Updated on 2022/03/31

写真a

 
UMENA Yasufumi
 
Organization
Synchrotron Radiation Research Center Division of Synchrotron Radiation Associate professor
Title
Associate professor

Degree 1

  1. 博士(理学) ( 2007.6   大阪大学 ) 

 

Papers 15

  1. Dynamic interactions in the l-lactate oxidase active site facilitate substrate binding at pH4.5. Reviewed

    Furubayashi N, Inaka K, Kamo M, Umena Y, Matsuoka T, Morimoto Y

    Biochemical and biophysical research communications   Vol. 568   page: 131 - 135   2021.9

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    DOI: 10.1016/j.bbrc.2021.06.078

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  2. Capturing structural changes of the S-1 to S-2 transition of photosystem II using time-resolved serial femtosecond crystallography Reviewed

    Li Hongjie, Nakajima Yoshiki, Nomura Takashi, Sugahara Michihiro, Yonekura Shinichiro, Chan Siu Kit, Nakane Takanori, Yamane Takahiro, Umena Yasufumi, Suzuki Mamoru, Masuda Tetsuya, Motomura Taiki, Naitow Hisashi, Matsuura Yoshinori, Kimura Tetsunari, Tono Kensuke, Owada Shigeki, Joti Yasumasa, Tanaka Rie, Nango Eriko, Akita Fusamichi, Kubo Minoru, Iwata So, Shen Jian-Ren, Suga Michihiro

    IUCRJ   Vol. 8 ( Pt 3 ) page: 431 - 443   2021.5

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    Photosystem II (PSII) catalyzes light-induced water oxidation through an S i-state cycle, leading to the generation of di-oxygen, protons and electrons. Pump-probe time-resolved serial femtosecond crystallography (TR-SFX) has been used to capture structural dynamics of light-sensitive proteins. In this approach, it is crucial to avoid light contamination in the samples when analyzing a particular reaction intermediate. Here, a method for determining a condition that avoids light contamination of the PSII microcrystals while minimizing sample consumption in TR-SFX is described. By swapping the pump and probe pulses with a very short delay between them, the structural changes that occur during the S1-to-S2 transition were examined and a boundary of the excitation region was accurately determined. With the sample flow rate and concomitant illumination conditions determined, the S2-state structure of PSII could be analyzed at room temperature, revealing the structural changes that occur during the S1-to-S2 transition at ambient temperature. Though the structure of the manganese cluster was similar to previous studies, the behaviors of the water molecules in the two channels (O1 and O4 channels) were found to be different. By comparing with the previous studies performed at low temperature or with a different delay time, the possible channels for water inlet and structural changes important for the water-splitting reaction were revealed.

    DOI: 10.1107/S2052252521002177

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  3. Estimation of the relative contributions to the electronic energy transfer rates based on Förster theory: The case of C-phycocyanin chromophores. Reviewed

    Mishima K, Shoji M, Umena Y, Boero M, Shigeta Y

    Biophysics and physicobiology   Vol. 18   page: 196 - 214   2021

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    DOI: 10.2142/biophysico.bppb-v18.021

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  4. Improvement Method by Laser-processing of Photosystem II Crystals for Valence Analysis of Mn-cluster Reviewed

    Umena Yasufumi, Kawakami Keisuke, Kawano Yoshiaki, Yamamoto Masaki, Kamiya Nobuo, Shen Jian-Ren

    SPring-8/SACLA Research Report   Vol. 9 ( 4 ) page: 177 - 181   2021

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    Language:Japanese   Publisher:Japan Synchrotron Radiation Research Institute  

    DOI: 10.18957/rr.9.4.177

  5. Formation of the High-Spin S-2 State Related to the Extrinsic Proteins in the Oxygen Evolving Complex of Photosystem II Reviewed

    Taguchi Shota, Shen Liangliang, Han Guangye, Umena Yasufumi, Shen Jian-Ren, Noguchi Takumi, Mino Hiroyuki

    JOURNAL OF PHYSICAL CHEMISTRY LETTERS   Vol. 11 ( 20 ) page: 8908 - 8913   2020.10

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    Language:Japanese   Publisher:Journal of Physical Chemistry Letters  

    The high-spin S2 state was investigated with photosystem II (PSII) from spinach, Thermosynechococcus vulcanus, and Cyanidioschyzon merolae. In extrinsic protein-depleted PSII, high-spin electron paramagnetic resonance (EPR) signals were not detected in either species, whereas all species showed g ∼5 signals in the presence of a high concentration of Ca2+ instead of the multiline signal. In the intact and PsbP/Q-depleted PSII from spinach, the g = 4.1 EPR signal was detected. These results show that formation of the high-spin S2 state of the manganese cluster is regulated by the extrinsic proteins through a charge located near the Mn4 atom in the Mn4CaO5 cluster but is independent of the intrinsic proteins. The shift to the g ∼5 state is caused by tilting of the z-axis in the Mn4 coordinates through hydrogen bonds or external divalent cations. The structural modification may allow insertion of an oxygen atom during the S2-to-S3 transition.

    DOI: 10.1021/acs.jpclett.0c02411

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  6. X-ray fluorescence holography for soft matter Reviewed

    Ang Artoni Kevin R., Sato-Tomita Ayana, Shibayama Naoya, Umena Yasufumi, Happo Naohisa, Marumi Riho, Kimura Koji, Matsushita Tomohiro, Akagi Kazuto, Sasaki Takahiko, Sasaki Yuji C., Hayashi Kouichi

    JAPANESE JOURNAL OF APPLIED PHYSICS   Vol. 59 ( 1 )   2020.1

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    Language:Japanese   Publisher:Japanese Journal of Applied Physics  

    X-ray fluorescence holography (XFH) is a technique that can directly image the 3D arrangement of atoms around an element in a sample. The holograms contain both intensity and phase information, allowing atomic reconstruction without needing prior structural information or a tentative structural model. XFH has already been used to reveal the local structures of various inorganic samples, and recently, work has begun on XFH for soft matter. In this paper, we review the progress of XFH on soft materials. First, we review the fundamental principles of XFH. Second, we review inverse mode XFH on soft materials, and the results of the experiments on hemoglobin, myoglobin, and κ-(BEDT-TTF)2Cu[N(CN)2]Br crystals. In the last section, we report the progress of the development of normal mode holography for soft materials. The new apparatus and scanning method is described, and results of the initial tests on the protein Photosystem II are discussed.

    DOI: 10.7567/1347-4065/ab5d55

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  7. An alternative plant-like cyanobacterial ferredoxin with unprecedented structural and functional properties Reviewed

    Motomura Taiki, Zuccarello Lidia, Setif Pierre, Boussac Alain, Umena Yasufumi, Lemaire David, Tripathy Jatindra N., Sugiura Miwa, Hienerwadel Rainer, Shen Jian-Ren, Berthomieu Catherine

    BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS   Vol. 1860 ( 11 ) page: 148084   2019.11

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    Language:Japanese   Publisher:Biochimica et Biophysica Acta - Bioenergetics  

    Photosynthetic [2Fe-2S] plant-type ferredoxins have a central role in electron transfer between the photosynthetic chain and various metabolic pathways. Several genes are coding for [2Fe–2S] ferredoxins in cyanobacteria, with four in the thermophilic cyanobacterium Thermosynechococcus elongatus. The structure and functional properties of the major ferredoxin Fd1 are well known but data on the other ferredoxins are scarce. We report the structural and functional properties of a novel minor type ferredoxin, Fd2 of T. elongatus, homologous to Fed4 from Synechocystis sp. PCC 6803. Remarkably, the midpoint potential of Fd2, Em = −440 mV, is lower than that of Fd1, Em = −372 mV. However, while Fd2 can efficiently react with photosystem I or nitrite reductase, time-resolved spectroscopy shows that Fd2 has a very low capacity to reduce ferredoxin-NADP+ oxidoreductase (FNR). These unique Fd2 properties are discussed in relation with its structure, solved at 1.38 Å resolution. The Fd2 structure significantly differs from other known ferredoxins structures in loop 2, N-terminal region, hydrogen bonding networks and surface charge distributions. UV–Vis, EPR, and Mid- and Far-IR data also show that the electronic properties of the [2Fe–2S] cluster of Fd2 and its interaction with the protein differ from those of Fd1 both in the oxidized and reduced states. The structural analysis allows to propose that valine in the motif Cys53ValAsnCys56 of Fd2 and the specific orientation of Phe72, explain the electron transfer properties of Fd2. Strikingly, the nature of these residues correlates with different phylogenetic groups of cyanobacterial Fds. With its low redox potential and its discrimination against FNR, Fd2 exhibits a unique capacity to direct efficiently photosynthetic electrons to metabolic pathways not dependent on FNR.

    DOI: 10.1016/j.bbabio.2019.148084

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

    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, Shen Jian-Ren

    SCIENCE   Vol. 366 ( 6463 ) page: 334 - +   2019.10

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

    Suga M., Akita F., Yamashita K., Nakajima Y., Ueno G., Li H., Yamane T., Hirata K., Umena Y., Yonekura S., Yu L.J., Murakami H., Nomura T., Kimura T., Kubo M., Baba S., Kumasaka T., Tono K., Yabashi M., Isobe H., Yamaguchi K., Yamamoto M., Ago H., Shen J.R.

    Science   Vol. 366 ( 6463 ) page: 334 - 338   2019.10

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    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 reve cooperative action of substrate water access, proton release, and dioxygen formation in photosynthetic water oxidation.

    DOI: 10.1126/science.aax6998

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  10. A versatile experimental system for tracking ultrafast chemical reactions with X-ray free-electron lasers Reviewed

    Katayama Tetsuo, Nozawa Shunsuke, Umena Yasufumi, Lee SungHee, Togashi Tadashi, Owada Shigeki, Yabashi Makina

    STRUCTURAL DYNAMICS-US   Vol. 6 ( 5 ) page: 054302   2019.9

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    Language:English   Publisher:Structural Dynamics  

    An experimental system, SPINETT (SACLA Pump-probe INstrumEnt for Tracking Transient dynamics), dedicated for ultrafast pump-probe experiments using X-ray free-electron lasers has been developed. SPINETT consists of a chamber operated under 1 atm helium pressure, two Von Hamos spectrometers, and a large two-dimensional detector having a short work distance. This platform covers complementary X-ray techniques; one can perform time-resolved X-ray absorption spectroscopy, time-resolved X-ray emission spectroscopy, and time-resolved X-ray diffuse scattering. Two types of liquid injectors have been prepared for low-viscosity chemical solutions and for protein microcrystals embedded in a matrix. We performed a test experiment at SPring-8 Angstrom Compact free-electron LAser and demonstrated the capability of SPINETT to obtain the local electronic structure and geometrical information simultaneously.

    DOI: 10.1063/1.5111795

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  11. Novel Mechanism of Cl-Dependent Proton Dislocation in Photosystem II (PSII): Hybrid Ab initio Quantum Mechanics/Molecular Mechanics Molecular Dynamics Simulation Reviewed

    Nakamura Atsushi, Kang Jiyoung, Terada Ryu-ichiro, Kino Hiori, Umena Yasufumi, Kawakami Keisuke, Shen Jian-Ren, Kamiya Nobuo, Tateno Masaru

    JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN   Vol. 88 ( 8 )   2019.8

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    Language:Japanese   Publisher:Journal of the Physical Society of Japan  

    The photosynthetic water oxidation reaction in photosystem II (PSII) causes the ejection of four protons (H+) and electrons from the substrate water bound to the Mn4CaO5 cluster, denoting the catalytic center of the system. Two Cl− ions, Cl1 and Cl2 sites, were found in the vicinity of the Mn4CaO5 moiety. Herein, a novel H+ transfer mechanism (amide H+ exchange-driven scheme) was identified to operate in the Cl2 pathway based on the hybrid ab initio quantum mechanics (QM) molecular dynamics (MD) simulations of PSII. The analysis revealed that H+ can be displaced across the peptide bond of the D1-His337 and D1-Asn338 backbones, interrupting the hydrogen bond network spanning to the lumenal side in the crystal structure. The estimated energy barrier was consistent with the previous kinetic data. This is the first report to address unidirectional H+ transfer through a peptide bond based on the theoretical analysis involving the environmental protein structure.

    DOI: 10.7566/JPSJ.88.084802

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  12. beta-Carotene Probes the Energy Transfer Pathway in the Photosystem II Core Complex Reviewed

    Yoneda Yusuke, Nagasawa Yutaka, Umena Yasufumi, Miyasaka Hiroshi

    JOURNAL OF PHYSICAL CHEMISTRY LETTERS   Vol. 10 ( 13 ) page: 3710 - 3714   2019.7

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    Language:Japanese   Publisher:Journal of Physical Chemistry Letters  

    The dynamics of the intact photosystem II core complex (PSII-CC) has been investigated extensively to elucidate its excellent photofunction. However, it is significantly difficult to observe the primary photosynthetic processes in PSII-CC because a vast number of chlorophylls (Chl) in the core complex show similar spectral features. In the present work, the dynamics of the energy transfer (ET) from β-carotene (Bcr) in intact PSII-CC followed by charge separation (CS) at the reaction center (RC) with different excitation wavelengths were compared. Upon excitation at 510 nm, which selectively excites Bcr (Bcr651) inside of the D1-D2 RC, the pheophytin anion absorption band appeared within 9.6 ps. On the other hand, upon excitation at 490 nm, mainly exciting unspecified Bcr in the antenna complex, the anion band appeared after 20 ps. These excitation wavelength dependence experiments revealed a new ET pathway of PSII-CC, which indicates that the initial CS of PSII-CC is limited by ET to the RC.

    DOI: 10.1021/acs.jpclett.9b01072

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  13. Structural basis for blue-green light harvesting and energy dissipation in diatoms

    Wang Wenda, Yu Long-Jiang, Xu Caizhe, Tomizaki Takashi, Zhao Songhao, Umena Yasufumi, Chen Xiaobo, Qin Xiaochun, Xin Yueyong, Suga Michihiro, Han Guangye, Kuang Tingyun, Shen Jian-Ren

    SCIENCE   Vol. 363 ( 6427 ) page: 598 - +   2019.2

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    Diatoms are abundant photosynthetic organisms in aquatic environments and contribute 40% of its primary productivity. An important factor that contributes to the success of diatoms is their fucoxanthin chlorophyll a/c-binding proteins (FCPs), which have exceptional light-harvesting and photoprotection capabilities. Here, we report the crystal structure of an FCP from the marine diatom Phaeodactylum tricornutum, which reveals the binding of seven chlorophylls (Chls) a, two Chls c, seven fucoxanthins (Fxs), and probably one diadinoxanthin within the protein scaffold. Efficient energy transfer pathways can be found between Chl a and c, and each Fx is surrounded by Chls, enabling the energy transfer and quenching via Fx highly efficient. The structure provides a basis for elucidating the mechanisms of blue-green light harvesting, energy transfer, and dissipation in diatoms.

    DOI: 10.1126/science.aav0365

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  14. Crystallographic study on estimation of the valence of each of the four Mn atoms in Photosystem II using anomalous diffraction techniques

    Umena Yasufumi, Kawakami Keisuke, Kamiya Nobuo, Kawano Yoshiaki, Yamashita Keitaro, Ago Hideo, Yamamoto Masaki, Shen Jian-Ren

    ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES   Vol. 75   page: A363 - A363   2019

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    DOI: 10.1107/S010876731909648X

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  15. Theoretical Elucidation of Geometrical Structures of the CaMn4O5 Cluster in Oxygen Evolving Complex of Photosystem II Scope and Applicability of Estimation Formulae of Structural Deformations via the Mixed-Valence and Jahn-Teller Effects Reviewed

    Shoji Mitsuo, Isobe Hiroshi, Yamanaka Shusuke, Umena Yasufumi, Kawakami Keisuke, Kamiya Nobuo, Yamaguchi Kizashi

    QUANTUM SYSTEMS IN PHYSICS, CHEMISTRY AND BIOLOGY - THEORY, INTERPRETATION, AND RESULTS   Vol. 78   page: 307 - 451   2019

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    Language:Japanese   Publisher:Advances in Quantum Chemistry  

    Atmospheric oxygenation and evolution of aerobic life on our earth are a result of water oxidation by oxygenic photosynthesis in photosystem II (PSII) of plants, algae, and cyanobacteria. The water oxidation in the oxygen-evolving complex (OEC) of PSII is expected to proceed through five oxidation states, known as the Si (i = 0, 1, 2, 3, and 4) states in the Kok cycle, with the S1 being the most stable state in the dark. The OEC in PSII involves the active catalytic site made of four Mn ions and one Ca ion, namely the CaMn4O5 cluster. Past decades, molecular structures of the CaMn4O5 cluster in OEC of PSII have been investigated by the extended X-ray absorption fine structure (EXAFS). The magnetostructural correlations were extensively investigated by EPR spectroscopy. Recently, Kamiya and Shen groups made a great breakthrough for determination of the S1 structure of OEC of PSII by the X-ray diffraction (XRD) and X-ray free electron laser (XFEL) experiments, providing structural foundations that are crucial for theoretical investigations of structure and reactivity of the CaMn4O5 cluster. Large-scale QM/MM calculations starting from the XRD structures elucidated geometrical, electronic, and spin structures of the CaMn4O5 cluster, indicating an important role of the Jahn–Teller (JT) effect of Mn(III) ions. This review fully examines our theoretical formulae for estimation of the Jahn–Teller deformations of the CaMn4O5 cluster in OEC of PSII. Scope and applicability of the JT deformation formulae are elucidated in relation to several different structures of the CaMn4O5 cluster proposed by XRD, XFEL, EXAFS, and other experiments. Subtle differences among XRD, XFEL, and EXAFS structures in the S1 state are examined in relation to environmental effects for the CaMn4O5 cluster in OEC of PSII. The X-ray damage of the serial femtosecond crystallography (SFX) by XFEL is also examined in relation to the damage-free low-dose (LD) XRD structure. The JT deformation formulae are also applied to theoretical analysis of the S3 structures by SFX. Implications of the computational results are discussed for further refinements of geometrical parameters of the CaMn4O5 cluster in OEC of PSII and possible mechanisms of water oxidation in OEC of PSII.

    DOI: 10.1016/bs.aiq.2018.05.003

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Presentations 3

  1. Determination of the Mn Valence in Oxygen-Evolving Photosystem II

    Umena Yasufumi, Kawakami Keisuke, Shen Jian-Ren, Kamiya Nobuo

    SPring-8/SACLA Research Report  2020.3.26  Japan Synchrotron Radiation Research Institute

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    Language:Japanese  

    DOI: 10.18957/rr.8.1.1

    CiNii Research

  2. Improvement Method by Laser-processing of Photosystem II Crystals for Valence Analysis of Mn-cluster

    Umena Yasufumi, Kawakami Keisuke, Kawano Yoshiaki, Yamamoto Masaki, Kamiya Nobuo, Shen Jian-Ren

    SPring-8/SACLA Research Report  2021.6.30  Japan Synchrotron Radiation Research Institute

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    DOI: 10.18957/rr.9.4.177

    CiNii Research

  3. Novel Mechanism of Cl-Dependent Proton Dislocation in Photosystem Ⅱ (PSⅡ) : Hybrid Ab initio Quantum Mechanics Molecular Mechanics Molecular Dynamics Simulation

    Nakamura Atsushi, Kang Jiyoung, Terada Ryu-ichiro, Kino Hiori, Umena Yasufumi, Kawakami Keisuke, Shen Jian-Ren, Kamiya Nobuo, Tateno Masaru

    Journal of the Physical Society of Japan  2019.8  Physical Society of Japan

KAKENHI (Grants-in-Aid for Scientific Research) 3

  1. Structural analysis of various light-driven reaction mechanisms of light-sensitive proteins.

    Grant number:19H05779  2019.6 - 2024.3

    Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

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    Authorship:Coinvestigator(s) 

  2. Structural study on the function of chloride ion in photosystem II

    Grant number:18K06158  2018.4 - 2021.3

    Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (C)

    Umena Yasufumi

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    Authorship:Principal investigator 

    Grant amount:\4420000 ( Direct Cost: \3400000 、 Indirect Cost:\1020000 )

    In order to elucidate the role of chloride ion, which is an essential cofactor for water splitting in photosystem II (PSII) in photosynthesis reaction, we studied the inhibition mechanism from the crystal structure of PSII bound with molecular anions, which reduced PSII activity and to understand the original role of chloride ion from structural chemistry.
    This study succeeded in analyzing PSII crystals substituted with molecular anions azide, nitrate, and nitrite ions at 2-2.1 angstrom resolution. The inhibition mechanism was clarified from the common structural changes associated with these substitutions compared with the original structure. We concluded that the role of the chlorine ion in PSII is for supporting the proton transfer mechanism and for sustaining the structure of the active center of the Mn-cluster.

  3. Crystallographic study of water-spilitting reaction in photosystem II

    Grant number:16KT0058  2016.7 - 2020.3

    Umena Yasufumi

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    Authorship:Principal investigator 

    Grant amount:\18200000 ( Direct Cost: \14000000 、 Indirect Cost:\4200000 )

    Oxygen-evolving Photosystem II (PSII) protein in photosynthetic organisms has a Mn4CaO5 cluster as the reaction center of catalyzing a water-splitting reaction. In this study, the oxidation state in each of four Mn atoms in the cluster was investigated as well as the crystal structure of PSII in the four intermediate states of the reaction. To understand the detailed process of the water-splitting reaction in PSII, we developed a novel crystallographic analysis method using the wavelength of the absorption inflection point of a target metal atom. We prepared a lot of tinny PSII crystal, excited by pulse-laser, and then cryo-fixed. Both redox properties of each Mn atom in the cluster and crystal structure of PSII were simultaneously analyzed. As a result, we observed the redox changes in each Mn atom in the process of water-splitting reaction. Simultaneously with this redox analysis, we also captured the movements of water and proteins in PSII in the process of PSII.