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29 results on '"Suga, Michihiro"'

1. Oxygen-evolving photosystem II structures during S1–S2–S3 transitions

Author

Li, Hongjie, Nakajima, Yoshiki, Nango, Eriko, Owada, Shigeki, Yamada, Daichi, Hashimoto, Kana, Luo, Fangjia, Tanaka, Rie, Akita, Fusamichi, Kato, Koji, Kang, Jungmin, Saitoh, Yasunori, Kishi, Shunpei, Yu, Huaxin, Matsubara, Naoki, Fujii, Hajime, Sugahara, Michihiro, Suzuki, Mamoru, Masuda, Tetsuya, Kimura, Tetsunari, Thao, Tran Nguyen, Yonekura, Shinichiro, Yu, Long-Jiang, Tosha, Takehiko, Tono, Kensuke, Joti, Yasumasa, Hatsui, Takaki, Yabashi, Makina, Kubo, Minoru, Iwata, So, Isobe, Hiroshi, Yamaguchi, Kizashi, Suga, Michihiro, and Shen, Jian-Ren

Published
2024
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5. An oxyl/oxo mechanism for oxygen-oxygen coupling in PSII revealed by an x-ray free-electron laser

Author

Suga, Michihiro, Akita, Fusamichi, Yamashita, Keitaro, Nakajima, Yoshiki, Ueno, Go, Li, Hongjie, Yamane, Takahiro, Hirata, Kunio, Umena, Yasufumi, Yonekura, Shinichiro, Yu, Long-Jiang, Murakami, Hironori, Nomura, Takashi, Kimura, Tetsunari, Kubo, Minoru, Baba, Seiki, Kumasaka, Takashi, Tono, Kensuke, Yabashi, Makina, Isobe, Hiroshi, Yamaguchi, Kizashi, Yamamoto, Masaki, Ago, Hideo, and Shen, Jian-Ren

Published
2019

18. Structure and function of a silicic acid channel Lsi1

Author

Saitoh, Yasunori and Suga, Michihiro

Subjects
aquaporin, crystal structure, rice, transporter, channel, silicon, NIP, Plant Science, substrate selectivity
Abstract

Silicon is a beneficial element for plant growth and production, especially in rice. Plant roots take up silicon in the form of silicic acid. Silicic acid channels, which belong to the NIP subfamily of aquaporins, are responsible for silicic acid uptake. Accumulated experimental results have deepened our understanding of the silicic acid channel for its uptake mechanism, physiological function, localization, and other aspects. However, how the silicic acid channel efficiently and selectively permeates silicic acid remains to be elucidated. Recently reported crystal structures of the silicic acid channel enabled us to discuss the mechanism of silicic acid uptake by plant roots at an atomic level. In this mini-review, we focus on the crystal structures of the silicic acid channel and provide a detailed description of the structural determinants of silicic acid permeation and its transport mechanism, which are crucial for the rational creation of secure and sustainable crops.

Published
2022

19. Light-induced structural changes and the site of O=O bond formation in PSII caught by XFEL

Author

Suga, Michihiro, Akita, Fusamichi, Sugahara, Michihiro, Kubo, Minoru, Nakajima, Yoshiki, Nakane, Takanori, Yamashita, Keitaro, Umena, Yasufumi, Nakabayashi, Makoto, Yamane, Takahiro, Nakano, Takamitsu, Suzuki, Mamoru, Masuda, Tetsuya, Inoue, Shigeyuki, Kimura, Tetsunari, Nomura, Takashi, Yonekura, Shinichiro, Yu, Long-Jiang, Sakamoto, Tomohiro, Motomura, Taiki, Chen, Jing-Hua, Kato, Yuki, Noguchi, Takumi, Tono, Kensuke, Joti, Yasumasa, Kameshima, Takashi, Hatsui, Takaki, Nango, Eriko, Tanaka, Rie, Naitow, Hisashi, Matsuura, Yoshinori, Yamashita, Ayumi, Yamamoto, Masaki, Nureki, Osamu, Yabashi, Makina, Ishikawa, Tetsuya, Iwata, So, and Shen, Jian-Ren

Published
2017
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21. An oxyl/oxo mechanism for dioxygen bond formation in PSII revealed by X-ray free electron lasers

Author

Suga, Michihiro, Akita, Fusamichi, Yamashita, Keitaro, Nakajima, Yoshiki, Ueno, Go, Li, Hongjie, Yamane, Takahiro, Hirata, Kunio, Umena, Yasufumi, Yonekura, Shinichiro, Yu, Long-Jiang, Murakami, Hironori, Nomura, Takashi, Kimura, Tetsunari, Kubo, Minoru, Baba, Seiki, Kumasaka, Takashi, Tono, Kensuke, Yabashi, Makina, Isobe, Hiroshi, Yamaguchi, Kizashi, Yamamoto, Masaki, Ago, Hideo, and Shen, Jian-Ren

Abstract

Photosynthetic water oxidation is catalyzed by the Mn4CaO5 cluster of photosystem II (PSII) with linear progression through five S-state intermediates (S0 to S4). To reveal the mechanism of water oxidation, we analyzed structures of PSII in the S1, S2, and S3 states by x-ray free-electron laser serial crystallography. No insertion of water was found in S2, but flipping of D1 Glu189 upon transition to S3 leads to the opening of a water channel and provides a space for incorporation of an additional oxygen ligand, resulting in an open cubane Mn4CaO6 cluster with an oxyl/oxo bridge. Structural changes of PSII between the different S states reveal cooperative action of substrate water access, proton release, and dioxygen formation in photosynthetic water oxidation.

Published
2019

25. Novel features of LH1‐RC from Thermochromatium tepidum revealed from its atomic resolution structure.

Author

Yu, Long‐Jiang, Suga, Michihiro, Wang‐Otomo, Zheng‐Yu, and Shen, Jian‐Ren

Subjects
*MEMBRANE proteins, *PHOTOSYNTHETIC bacteria, *CHARGE exchange, *ENERGY transfer, *THERMAL stability
Abstract

Light‐harvesting‐1 (LH1)‐reaction center (RC) super‐complex is a membrane protein–pigment complex existing in purple photosynthetic bacteria, where LH1 absorbs light energy and transfers them rapidly and efficiently to RC to initiate the charge separation and electron transfer reactions. The structure of LH1‐RC has been reported at relatively low resolutions from several different species of bacteria previously, but was solved at an atomic resolution recently from a thermophilic photosynthetic bacterium Thermochromatium tepidum. This high‐resolution structure revealed the detailed organization of the super‐complex including a number of unique features that are important for its functioning, such as a more intact RC structure, transporting routes for quinones to replace the bound QB as well as for the in‐and‐out of the closed LH1 ring, detailed coordinating environment of the Ca2+ ions in LH1 important for the remarkable red shift of the absorption spectrum, as well as for the enhanced thermostability. These results thus greatly advance our understanding on the mechanisms of energy transfer, quinone exchange, the red shift in the LH1‐Qy transition and the enhanced thermal stability, in this super‐complex. Crystal structure of the light‐harvesting 1‐reaction center super‐complex from a photosynthetic purple bacterium at an atomic resolution reveals a number of novel features regarding the overall organization and detailed arrangement of pigments and cofactors, quinone exchange and proton transfer channels, and the coordination pattern of Ca2+ ions important for red shift and thermostability of the super‐complex. [ABSTRACT FROM AUTHOR]

Published
2018
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26. Large-scale QM/MM calculations of the CaMn4O5 cluster in the S3 state of the oxygen evolving complex of photosystem II. Comparison between water-inserted and no water-inserted structures.

Author

Shoji, Mitsuo, Isobe, Hiroshi, Nakajima, Takahito, Shigeta, Yasuteru, Suga, Michihiro, Akita, Fusamichi, Shen, Jian-Ren, and Yamaguchi, Kizashi

Abstract

Large-scale QM/MM calculations were performed to elucidate an optimized geometrical structure of a CaMn4O5 cluster with and without water insertion in the S3 state of the oxygen evolving complex (OEC) of photosystem II (PSII). The left (L)-opened structure was found to be stable under the assumption of no hydroxide anion insertion in the S3 state, whereas the right (R)-opened structure became more stable if one water molecule is inserted to the Mn4Ca cluster. The optimized Mna(4)–Mnd(1) distance determined by QM/MM was about 5.0 Å for the S3 structure without an inserted hydroxide anion, but this is elongated by 0.2–0.3 Å after insertion. These computational results are discussed in relation to the possible mechanisms of O–O bond formation in water oxidation by the OEC of PSII. [ABSTRACT FROM AUTHOR]

Published
2017
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27. Crystal structure at 1.5Å resolution of the PsbV2 cytochrome from the cyanobacterium Thermosynechococcus elongatus.

Author

Suga, Michihiro, Lai, Thanh-Lan, Sugiura, Miwa, Shen, Jian-Ren, and Boussac, Alain

Subjects
*THERMOSYNECHOCOCCUS elongatus, *CRYSTAL structure, *CYANOBACTERIA, *CYTOCHROME c, *ZINC-finger proteins, *TRANSCRIPTION factors
Abstract

Highlights: [•] PsbV2 is a cytochrome c in cyanobacteria with still unknown function. [•] The crystal structure of PsbV2 was resolved at a resolution of 1.5Å. [•] PsbV2 has an unusual His/Cys axial coordination. [ABSTRACT FROM AUTHOR]

Published
2013
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28. A description of the structural determination procedures of a gap junction channel at 3.5 Å resolution.

Author

Suga, Michihiro, Maeda, Shoji, Nakagawa, So, Yamashita, Eiki, and Tsukihara, Tomitake

Subjects
*GAP junctions (Cell biology), *MOLECULES, *PROTEINS, *ELECTRON microscopy, *LIGHT scattering, *HELICES (Algebraic topology)
Abstract

Intercellular signalling is an essential characteristic of multicellular organisms. Gap junctions, which consist of arrays of intercellular channels, permit the exchange of ions and small molecules between adjacent cells. Here, the structural determination of a gap junction channel composed of connexin 26 (Cx26) at 3.5 Å resolution is described. During each step of the purification process, the protein was examined using electron microscopy and/or dynamic light scattering. Dehydration of the crystals improved the resolution limits. Phase refinement using multi-crystal averaging in conjunction with noncrystallographic symmetry averaging based on strictly determined noncrystallographic symmetry operators resulted in an electron-density map for model building. The amino-acid sequence of a protomer structure consisting of the aminoterminal helix, four transmembrane helices and two extracellular loops was assigned to the electron-density map. The amino-acid assignment was confirmed using six selenomethionine (SeMet) sites in the difference Fourier map of the SeMet derivative and three intramolecular disulfide bonds in the anomalous difference Fourier map of the native crystal. [ABSTRACT FROM AUTHOR]

Published
2009
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29. Distinguishing between Cl- and Due to image rights restrictions, multiple line equation(s) cannot be graphically displayed. as the bridging element between Fe3+ and Cu2+ in resting-oxidized cytochrome c oxidase.

Author

Suga, Michihiro, Yano, Naomine, Muramoto, Kazumasa, Shinzawa-Itoh, Kyoko, Maeda, Tomoko, Yamashita, Eiki, Tsukihara, Tomitake, and Yoshikawa, Shinya

Subjects
*PROTONS, *CHARGE exchange, *CYTOCHROME oxidase, *PEROXIDES, *OXIDATION
Abstract

The article discusses an anomalous dispersion analysis of the mechanism of coupling the proton pumping process to the electron transfer reaction in resting-oxidized cytochrome c oxydase. The study suggests that peroxide moiety receives electron equivalents from cytochrome c without affecting the oxidation states of the metal sites. It further suggests that the metal site reduction is coupled to the proton pump.

Published
2011
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