free crystal structure of an X-ray-sensitive protein using an XFEL 査読

    Kunio Hirata, Kyoko Shinzawa-Itoh, Naomine Yano, Shuhei Takemura, Koji Kato, Miki Hatanaka, Kazumasa Muramoto, Takako Kawahara, Tomitake Tsukihara, Eiki Yamashita, Kensuke Tono, Go Ueno, Takaaki Hikima, Hironori Murakami, Yuichi Inubushi, Makina Yabashi, Tetsuya Ishikawa, Masaki Yamamoto, Takashi Ogura, Hiroshi Sugimoto, Jian-Ren Shen, Shinya Yoshikawa, Hideo Ago

    NATURE METHODS   11 ( 7 )   734 - U174   2014年7月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:NATURE PUBLISHING GROUP  

    We report a method of femtosecond crystallography for solving radiation damage-free crystal structures of large proteins at sub-angstrom spatial resolution, using a large single crystal and the femtosecond pulses of an X-ray free-electron laser (XFEL). We demonstrated the performance of the method by determining a 1.9-angstrom radiation damage-free structure of bovine cytochrome c oxidase, a large (420-kDa), highly radiation-sensitive membrane protein.

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  • Effective Pumping Proton Collection Facilitated by a Copper Site (CUB) of Bovine Heart Cytochrome c Oxidase, Revealed by a Newly Developed Time-resolved Infrared System 査読

    Minoru Kubo, Satoru Nakashima, Satoru Yamaguchi, Takashi Ogura, Masao Mochizuki, Jiyoung Kang, Masaru Tateno, Kyoko Shinzawa-Itoh, Koji Kato, Shinya Yoshikawa

    JOURNAL OF BIOLOGICAL CHEMISTRY   288 ( 42 )   30259 - 30269   2013年10月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC  

    Background: Cytochrome c oxidase reduces O-2 coupled with proton pumping. Results: A newly developed time-resolved infrared system reveals transient conformational changes in the proton-pumping pathway upon CO binding to Cu-B in the O-2 reduction site. Conclusion: Cu-B promotes proton collection and effective blockage of back-leak of pumping protons. Significance: These critical findings in bioenergetics stimulate the new infrared approach for mechanistic investigation of any other protein function.
    X-ray structural and mutational analyses have shown that bovine heart cytochrome c oxidase (CcO) pumps protons electrostatically through a hydrogen bond network using net positive charges created upon oxidation of a heme iron (located near the hydrogen bond network) for O-2 reduction. Pumping protons are transferred by mobile water molecules from the negative side of the mitochondrial inner membrane through a water channel into the hydrogen bond network. For blockage of spontaneous proton back-leak, the water channel is closed upon O-2 binding to the second heme (heme a(3)) after complete collection of the pumping protons in the hydrogen bond network. For elucidation of the structural bases for the mechanism of the proton collection and timely closure of the water channel, conformational dynamics after photolysis of CO (an O-2 analog)-bound CcO was examined using a newly developed time-resolved infrared system feasible for accurate detection of a single C=O stretch band of -helices of CcO in H2O medium. The present results indicate that migration of CO from heme a(3) to Cu-B in the O-2 reduction site induces an intermediate state in which a bulge conformation at Ser-382 in a transmembrane helix is eliminated to open the water channel. The structural changes suggest that, using a conformational relay system, including Cu-B, O-2, heme a(3), and two helix turns extending to Ser-382, Cu-B induces the conformational changes of the water channel that stimulate the proton collection, and senses complete proton loading into the hydrogen bond network to trigger the timely channel closure by O-2 transfer from Cu-B to heme a(3).

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  • 精密結晶構造解析によるチトクロム酸化酵素の反応機構の研究

    矢野 直峰, 新澤-伊藤 恭子, 畑中 美紀, 武村 修平, 藤澤 秀徳, 村本 和優, 加藤 公児, 山下 栄樹, 吉川 信也, 月原 冨武

    日本結晶学会誌   54 ( 0 )   s19 - s19   2012年

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    記述言語:日本語   出版者・発行元:日本結晶学会  

    DOI: 10.5940/jcrsj.54.s19

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  • Elucidation of the function based on the whole structure of rat liver vault, the largest ribonucleo-protein particle 査読

    Hideaki Tanaka, Koji Kato, Tomoyuki Sumizawa, Eiki Yamashita

    Seikagaku   83 ( 5 )   392 - 395   2011年

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    記述言語:日本語   掲載種別:研究論文(学術雑誌)   出版者・発行元:5  

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  • ラット肝由来の巨大なRNAタンパク質複合体vaultのX線結晶構造

    住澤知之, 加藤公児, 田中秀明

    J UOEH Univ Occup Environ Health   32 ( 1 )   113   2010年3月

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  • 25.ラット肝由来の巨大なRNAタンパク質複合体vaultのX線結晶構造(第27回産業医科大学学会総会 学術講演会記録)

    住澤 知之, 加藤 公児, 田中 秀明

    産業医科大学雑誌   32 ( 1 )   2010年3月

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    記述言語:日本語   出版者・発行元:産業医科大学学会  

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  • 分子量が1000万にも及ぶ生体内巨大分子に対する構造解析

    山下 栄樹, 加藤 公児, 田中 秀明

    放射光   22 ( 6 )   284 - 291   2009年11月

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    記述言語:日本語   出版者・発行元:日本放射光学会  

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  • ラット肝臓由来ボルトの3.5Å分解能での構造解析 招待

    加藤公児, 田中秀明, 月原冨武

    2009年10月

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  • [X-ray structure of vault: the largest ribonucleoprotein complex]. 査読

    Kato K, Tanaka H

    Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme   54   1159 - 1165   2009年7月

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  • 分子量約1000万の巨大粒子 vault のX線結晶構造解析

    田中 秀明, 加藤 公児, 山下 栄樹

    日本結晶学会誌   51 ( 3 )   189 - 194   2009年6月

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    記述言語:日本語   出版者・発行元:日本結晶学会  

    Vaults are among the largest cytoplasmic ribonucleoprotein particles and are found in numerous eukaryotic species. Although roles in multidrug resistance and innate immunity have been suggested, the cellular function remains unclear. We have determined the X-ray structure of rat liver vault at 3.5 Å resolution. A vault particle shell was composed of 78 MVP (Major vault protein) chains with 39-fold dihedral symmetry. The shoulder domain of MVP is structurally similar to SPFH (stomatin/prohibitin/flotillin/HflK/C) domain involved in lipid raft association.

    DOI: 10.5940/jcrsj.51.189

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  • X-ray crystal structural determination of rat vault, a large nucleoprotein complex at 3.5Å resolution. 招待

    H. Tanaka, K. Kato, E. Yamashita, T. Sumizawa, Y. Zhou, M. Yao, K. Iwasaki, M. Yoshimura, T. Tsukihara

    2009年3月

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  • The Structure of Rat Liver Vault at 3.5 Angstrom Resolution 査読

    Hideaki Tanaka, Koji Kato, Eiki Yamashita, Tomoyuki Sumizawa, Yong Zhou, Min Yao, Kenji Iwasaki, Masato Yoshimura, Tomitake Tsukihara

    SCIENCE   323 ( 5912 )   384 - 388   2009年1月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER ASSOC ADVANCEMENT SCIENCE  

    Vaults are among the largest cytoplasmic ribonucleoprotein particles and are found in numerous eukaryotic species. Roles in multidrug resistance and innate immunity have been suggested, but the cellular function remains unclear. We have determined the x-ray structure of rat liver vault at 3.5 angstrom resolution and show that the cage structure consists of a dimer of half-vaults, with each half-vault comprising 39 identical major vault protein (MVP) chains. Each MVP monomer folds into 12 domains: nine structural repeat domains, a shoulder domain, a cap-helix domain, and a cap-ring domain. Interactions between the 42-turn-long cap-helix domains are key to stabilizing the particle. The shoulder domain is structurally similar to a core domain of stomatin, a lipid-raft component in erythrocytes and epithelial cells.

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  • Purification, characterization, and sequencing of antimicrobial peptides, Cy-AMP1, Cy-AMP2, and Cy-AMP3, from the Cycad (Cycas reuoluta) seeds 査読

    Seiya Yokoyama, Kouji Kato, Atsuko Koba, Yuji Minami, Keiichi Watanabec, Fumio Yagi

    PEPTIDES   29 ( 12 )   2110 - 2117   2008年12月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE INC  

    Novel antimicrobial peptides (AMP), designated Cy-AMP1, Cy-AMP2, and Cy-AMP3, were purified from seeds of the cycad (Cycas revoluta) by a CM cellulofine column, ion-exchange HPLC on SP COSMOGEL, and reverse-phase HPLC. They had molecular masses of 4583.2 Da, 4568.9 Da and 9275.8 Da, respectively, by MALDI-TOF MS analysis. Half of the amino acid residues of Cy-AMP1 and Cy-AMP2 were cysteine, glycine and proline, and their sequences were similar. The sequence of Cy-AMP3 showed high homology to various lipid transfer proteins. For Cy-AMP1 and Cy-AMP2, the concentrations of peptides required for 50% inhibition (IC(50)) of the growth of plant pathogenic fungi, Gram-positive and Gram-negative bacteria were 7.0-8.9 mu g/ml. The Cy-AMP3 had weak antimicrobial activity. The structural and antimicrobial characteristics of Cy-AMP1 and Cy-AMP2 indicated that they are a novel type of antimicrobial peptide belonging to a plant defensin family. (c) 2008 Elsevier Inc. All rights reserved.

    DOI: 10.1016/j.peptides.2008.08.007

    Web of Science

    PubMed

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  • X-ray structure of the vault purified from rat liver 招待

    田中秀明, 加藤公児, 住澤知之, 山下栄樹, 吉村政人, 周勇, 姚閔, 岩崎憲治, 月原冨武

    2008年12月

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    記述言語:日本語   掲載種別:研究論文(その他学術会議資料等)  

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  • A vault ribonucleoprotein particle exhibiting 39-fold dihedral symmetry 査読

    Koji Kato, Hideaki Tanaka, Tomoyuki Sumizawa, Masato Yoshimura, Eiki Yamashita, Kenji Iwasaki, Tomitake Tsukihara

    ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY   64   525 - 531   2008年5月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:BLACKWELL PUBLISHING  

    Vault is a 12.9 MDa ribonucleoprotein particle with a barrel-like shape, two protruding caps and an invaginated waist structure that is highly conserved in a wide variety of eukaryotes. Multimerization of the major vault protein (MVP) is sufficient to assemble the entire exterior shell of the barrel-shaped vault particle. Multiple copies of two additional proteins, vault poly(ADP-ribose) polymerase (VPARP) and telomerase-associated protein 1 (TEP1), as well as a small vault RNA (vRNA), are also associated with vault. Here, the crystallization of vault particles is reported. The crystals belong to space group C2, with unit-cell parameters a = 708.0, b = 385.0, c = 602.9 angstrom, beta = 124.8 degrees. Rotational symmetry searches based on the R factor and correlation coefficient from noncrystallographic symmetry (NCS) averaging indicated that the particle has 39-fold dihedral symmetry.

    DOI: 10.1107/S0907444908004277

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    PubMed

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MISC

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講演・口頭発表等

  • 立体構造解析のイロハ ~光化学系膜タンパク質複合体を例に~ 招待

    加藤 公児

    第28回「光合成セミナー 2021」  2021年6月26日 

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    開催年月日: 2021年6月26日

    記述言語:日本語   会議種別:口頭発表(招待・特別)  

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  • 高分解能クライオ電顕マップを用いた補因子の同定

    加藤 公児, 長尾 遼, 沈 建仁, 秋田 総理, 宮崎 直幸

    第21回日本蛋白質科学会年会  2021年6月18日 

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    開催年月日: 2021年6月16日 - 2021年6月18日

    記述言語:日本語   会議種別:口頭発表(一般)  

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  • アナベナ由来光化学系I四量体のボルタ位相差クライオ電顕構造解析

    加藤公児

    日本顕微鏡学会第75回学術講演会  2019年6月17日 

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    記述言語:英語   会議種別:ポスター発表  

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  • 珪藻PSII-FCPII複合体のクライオ電子顕微鏡単粒子解析

    加藤公児, 秋田総理, 長尾遼, 宮崎直幸, 沈建仁

    生理研研究会NIPS EM Workshop  2018年11月 

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    記述言語:日本語   会議種別:ポスター発表  

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  • 精密X線回折データ測定のための溶液フリーマウント法の自動化

    加藤公児, 篠田晃, ユイジェン, 姚閔, 田中勲

    平成29年度日本結晶学会年会  2017年11月 

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    記述言語:日本語   会議種別:ポスター発表  

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  • Encapsulation of Biomacromolecule into Porous Crystal of a Huge Protein Complex Hemocyanin

    加藤公児

    The 5th International Symposium on Dynamical Ordering of Biomolecular Systems for Creation of Integrated Function  2017年1月 

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    記述言語:英語   会議種別:ポスター発表  

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  • 巨大生体分子の構造生物学:超分子複合体を見る 招待

    加藤公児

    生物物理学会若手の会夏の学校  2016年9月 

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    記述言語:日本語   会議種別:口頭発表(招待・特別)  

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  • スルメイカヘモシアニンの結晶構造解析

    田中良和, 加藤公児, 蓋作啓, 田中深雪, 田中勲, 姚閔, 加藤佑基, 清水健志, 宮部好克, 菅野岳, 岸村栄毅, 吉岡武也, 加藤早苗

    日本水産学会大会講演要旨集  2014年3月27日 

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    記述言語:日本語  

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  • スルメイカ由来巨大ヘモシアニンの構造生物学

    加藤公児

    2013年合同シンポジウム  2013年11月22日 

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    記述言語:日本語   会議種別:口頭発表(一般)  

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  • 分子量4MDaの巨大酸素運搬蛋白質会合体ヘモシアニンの結晶構造解析

    田中良和, 加藤公児, 蓋作啓, 田中深雪, 加藤早苗, 清水健志, 岸村栄毅, 菅野岳, 宮部好克, 岩崎憲治, 田中勲, 姚閔

    日本結晶学会年会講演要旨集  2013年10月12日 

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    記述言語:日本語  

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  • SACLAによるウシ心筋チトクロム酸化酵素の無損傷高分解能結晶構造解析

    吾郷日出夫, 平田邦生, 上野剛, 村上博則, 山本雅貴, 山下栄樹, 伊藤(新澤)恭子, 加藤公児, 畑中美樹, 武村修平, 矢野直峰, 吉川信也, 月原冨武

    日本結晶学会年会講演要旨集  2013年10月12日 

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    記述言語:日本語  

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  • ウシ心筋チトクロム酸化酵素の酸性アミノ酸残基のイオン化状態のX線結晶学的解析

    武村秀平, 加藤公児, 矢野直峰, 山下栄樹, 村本和優, 伊藤(新澤)恭子, 月原富武, 吉川信也

    日本蛋白質科学会年会プログラム・要旨集  2013年5月31日 

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    記述言語:日本語  

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  • ウシ心筋チトクロム酸化酵素のMgを含む水クラスターの機能の高分解能X線結晶構造解析による研究

    矢野直峰, 加藤公児, 山下栄樹, 村本和優, 伊藤(新澤)恭子, 月原冨武, 吉川信也

    日本蛋白質科学会年会プログラム・要旨集  2013年5月31日 

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    記述言語:日本語  

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  • 精密結晶構造解析によるチトクロム酸化酵素の反応機構の研究

    矢野直峰, 新澤(伊藤)恭子, 畑中美紀, 武村修平, 藤澤秀徳, 村本和優, 加藤公児, 山下栄樹, 吉川信也, 月原冨武

    日本結晶学会年会講演要旨集  2012年10月25日 

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    記述言語:日本語  

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  • 巨大な超分子複合体を見る

    加藤公児, 田中秀明, 山下栄樹, 住澤知之, 周勇, 姚閔, 岩崎憲治, 吉村政人, 月原冨武

    日本蛋白質科学会年会プログラム・要旨集  2010年5月15日 

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    記述言語:日本語  

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  • 超巨大タンパク質‐核酸複合体vaultの構造解析

    山下栄樹, 加藤公児, 田中秀明

    日本放射光学会年会・放射光科学合同シンポジウム予稿集  2009年12月10日 

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    記述言語:日本語  

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  • 3.5Å分解能でのラット肝臓由来vaultのX線結晶構造解析

    加藤公児

    第47回日本生物物理学会  2009年10月30日 

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    記述言語:英語   会議種別:口頭発表(一般)  

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  • 3.5Å分解能でのラット肝臓由来vaultの構造 招待

    加藤公児

    2009年6月22日 

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    記述言語:英語   会議種別:口頭発表(一般)  

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  • ラット肝臓由来vaultのX線結晶構造解析

    加藤公児

    生命科学系グローバルCOEネットワーク  2009年2月14日 

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    記述言語:日本語   会議種別:ポスター発表  

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  • ラット肝臓由来vaultの構造解析

    加藤公児

    第21回国際結晶学会  2008年8月23日 

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    記述言語:英語   会議種別:ポスター発表  

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  • 巨大RNAタンパク質複合体vaultの構造解析

    加藤公児

    生体防御医学研究所第17回ホットスプリングハーバー国際シンポジウム/第3回研究所ネットワーク国際シンポジウム合同シンポジウム  2008年2月1日 

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    記述言語:英語   会議種別:ポスター発表  

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受賞

  • 第27回井上研究奨励賞

    2011年2月   井上科学振興財団   3.5Å分解能でのラット肝臓由来vaultの構造解析

    加藤公児

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共同研究・競争的資金等の研究

  • フィコビリソーム-四量体光化学系I超複合体の構造生物学的研究

    研究課題/領域番号:20H02914  2020年04月 - 2023年03月

    日本学術振興会  科学研究費助成事業 基盤研究(B)  基盤研究(B)

    加藤 公児, 長尾 遼

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    配分額:17940000円 ( 直接経費:13800000円 、 間接経費:4140000円 )

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  • 褐藻由来光化学系アンテナ超複合体の単粒子構造解析

    研究課題/領域番号:20H03194  2020年04月 - 2023年03月

    日本学術振興会  科学研究費助成事業 基盤研究(B)  基盤研究(B)

    秋田 総理, 宮崎 直幸, 加藤 公児

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    配分額:18200000円 ( 直接経費:14000000円 、 間接経費:4200000円 )

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  • クライオ電子顕微鏡を用いた光化学系II複合体の反応中間体の構造解析

    研究課題/領域番号:19K22396  2019年06月 - 2021年03月

    日本学術振興会  科学研究費助成事業 挑戦的研究(萌芽)  挑戦的研究(萌芽)

    秋田 総理, 宮崎 直幸, 加藤 公児

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    配分額:6500000円 ( 直接経費:5000000円 、 間接経費:1500000円 )

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  • 4者複合体の構造解析によるtranssulfursomeのtRNA変換機構の解明

    研究課題/領域番号:17H03637  2017年04月 - 2020年03月

    日本学術振興会  科学研究費助成事業 基盤研究(B)  基盤研究(B)

    姚 閔, 尾瀬 農之, 田中 良和, 加藤 公児

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    配分額:17420000円 ( 直接経費:13400000円 、 間接経費:4020000円 )

    古細菌におけるCys-tRNA(Cys) の生合成は,2 つの酵素,SepRS とSepCysS が,それぞれ触媒する2段階の反応から成り立っている.申請者らは,この反応を推進するためには,第3のタンパク質SepCysE がSepRS とSepCysS をつないで3者複合体(transsulfursome)を形成することが必須であることを明らかにした.本研究では,そのtranssulfursome とtRNA から成る4者複合体の構造解析により,transsulfursomeが2つのリンカーを利用して動的なtRNAをプロセスする分子機構を明らかにする.そのために,H29年度に引き続き,H30年度に下記のように研究を進めた.
    H30年度に,transsulfursomeとtRNAの結合実験で確認しながら,各反応段階を反映するtranssulfursomeとtRNAの変異体作製を続き,精製できた第1段階反応状態を反映するtranssulfursome変異体SepRS-SepCysE(H)とtRNA複合体を結晶化し,初期結晶を得た.現在に,その結晶の条件最適化を行っている.また,transsulfursome-tRNA複合体のクライオ電子顕微鏡の測定について,当学科に既存の共用透過型電子顕微鏡(Hitachi社製 H7650)を用いて,硝酸ウランを用いたネガティブ染色法によりtranssulfursome-tRNA複合体の確認を行ったところで,tRNA結合状態のtranssulfursomeが単体より,まっすぐのような形が多かったということが分かった.さらに,放射光施設PFにて,凍結条件のスクリーニングを実施した.その結果,transsulfursome-tRNA複合体が沈殿しやすい,クライオ電子顕微鏡の測定に適切なグリッドの作製が困難であることが分かった.

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  • tRNAスプライシングにおける多機能性tRNAリガーゼの分子機構解明

    研究課題/領域番号:16K18498  2016年04月 - 2018年03月

    日本学術振興会  科学研究費助成事業 若手研究(B)  若手研究(B)

    加藤 公児, 桜井 直文, 鈴木 稚菜

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    配分額:4290000円 ( 直接経費:3300000円 、 間接経費:990000円 )

    Trl1リガーセドメイン(Trl1-LD)- GMP複合体の構造を2.75オングストローム分解能で決定した。Trl1-LDの活性中心付近に2分子のGMP がスタックして結合していた。その複合体構造を詳細に解析した結果、2分子のGMPの周辺には塩基性のアミノ酸が集中していた。このことから、これらのGMPはライゲーション過程のtRNAエキソンをミミックしているものと考えられた。これによりTrl1-LDのtRNAの結合様式を類推することが可能となった。

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  • 熱応答ゲル化ポリマーを利用した,中性子線構造解析のための大型結晶作製法の開発

    研究課題/領域番号:16K14677  2016年04月 - 2018年03月

    日本学術振興会  科学研究費助成事業 挑戦的萌芽研究  挑戦的萌芽研究

    姚 閔, 加藤 公児, 安達 基泰

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    配分額:3770000円 ( 直接経費:2900000円 、 間接経費:870000円 )

    本研究では,中性子線構造解析のために,タンパク質の良質な大型結晶の作製技術を確立することを目的とする.研究期間で,LCST型温度応答ポリマーを利用して,数種類のサンプルの大型結晶を成長させた.そのうち,分子量110kDaであるGatCABと基質の複合体の中性子構造も得られ,そのポリマーが結晶の成長に有効であることが確認できた.また,LCST型温度応答ポリマーが結晶成長に与える影響を検討したところ,結晶成長中に溶液のエントロピー変化量の変化が見られた.これは,結晶成長とともに生じていた温度変化によってポリマーの相転移が起こり,タンパク質結晶の周辺にある水分子に影響を与えたと考えられる.

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  • 分子量4MDaの巨大酸素運搬蛋白質ヘモシアニンの構造生物学研究

    研究課題/領域番号:26291008  2014年04月 - 2017年03月

    日本学術振興会  科学研究費助成事業 基盤研究(B)  基盤研究(B)

    田中 良和, 姚 閔, 加藤 公児

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    配分額:16770000円 ( 直接経費:12900000円 、 間接経費:3870000円 )

    スルメイカ由来ヘモシアニンの結晶化に成功し,その構造を3.0オングストローム分解能で決定した.明らかになった構造から,スルメイカヘモシアニンが円筒型の外壁領域と,5つの内部領域から構成される,10量体の会合体であることがわかった.巨大な10量体は,2つのドメインが会合したドメイン2量体が一つの構造単位となり,それが複雑に会合することで形成されていた.サユブニット同士の界面に糖鎖修飾クラスターが存在していることがわかり,生化学実験の結果を考え合わせた結果,この糖鎖クラスターがサブユニット同士の会合に貢献していることがわかった.

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  • 大腸菌リボソーム駆動部構成蛋白質のカセット交換による真核型合成速度の実現

    研究課題/領域番号:26650013  2014年04月 - 2016年03月

    日本学術振興会  科学研究費助成事業 挑戦的萌芽研究  挑戦的萌芽研究

    姚 閔, 内海 利男, 加藤 公児

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    配分額:4030000円 ( 直接経費:3100000円 、 間接経費:930000円 )

    本研究では,大腸菌のストークタンパク質の一部を真核型に変換したキメラストーク複合体を用いて,真核型タンパク質のフォールド速度に対応した減速型(真核型)発現系に変更させることによって,真核生物タンパク質の可溶化発現の改善を目指す.この目的を達成するために,大腸菌由来のストーク複合体の背骨タンパク質L10のキメラ体をin vitro作製を試み,L10の変異体L10ΔCHと2種類のL10P0キメラL10ΔCH-P0H2CTD/H3CTDの可溶化発現に成功した.また,そのL10P0キメラを精製し,P1との結合実験を行い,大腸菌のキメラリボソームストーク複合体を創製する可能性が示唆された.

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  • 巨大タンパク質ー核酸複合体ボルトの結晶構造解析

    研究課題/領域番号:21770111  2009年 - 2010年

    日本学術振興会  科学研究費助成事業 若手研究(B)  若手研究(B)

    加藤 公児

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    担当区分:研究代表者  資金種別:競争的資金

    配分額:4550000円 ( 直接経費:3500000円 、 間接経費:1050000円 )

    昆虫細胞-バキュロウイルス大量発現系を構築し、結晶化条件を再検討することにより、良質の結晶が得られており、SPring-8のビームラインBL44XUにおいて、最高で2.9Å分解能の回折点を確認することができた。これらの結果は、今後、高分解能でボルトの全体構造を解析し、ボルトの生体内における機能を解明する上で重要な足がかりになると期待される

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  • 学際基礎科学概論2 (2021年度) 前期  - 水1,水2