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Yasufumi Umena

Bio: Yasufumi Umena is an academic researcher from Okayama University. The author has contributed to research in topics: Photosystem II & Oxygen-evolving complex. The author has an hindex of 24, co-authored 49 publications receiving 5435 citations. Previous affiliations of Yasufumi Umena include Osaka University & Osaka City University.


Papers
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Journal ArticleDOI
05 May 2011-Nature
TL;DR: The crystal structure of photosystem II is reported, finding that five oxygen atoms served as oxo bridges linking the five metal atoms, and that four water molecules were bound to the Mn4CaO5 cluster; some of them may therefore serve as substrates for dioxygen formation.
Abstract: Photosystem II is the site of photosynthetic water oxidation and contains 20 subunits with a total molecular mass of 350 kDa. The structure of photosystem II has been reported at resolutions from 3.8 to 2.9 angstrom. These resolutions have provided much information on the arrangement of protein subunits and cofactors but are insufficient to reveal the detailed structure of the catalytic centre of water splitting. Here we report the crystal structure of photosystem II at a resolution of 1.9 angstrom. From our electron density map, we located all of the metal atoms of the Mn(4)CaO(5) cluster, together with all of their ligands. We found that five oxygen atoms served as oxo bridges linking the five metal atoms, and that four water molecules were bound to the Mn(4)CaO(5) cluster; some of them may therefore serve as substrates for dioxygen formation. We identified more than 1,300 water molecules in each photosystem II monomer. Some of them formed extensive hydrogen-bonding networks that may serve as channels for protons, water or oxygen molecules. The determination of the high-resolution structure of photosystem II will allow us to analyse and understand its functions in great detail.

3,325 citations

Journal ArticleDOI
02 Mar 2017-Nature
TL;DR: The structural changes in PSII induced by two-flash illumination at room temperature at a resolution of 2.35 Å are described, providing a mechanism for the O=O bond formation consistent with that proposed previously.
Abstract: Photosystem II (PSII) is a huge membrane-protein complex consisting of 20 different subunits with a total molecular mass of 350 kDa for a monomer. It catalyses light-driven water oxidation at its catalytic centre, the oxygen-evolving complex (OEC). The structure of PSII has been analysed at 1.9 A resolution by synchrotron radiation X-rays, which revealed that the OEC is a Mn4CaO5 cluster organized in an asymmetric, 'distorted-chair' form. This structure was further analysed with femtosecond X-ray free electron lasers (XFEL), providing the 'radiation damage-free' structure. The mechanism of O=O bond formation, however, remains obscure owing to the lack of intermediate-state structures. Here we describe the structural changes in PSII induced by two-flash illumination at room temperature at a resolution of 2.35 A using time-resolved serial femtosecond crystallography with an XFEL provided by the SPring-8 angstrom compact free-electron laser. An isomorphous difference Fourier map between the two-flash and dark-adapted states revealed two areas of apparent changes: around the QB/non-haem iron and the Mn4CaO5 cluster. The changes around the QB/non-haem iron region reflected the electron and proton transfers induced by the two-flash illumination. In the region around the OEC, a water molecule located 3.5 A from the Mn4CaO5 cluster disappeared from the map upon two-flash illumination. This reduced the distance between another water molecule and the oxygen atom O4, suggesting that proton transfer also occurred. Importantly, the two-flash-minus-dark isomorphous difference Fourier map showed an apparent positive peak around O5, a unique μ4-oxo-bridge located in the quasi-centre of Mn1 and Mn4 (refs 4,5). This suggests the insertion of a new oxygen atom (O6) close to O5, providing an O=O distance of 1.5 A between these two oxygen atoms. This provides a mechanism for the O=O bond formation consistent with that proposed previously

455 citations

Journal ArticleDOI
TL;DR: Results indicate that these 2 Cl− anions are required to maintain the coordination structure of the Mn4Ca cluster as well as the proposed proton channel, thereby keeping the oxygen-evolving complex fully active.
Abstract: The chloride ion, Cl−, is an essential cofactor for oxygen evolution of photosystem II (PSII) and is closely associated with the Mn4Ca cluster Its detailed location and function have not been identified, however We substituted Cl− with a bromide ion (Br−) or an iodide ion (I−) in PSII and analyzed the crystal structures of PSII with Br− and I− substitutions Substitution of Cl− with Br− did not inhibit oxygen evolution, whereas substitution of Cl− with I− completely inhibited oxygen evolution, indicating the efficient replacement of Cl− by I− PSII with Br− and I− substitutions were crystallized, and their structures were analyzed The results showed that there are 2 anion-binding sites in each PSII monomer; they are located on 2 sides of the Mn4Ca cluster at equal distances from the metal cluster Anion-binding site 1 is close to the main chain of D1-Glu-333, and site 2 is close to the main chain of CP43-Glu-354; these 2 residues are coordinated directly with the Mn4Ca cluster In addition, site 1 is located in the entrance of a proton exit channel These results indicate that these 2 Cl− anions are required to maintain the coordination structure of the Mn4Ca cluster as well as the proposed proton channel, thereby keeping the oxygen-evolving complex fully active

219 citations

Journal ArticleDOI
18 Oct 2019-Science
TL;DR: To reveal the mechanism of water oxidation, structures of PSII in the S1, S2, and S3 states by x-ray free-electron laser serial crystallography reveal details of photosynthetic oxygen evolution.
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.

205 citations

Journal ArticleDOI
TL;DR: The results provide refined intermetallic distances within the Mn cluster and suggest that the XRD model most likely corresponds to a mixture of oxidation states, including species more reduced than those observed in the catalytic cycle of water splitting.
Abstract: We introduce a quantum mechanics/molecular mechanics model of the oxygen-evolving complex of photosystem II in the S1 Mn4(IV,III,IV,III) state, where Ca2+ is bridged to manganese centers by the carboxylate moieties of D170 and A344 on the basis of the new X-ray diffraction (XRD) model recently reported at 19 A resolution The model is also consistent with high-resolution spectroscopic data, including polarized extended X-ray absorption fine structure data of oriented single crystals Our results provide refined intermetallic distances within the Mn cluster and suggest that the XRD model most likely corresponds to a mixture of oxidation states, including species more reduced than those observed in the catalytic cycle of water splitting

204 citations


Cited by
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Journal ArticleDOI
05 May 2011-Nature
TL;DR: The crystal structure of photosystem II is reported, finding that five oxygen atoms served as oxo bridges linking the five metal atoms, and that four water molecules were bound to the Mn4CaO5 cluster; some of them may therefore serve as substrates for dioxygen formation.
Abstract: Photosystem II is the site of photosynthetic water oxidation and contains 20 subunits with a total molecular mass of 350 kDa. The structure of photosystem II has been reported at resolutions from 3.8 to 2.9 angstrom. These resolutions have provided much information on the arrangement of protein subunits and cofactors but are insufficient to reveal the detailed structure of the catalytic centre of water splitting. Here we report the crystal structure of photosystem II at a resolution of 1.9 angstrom. From our electron density map, we located all of the metal atoms of the Mn(4)CaO(5) cluster, together with all of their ligands. We found that five oxygen atoms served as oxo bridges linking the five metal atoms, and that four water molecules were bound to the Mn(4)CaO(5) cluster; some of them may therefore serve as substrates for dioxygen formation. We identified more than 1,300 water molecules in each photosystem II monomer. Some of them formed extensive hydrogen-bonding networks that may serve as channels for protons, water or oxygen molecules. The determination of the high-resolution structure of photosystem II will allow us to analyse and understand its functions in great detail.

3,325 citations

Journal ArticleDOI
TL;DR: The battery electrochemistry and catalytic mechanism of oxygen reduction reactions are discussed on the basis of aqueous and organic electrolytes, and the design and optimization of air-electrode structure are outlined.
Abstract: Because of the remarkably high theoretical energy output, metal–air batteries represent one class of promising power sources for applications in next-generation electronics, electrified transportation and energy storage of smart grids. The most prominent feature of a metal–air battery is the combination of a metal anode with high energy density and an air electrode with open structure to draw cathode active materials (i.e., oxygen) from air. In this critical review, we present the fundamentals and recent advances related to the fields of metal–air batteries, with a focus on the electrochemistry and materials chemistry of air electrodes. The battery electrochemistry and catalytic mechanism of oxygen reduction reactions are discussed on the basis of aqueous and organic electrolytes. Four groups of extensively studied catalysts for the cathode oxygen reduction/evolution are selectively surveyed from materials chemistry to electrode properties and battery application: Pt and Pt-based alloys (e.g., PtAu nanoparticles), carbonaceous materials (e.g., graphene nanosheets), transition-metal oxides (e.g., Mn-based spinels and perovskites), and inorganic–organic composites (e.g., metal macrocycle derivatives). The design and optimization of air-electrode structure are also outlined. Furthermore, remarks on the challenges and perspectives of research directions are proposed for further development of metal–air batteries (219 references).

2,211 citations

Journal ArticleDOI
TL;DR: Proton-coupled electron transfer is an important mechanism for charge transfer in a wide variety of systems including biology- and materials-oriented venues and several are reviewed.
Abstract: ▪ Abstract Proton-coupled electron transfer (PCET) is an important mechanism for charge transfer in a wide variety of systems including biology- and materials-oriented venues. We review several are...

2,182 citations

Journal ArticleDOI
TL;DR: In this paper, a vision for a future sustainable hydrogen fuel community based on artificial photosynthesis is outlined and current progress towards artificial photosynthetic devices is reviewed, with particular focus on visible light active nanostructures.
Abstract: Hydrogen from solar-driven water splitting has the potential to provide clean energy. Current progress towards artificial photosynthetic devices is reviewed, with particular focus on visible light active nanostructures. A vision for a future sustainable hydrogen fuel community based on artificial photosynthesis is outlined.

1,703 citations

Journal ArticleDOI
04 Nov 2011-Science
TL;DR: The development of solar water-splitting cells comprising earth-abundant elements that operate in near-neutral pH conditions, both with and without connecting wires are described, allowing for direct solar-to-fuels conversion that captures many of the basic functional elements of a leaf.
Abstract: We describe the development of solar water-splitting cells comprising earth-abundant elements that operate in near-neutral pH conditions, both with and without connecting wires. The cells consist of a triple junction, amorphous silicon photovoltaic interfaced to hydrogen- and oxygen-evolving catalysts made from an alloy of earth-abundant metals and a cobalt|borate catalyst, respectively. The devices described here carry out the solar-driven water-splitting reaction at efficiencies of 4.7% for a wired configuration and 2.5% for a wireless configuration when illuminated with 1 sun (100 milliwatts per square centimeter) of air mass 1.5 simulated sunlight. Fuel-forming catalysts interfaced with light-harvesting semiconductors afford a pathway to direct solar-to-fuels conversion that captures many of the basic functional elements of a leaf.

1,535 citations