start-ver=1.4
cd-journal=joma
no-vol=16
cd-vols=
no-issue=26
article-no=
start-page=12024
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2025
dt-pub=2025
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Collective motions in the primary coordination sphere: a critical functional framework for catalytic activity of the oxygen-evolving complex of photosystem II
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=Photosynthetic water oxidation, vital for dioxygen production and light energy conversion, is catalyzed by the oxygen-evolving complex of photosystem II, where the inorganic Mn4CaO5 cluster acts as the catalytic core. In this study, we investigate the functional significance of collective motions of amino acid side chains within the primary coordination sphere of the Mn cluster, focusing on their role in modulating the energetic demands for catalytic transformations in the S3 state. We applied regularized canonical correlation analysis to quantitatively correlate the three-dimensional arrangement of coordinating atoms with catalytic driving forces computed via density functional theory. Our analysis reveals that distinct collective side chain motions profoundly influence the energetic requirements for structural reconfigurations of the Mn cluster, achieved through expansion and contraction of the ligand cavity while fine-tuning its geometry to stabilize key intermediates. Complementary predictions from a neural network-based machine learning model indicate that the coordination sphere exerts a variable energetic impact on the catalytic transformations of the Mn cluster, depending on the S-state environment. Integrated computational analyses suggest that the extended lifetime of the S3YZ˙ state, consistently observed after three flash illuminations, may result from slow, progressive protein dynamics that continuously reshape the energy landscape, thereby shifting the equilibrium positions of rapid, reversible chemical processes over time. Overall, our findings demonstrate that collective motions in the primary coordination sphere constitute an active, dynamic framework essential for the efficient execution of multi-electron catalysis under ambient conditions, while simultaneously achieving a high selectivity with irreversible nature required for effective 3O2 evolution.
en-copyright=
kn-copyright=
en-aut-name=IsobeHiroshi
en-aut-sei=Isobe
en-aut-mei=Hiroshi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=
en-aut-name=SuzukiTakayoshi
en-aut-sei=Suzuki
en-aut-mei=Takayoshi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=
en-aut-name=SugaMichihiro
en-aut-sei=Suga
en-aut-mei=Michihiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=
en-aut-name=ShenJian-Ren
en-aut-sei=Shen
en-aut-mei=Jian-Ren
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=
en-aut-name=YamaguchiKizashi
en-aut-sei=Yamaguchi
en-aut-mei=Kizashi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=5
ORCID=
affil-num=1
en-affil=
kn-affil=
affil-num=2
en-affil=Research Institute for Interdisciplinary Science, Okayama University
kn-affil=
affil-num=3
en-affil=Research Institute for Interdisciplinary Science, Okayama University
kn-affil=
affil-num=4
en-affil=Research Institute for Interdisciplinary Science, Okayama University
kn-affil=
affil-num=5
en-affil=Center for Quantum Information and Quantum Biology, Osaka University
kn-affil=
END
start-ver=1.4
cd-journal=joma
no-vol=9
cd-vols=
no-issue=50
article-no=
start-page=50041
end-page=50048
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2024
dt-pub=20241205
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Conformational Flexibility of D1-Glu189: A Crucial Determinant in Substrate Water Selection, Positioning, and Stabilization within the Oxygen-Evolving Complex of Photosystem II
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=Photosynthetic water oxidation is a vital process responsible for producing dioxygen and supplying the energy necessary to sustain life on Earth. This fundamental reaction is catalyzed by the oxygen-evolving complex (OEC) of photosystem II, which houses the Mn4CaO5 cluster as its catalytic core. In this study, we specifically focus on the D1-Glu189 amino acid residue, which serves as a direct ligand to the Mn4CaO5 cluster. Our primary goal is to explore, using density functional theory (DFT), how the conformational flexibility of the D1-Glu189 side chain influences crucial catalytic processes, particularly the selection, positioning, and stabilization of a substrate water molecule within the OEC. Our investigation is based on a hypothesis put forth by Li et al. (Nature, 2024, 626, 670), which suggests that during the transition from the S2 to S3 state, a specific water molecule temporarily coordinating with the Ca ion, referred to as O6*, may exist as a hydroxide ion (OH-). Our results demonstrate a key mechanism by which the detachment of the D1-Glu189 carboxylate group from its coordination with the Ca ion allows the creation of a specialized microenvironment within the OEC that enables the selective attraction of O6* in its deprotonated form (OH-) and stabilizes it at the catalytic metal (MnD) site. Our findings indicate that D1-Glu189 is not only a structural ligand for the Ca ion but may also play an active and dynamic role in the catalytic process, positioning O6* optimally for its subsequent participation in the oxidation sequence during the water-splitting cycle.
en-copyright=
kn-copyright=
en-aut-name=IsobeHiroshi
en-aut-sei=Isobe
en-aut-mei=Hiroshi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=
en-aut-name=SuzukiTakayoshi
en-aut-sei=Suzuki
en-aut-mei=Takayoshi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=
en-aut-name=SugaMichihiro
en-aut-sei=Suga
en-aut-mei=Michihiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=
en-aut-name=ShenJian-Ren
en-aut-sei=Shen
en-aut-mei=Jian-Ren
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=
en-aut-name=YamaguchiKizashi
en-aut-sei=Yamaguchi
en-aut-mei=Kizashi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=5
ORCID=
affil-num=1
en-affil=Research Institute for Interdisciplinary Science, Okayama University
kn-affil=
affil-num=2
en-affil=Research Institute for Interdisciplinary Science, Okayama University
kn-affil=
affil-num=3
en-affil=Research Institute for Interdisciplinary Science, Okayama University
kn-affil=
affil-num=4
en-affil=Research Institute for Interdisciplinary Science, Okayama University
kn-affil=
affil-num=5
en-affil=Center for Quantum Information and Quantum Biology, Osaka University
kn-affil=
END
start-ver=1.4
cd-journal=joma
no-vol=626
cd-vols=
no-issue=7999
article-no=
start-page=670
end-page=677
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2024
dt-pub=20240131
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Oxygen-evolving photosystem II structures during S1–S2–S3 transitions
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=Photosystem II (PSII) catalyses the oxidation of water through a four-step cycle of Si states (i = 0–4) at the Mn4CaO5 cluster1,2,3, during which an extra oxygen (O6) is incorporated at the S3 state to form a possible dioxygen4,5,6,7. Structural changes of the metal cluster and its environment during the S-state transitions have been studied on the microsecond timescale. Here we use pump-probe serial femtosecond crystallography to reveal the structural dynamics of PSII from nanoseconds to milliseconds after illumination with one flash (1F) or two flashes (2F). YZ, a tyrosine residue that connects the reaction centre P680 and the Mn4CaO5 cluster, showed structural changes on a nanosecond timescale, as did its surrounding amino acid residues and water molecules, reflecting the fast transfer of electrons and protons after flash illumination. Notably, one water molecule emerged in the vicinity of Glu189 of the D1 subunit of PSII (D1-E189), and was bound to the Ca2+ ion on a sub-microsecond timescale after 2F illumination. This water molecule disappeared later with the concomitant increase of O6, suggesting that it is the origin of O6. We also observed concerted movements of water molecules in the O1, O4 and Cl-1 channels and their surrounding amino acid residues to complete the sequence of electron transfer, proton release and substrate water delivery. These results provide crucial insights into the structural dynamics of PSII during S-state transitions as well as O–O bond formation.
en-copyright=
kn-copyright=
en-aut-name=LiHongjie
en-aut-sei=Li
en-aut-mei=Hongjie
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=
en-aut-name=NakajimaYoshiki
en-aut-sei=Nakajima
en-aut-mei=Yoshiki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=
en-aut-name=NangoEriko
en-aut-sei=Nango
en-aut-mei=Eriko
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=
en-aut-name=OwadaShigeki
en-aut-sei=Owada
en-aut-mei=Shigeki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=
en-aut-name=YamadaDaichi
en-aut-sei=Yamada
en-aut-mei=Daichi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=5
ORCID=
en-aut-name=HashimotoKana
en-aut-sei=Hashimoto
en-aut-mei=Kana
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=6
ORCID=
en-aut-name=LuoFangjia
en-aut-sei=Luo
en-aut-mei=Fangjia
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=7
ORCID=
en-aut-name=TanakaRie
en-aut-sei=Tanaka
en-aut-mei=Rie
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=8
ORCID=
en-aut-name=AkitaFusamichi
en-aut-sei=Akita
en-aut-mei=Fusamichi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=9
ORCID=
en-aut-name=KatoKoji
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kn-aut-sei=
kn-aut-mei=
aut-affil-num=10
ORCID=
en-aut-name=KangJungmin
en-aut-sei=Kang
en-aut-mei=Jungmin
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=11
ORCID=
en-aut-name=SaitohYasunori
en-aut-sei=Saitoh
en-aut-mei=Yasunori
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=12
ORCID=
en-aut-name=KishiShunpei
en-aut-sei=Kishi
en-aut-mei=Shunpei
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=13
ORCID=
en-aut-name=YuHuaxin
en-aut-sei=Yu
en-aut-mei=Huaxin
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=14
ORCID=
en-aut-name=MatsubaraNaoki
en-aut-sei=Matsubara
en-aut-mei=Naoki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=15
ORCID=
en-aut-name=FujiiHajime
en-aut-sei=Fujii
en-aut-mei=Hajime
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=16
ORCID=
en-aut-name=SugaharaMichihiro
en-aut-sei=Sugahara
en-aut-mei=Michihiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=17
ORCID=
en-aut-name=SuzukiMamoru
en-aut-sei=Suzuki
en-aut-mei=Mamoru
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=18
ORCID=
en-aut-name=MasudaTetsuya
en-aut-sei=Masuda
en-aut-mei=Tetsuya
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=19
ORCID=
en-aut-name=KimuraTetsunari
en-aut-sei=Kimura
en-aut-mei=Tetsunari
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=20
ORCID=
en-aut-name=ThaoTran Nguyen
en-aut-sei=Thao
en-aut-mei=Tran Nguyen
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=21
ORCID=
en-aut-name=YonekuraShinichiro
en-aut-sei=Yonekura
en-aut-mei=Shinichiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=22
ORCID=
en-aut-name=YuLong-Jiang
en-aut-sei=Yu
en-aut-mei=Long-Jiang
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=23
ORCID=
en-aut-name=ToshaTakehiko
en-aut-sei=Tosha
en-aut-mei=Takehiko
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=24
ORCID=
en-aut-name=TonoKensuke
en-aut-sei=Tono
en-aut-mei=Kensuke
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=25
ORCID=
en-aut-name=JotiYasumasa
en-aut-sei=Joti
en-aut-mei=Yasumasa
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=26
ORCID=
en-aut-name=HatsuiTakaki
en-aut-sei=Hatsui
en-aut-mei=Takaki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=27
ORCID=
en-aut-name=YabashiMakina
en-aut-sei=Yabashi
en-aut-mei=Makina
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=28
ORCID=
en-aut-name=KuboMinoru
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en-aut-mei=Minoru
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=29
ORCID=
en-aut-name=IwataSo
en-aut-sei=Iwata
en-aut-mei=So
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=30
ORCID=
en-aut-name=IsobeHiroshi
en-aut-sei=Isobe
en-aut-mei=Hiroshi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=31
ORCID=
en-aut-name=YamaguchiKizashi
en-aut-sei=Yamaguchi
en-aut-mei=Kizashi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=32
ORCID=
en-aut-name=SugaMichihiro
en-aut-sei=Suga
en-aut-mei=Michihiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=33
ORCID=
en-aut-name=ShenJian-Ren
en-aut-sei=Shen
en-aut-mei=Jian-Ren
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=34
ORCID=
affil-num=1
en-affil=Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=2
en-affil=Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=3
en-affil=Institute of Multidisciplinary Research for Advanced Materials, Tohoku University
kn-affil=
affil-num=4
en-affil=Japan Synchrotron Radiation Research Institute
kn-affil=
affil-num=5
en-affil=Department of Picobiology, Graduate School of Life Science, University of Hyogo
kn-affil=
affil-num=6
en-affil=Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=7
en-affil=Japan Synchrotron Radiation Research Institute
kn-affil=
affil-num=8
en-affil=RIKEN SPring-8 Center
kn-affil=
affil-num=9
en-affil=Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=10
en-affil=Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=11
en-affil=RIKEN SPring-8 Center
kn-affil=
affil-num=12
en-affil=Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=13
en-affil=Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=14
en-affil=Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=15
en-affil=Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=16
en-affil=Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=17
en-affil=Japan Synchrotron Radiation Research Institute
kn-affil=
affil-num=18
en-affil=Institute for Protein Research, Osaka University
kn-affil=
affil-num=19
en-affil=Division of Food and Nutrition, Faculty of Agriculture, Ryukoku University
kn-affil=
affil-num=20
en-affil=Department of Chemistry, Graduate School of Science, Kobe University
kn-affil=
affil-num=21
en-affil=Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=22
en-affil=Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=23
en-affil=Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=24
en-affil=RIKEN SPring-8 Center
kn-affil=
affil-num=25
en-affil=Japan Synchrotron Radiation Research Institute
kn-affil=
affil-num=26
en-affil=Japan Synchrotron Radiation Research Institute
kn-affil=
affil-num=27
en-affil=Japan Synchrotron Radiation Research Institute
kn-affil=
affil-num=28
en-affil=Japan Synchrotron Radiation Research Institute
kn-affil=
affil-num=29
en-affil=Department of Picobiology, Graduate School of Life Science, University of Hyogo
kn-affil=
affil-num=30
en-affil=RIKEN SPring-8 Center
kn-affil=
affil-num=31
en-affil=Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=32
en-affil=Center for Quantum Information and Quantum Biology, Osaka University
kn-affil=
affil-num=33
en-affil=Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=34
en-affil=Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University
kn-affil=
END
start-ver=1.4
cd-journal=joma
no-vol=298
cd-vols=
no-issue=12
article-no=
start-page=102668
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2022
dt-pub=202212
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Crystal structures of photosystem II from a cyanobacterium expressing psbA2 in comparison to psbA3 reveal differences in the D1 subunit
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=Three psbA genes (psbA1, psbA2, and psbA3) encoding the D1 subunit of photosystem II (PSII) are present in the ther-mophilic cyanobacterium Thermosynechococcus elongatus and are expressed differently in response to changes in the growth environment. To clarify the functional differences of the D1 protein expressed from these psbA genes, PSII dimers from two strains, each expressing only one psbA gene (psbA2 or psbA3), were crystallized, and we analyzed their structures at resolu-tions comparable to previously studied PsbA1-PSII. Our results showed that the hydrogen bond between pheophytin/D1 (PheoD1) and D1-130 became stronger in PsbA2-and PsbA3-PSII due to change of Gln to Glu, which partially explains the increase in the redox potential of PheoD1 observed in PsbA3. In PsbA2, one hydrogen bond was lost in PheoD1 due to the change of D1-Y147F, which may explain the decrease in stability of PheoD1 in PsbA2. Two water molecules in the Cl-1 channel were lost in PsbA2 due to the change of D1-P173M, leading to the narrowing of the channel, which may explain the lower efficiency of the S-state transition beyond S2 in PsbA2-PSII. In PsbA3-PSII, a hydrogen bond between D1-Ser270 and a sulfoquinovosyl-diacylglycerol molecule near QB dis-appeared due to the change of D1-Ser270 in PsbA1 and PsbA2 to D1-Ala270. This may result in an easier exchange of bound QB with free plastoquinone, hence an enhancement of oxygen evolution in PsbA3-PSII due to its high QB exchange efficiency. These results provide a structural basis for further functional examination of the three PsbA variants.
en-copyright=
kn-copyright=
en-aut-name=NakajimaYoshiki
en-aut-sei=Nakajima
en-aut-mei=Yoshiki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=
en-aut-name=Ugai-AmoNatsumi
en-aut-sei=Ugai-Amo
en-aut-mei=Natsumi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=
en-aut-name=ToneNaoki
en-aut-sei=Tone
en-aut-mei=Naoki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=
en-aut-name=NakagawaAkiko
en-aut-sei=Nakagawa
en-aut-mei=Akiko
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=
en-aut-name=IwaiMasako
en-aut-sei=Iwai
en-aut-mei=Masako
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=5
ORCID=
en-aut-name=IkeuchiMasahiko
en-aut-sei=Ikeuchi
en-aut-mei=Masahiko
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=6
ORCID=
en-aut-name=SugiuraMiwa
en-aut-sei=Sugiura
en-aut-mei=Miwa
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=7
ORCID=
en-aut-name=SugaMichihiro
en-aut-sei=Suga
en-aut-mei=Michihiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=8
ORCID=
en-aut-name=Jian-RenShen
en-aut-sei=Jian-Ren
en-aut-mei=Shen
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=9
ORCID=
affil-num=1
en-affil=Research Institute for Interdisciplinary Science, Okayama University
kn-affil=
affil-num=2
en-affil=Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=3
en-affil=Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=4
en-affil=Proteo-Science Research Center, Ehime University
kn-affil=
affil-num=5
en-affil=Graduate School and College of Arts and Sciences, The University of Tokyo
kn-affil=
affil-num=6
en-affil=Graduate School and College of Arts and Sciences, The University of Tokyo
kn-affil=
affil-num=7
en-affil=Proteo-Science Research Center, Ehime University
kn-affil=
affil-num=8
en-affil=Research Institute for Interdisciplinary Science, Okayama University
kn-affil=
affil-num=9
en-affil=Research Institute for Interdisciplinary Science, Okayama University
kn-affil=
END
start-ver=1.4
cd-journal=joma
no-vol=471
cd-vols=
no-issue=
article-no=
start-page=214742
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2022
dt-pub=202211
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Geometric, electronic and spin structures of the CaMn4O5 catalyst for water oxidation in oxygen-evolving photosystem II. Interplay between experiments and theoretical computations
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=The aim of this review is to elucidate geometric structures of the catalytic CaMn4Ox (x = 5, 6) cluster in the Kok cycle for water oxidation in the oxygen evolving complex (OEC) of photosystem II (PSII) based on the high-resolution (HR) X-ray diffraction (XRD) and serial femtosecond crystallography (SFX) experiments using the X-ray free-electron laser (XFEL). Quantum mechanics (QM) and QM/molecular mechanics (MM) computations are performed to elucidate the electronic and spin structures of the CaMn4Ox (x = 5, 6) cluster in five states S-i (i = 0 similar to 4) on the basis of the X-ray spectroscopy, electron paramagnetic resonance (EPR) and related experiments. Interplay between the experiments and theoretical computations has been effective to elucidate the coordination structures of the CaMn4Ox (x = 5, 6) cluster ligated by amino acid residues of the protein matrix of PSII, valence states of the four Mn ions and total spin states by their exchange-couplings, and proton-shifted isomers of the CaMn4Ox (x = 5, 6) cluster. The HR XRD and SFX XFEL experiments have also elucidated the biomolecular systems structure of OEC of PSII and the hydrogen bonding networks consisting of water molecules, chloride anions, etc., for water inlet and proton release pathways in PSII. Large-scale QM/MM computations have been performed for elucidation of the hydrogen bonding distances and angles by adding invisible hydrogen atoms to the HR XRD structure. Full geometry optimizations by the QM and QM/MM methods have been effective for elucidation of the molecular systems structure around the CaMn4Ox (x = 5, 6) cluster in OEC. DLPNO-CCSD(T-0) method has been applied to elucidate relative energies of possible intermediates in each state of the Kok cycle for water oxidation. Implications of these results are discussed in relation to the blueprint for developments of artificial catalysts for water oxidation.
en-copyright=
kn-copyright=
en-aut-name=YamaguchiKizashi
en-aut-sei=Yamaguchi
en-aut-mei=Kizashi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=
en-aut-name=ShojiMitsuo
en-aut-sei=Shoji
en-aut-mei=Mitsuo
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=
en-aut-name=IsobeHiroshi
en-aut-sei=Isobe
en-aut-mei=Hiroshi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=
en-aut-name=KawakamiTakashi
en-aut-sei=Kawakami
en-aut-mei=Takashi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=
en-aut-name=MiyagawaKoichi
en-aut-sei=Miyagawa
en-aut-mei=Koichi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=5
ORCID=
en-aut-name=SugaMichihiro
en-aut-sei=Suga
en-aut-mei=Michihiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=6
ORCID=
en-aut-name=AkitaFusamichi
en-aut-sei=Akita
en-aut-mei=Fusamichi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=7
ORCID=
en-aut-name=ShenJian-Ren
en-aut-sei=Shen
en-aut-mei=Jian-Ren
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=8
ORCID=
affil-num=1
en-affil=Center for Quantum Information and Quantum Biology, Osaka University
kn-affil=
affil-num=2
en-affil=Center of Computational Sciences, Tsukuba University
kn-affil=
affil-num=3
en-affil=Research Institute for Interdisciplinary Science, and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=4
en-affil=RIKEN Center for Computational Science
kn-affil=
affil-num=5
en-affil=Center of Computational Sciences, Tsukuba University
kn-affil=
affil-num=6
en-affil=Research Institute for Interdisciplinary Science, and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=7
en-affil=Research Institute for Interdisciplinary Science, and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=8
en-affil=Research Institute for Interdisciplinary Science, and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
en-keyword=Water oxidation
kn-keyword=Water oxidation
en-keyword=Oxygen evolution
kn-keyword=Oxygen evolution
en-keyword=Photosystem II
kn-keyword=Photosystem II
en-keyword=HR XRD
kn-keyword=HR XRD
en-keyword=SFX XFEL
kn-keyword=SFX XFEL
en-keyword=QM/MM calculation
kn-keyword=QM/MM calculation
en-keyword=DLPNO CCSD(T-0) computations, Oxyl radical character
kn-keyword=DLPNO CCSD(T-0) computations, Oxyl radical character
END
start-ver=1.4
cd-journal=joma
no-vol=13
cd-vols=
no-issue=
article-no=
start-page=982068
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2022
dt-pub=20220912
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Structure and function of a silicic acid channel Lsi1
en-subtitle=
kn-subtitle=
en-abstract=
kn-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.
en-copyright=
kn-copyright=
en-aut-name=SaitohYasunori
en-aut-sei=Saitoh
en-aut-mei=Yasunori
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=
en-aut-name=SugaMichihiro
en-aut-sei=Suga
en-aut-mei=Michihiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=
affil-num=1
en-affil=Research Institute for Interdisciplinary Science, Okayama University
kn-affil=
affil-num=2
en-affil=Research Institute for Interdisciplinary Science, Okayama University
kn-affil=
en-keyword=silicon
kn-keyword=silicon
en-keyword=aquaporin
kn-keyword=aquaporin
en-keyword=NIP
kn-keyword=NIP
en-keyword=rice
kn-keyword=rice
en-keyword=crystal structure
kn-keyword=crystal structure
en-keyword=substrate selectivity
kn-keyword=substrate selectivity
en-keyword=channel
kn-keyword=channel
en-keyword=transporter
kn-keyword=transporter
END
start-ver=1.4
cd-journal=joma
no-vol=12
cd-vols=
no-issue=1
article-no=
start-page=6236
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2021
dt-pub=20211029
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Structural basis for high selectivity of a rice silicon channel Lsi1
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=Silicon (Si), the most abundant mineral element in the earth’s crust, is taken up by plant roots
in the form of silicic acid through Low silicon rice 1 (Lsi1). Lsi1 belongs to the Nodulin 26-like
intrinsic protein subfamily in aquaporin and shows high selectivity for silicic acid. To uncover
the structural basis for this high selectivity, here we show the crystal structure of the rice Lsi1
at a resolution of 1.8 Å. The structure reveals transmembrane helical orientations different
from other aquaporins, characterized by a unique, widely opened, and hydrophilic selectivity
filter (SF) composed of five residues. Our structural, functional, and theoretical investigations
provide a solid structural basis for the Si uptake mechanism in plants, which will contribute to
secure and sustainable rice production by manipulating Lsi1 selectivity for different
metalloids.
en-copyright=
kn-copyright=
en-aut-name=SaitohYasunori
en-aut-sei=Saitoh
en-aut-mei=Yasunori
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=
en-aut-name=Mitani-UenoNamiki
en-aut-sei=Mitani-Ueno
en-aut-mei=Namiki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=
en-aut-name=SaitoKeisuke
en-aut-sei=Saito
en-aut-mei=Keisuke
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=
en-aut-name=MatsukiKengo
en-aut-sei=Matsuki
en-aut-mei=Kengo
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=
en-aut-name=HuangSheng
en-aut-sei=Huang
en-aut-mei=Sheng
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=5
ORCID=
en-aut-name=YangLingli
en-aut-sei=Yang
en-aut-mei=Lingli
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=6
ORCID=
en-aut-name=YamajiNaoki
en-aut-sei=Yamaji
en-aut-mei=Naoki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=7
ORCID=
en-aut-name=IshikitaHiroshi
en-aut-sei=Ishikita
en-aut-mei=Hiroshi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=8
ORCID=
en-aut-name=ShenJian-Ren
en-aut-sei=Shen
en-aut-mei=Jian-Ren
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=9
ORCID=
en-aut-name=MaJian Feng
en-aut-sei=Ma
en-aut-mei=Jian Feng
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=10
ORCID=
en-aut-name=SugaMichihiro
en-aut-sei=Suga
en-aut-mei=Michihiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=11
ORCID=
affil-num=1
en-affil=Research Institute for Interdisciplinary Science, Okayama University
kn-affil=
affil-num=2
en-affil=Institute of Plant Science and Resources, Okayama University
kn-affil=
affil-num=3
en-affil=Research Center for Advanced Science and Technology, The University of Tokyo
kn-affil=
affil-num=4
en-affil=Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=5
en-affil=Institute of Plant Science and Resources, Okayama University
kn-affil=
affil-num=6
en-affil=Research Institute for Interdisciplinary Science, Okayama University
kn-affil=
affil-num=7
en-affil=Institute of Plant Science and Resources, Okayama University
kn-affil=
affil-num=8
en-affil=Research Center for Advanced Science and Technology, The University of Tokyo
kn-affil=
affil-num=9
en-affil=Research Institute for Interdisciplinary Science, Okayama University
kn-affil=
affil-num=10
en-affil=Institute of Plant Science and Resources, Okayama University
kn-affil=
affil-num=11
en-affil=Research Institute for Interdisciplinary Science, Okayama University
kn-affil=
END
start-ver=1.4
cd-journal=joma
no-vol=1864
cd-vols=
no-issue=2
article-no=
start-page=129466
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2020
dt-pub=20200229
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Time-resolved studies of metalloproteins using X-ray free electron laser radiation at SACLA
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=Background: The invention of the X-ray free-electron laser (XFEL) has provided unprecedented new opportunities for structural biology. The advantage of XFEL is an intense pulse of X-rays and a very short pulse duration (<10 fs) promising a damage-free and time-resolved crystallography approach.
Scope of review: Recent time-resolved crystallographic analyses in XFEL facility SACLA are reviewed. Specifically, metalloproteins involved in the essential reactions of bioenergy conversion including photosystem II, cytochrome c oxidase and nitric oxide reductase are described.
Major conclusions: XFEL with pump-probe techniques successfully visualized the process of the reaction and the dynamics of a protein. Since the active center of metalloproteins is very sensitive to the X-ray radiation, damage-free structures obtained by XFEL are essential to draw mechanistic conclusions. Methods and tools for sample delivery and reaction initiation are key for successful measurement of the time-resolved data.
General significance: XFEL is at the center of approaches to gain insight into complex mechanism of structural dynamics and the reactions catalyzed by biological macromolecules. Further development has been carried out to expand the application of time-resolved X-ray crystallography. This article is part of a Special Issue entitled Novel measurement techniques for visualizing 'live' protein molecules.
en-copyright=
kn-copyright=
en-aut-name=SugaMichihiro
en-aut-sei=Suga
en-aut-mei=Michihiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=
en-aut-name=ShimadaAtsuhiro
en-aut-sei=Shimada
en-aut-mei=Atsuhiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=
en-aut-name=AkitaFusamichi
en-aut-sei=Akita
en-aut-mei=Fusamichi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=
en-aut-name=ShenJian-Ren
en-aut-sei=Shen
en-aut-mei=Jian-Ren
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=
en-aut-name=ToshaTakehiko
en-aut-sei=Tosha
en-aut-mei=Takehiko
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=5
ORCID=
en-aut-name=SugimotoHiroshi
en-aut-sei=Sugimoto
en-aut-mei=Hiroshi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=6
ORCID=
affil-num=1
en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=2
en-affil=Graduate School of Applied Biological Sciences and Faculty of Applied Biological Sciences, Gifu University
kn-affil=
affil-num=3
en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=4
en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=5
en-affil=Synchrotron Radiation Life Science Instrumentation Team, RIKEN SPring-8 Center
kn-affil=
affil-num=6
en-affil=Synchrotron Radiation Life Science Instrumentation Team, RIKEN SPring-8 Center
kn-affil=
en-keyword=Heme
kn-keyword=Heme
en-keyword=Metalloproteins
kn-keyword=Metalloproteins
en-keyword=Proton pump
kn-keyword=Proton pump
en-keyword=Radiation damage
kn-keyword=Radiation damage
en-keyword=Serial femtosecond crystallography
kn-keyword=Serial femtosecond crystallography
en-keyword=X-ray free-electron laser
kn-keyword=X-ray free-electron laser
END
start-ver=1.4
cd-journal=joma
no-vol=366
cd-vols=
no-issue=6463
article-no=
start-page=334
end-page=338
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2019
dt-pub=20191018
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=An oxyl/oxo mechanism for dioxygen bond formation in PSII revealed by X-ray free electron lasers
en-subtitle=
kn-subtitle=
en-abstract=
kn-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.
en-copyright=
kn-copyright=
en-aut-name=SugaMichihiro
en-aut-sei=Suga
en-aut-mei=Michihiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=
en-aut-name=AkitaFusamichi
en-aut-sei=Akita
en-aut-mei=Fusamichi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=
en-aut-name=YamashitaKeitaro
en-aut-sei=Yamashita
en-aut-mei=Keitaro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=
en-aut-name=NakajimaYoshiki
en-aut-sei=Nakajima
en-aut-mei=Yoshiki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=
en-aut-name=UenoGo
en-aut-sei=Ueno
en-aut-mei=Go
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=5
ORCID=
en-aut-name=LiHongjie
en-aut-sei=Li
en-aut-mei=Hongjie
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=6
ORCID=
en-aut-name=YamaneTakahiro
en-aut-sei=Yamane
en-aut-mei=Takahiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=7
ORCID=
en-aut-name=HirataKunio
en-aut-sei=Hirata
en-aut-mei=Kunio
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=8
ORCID=
en-aut-name=UmenaYasufumi
en-aut-sei=Umena
en-aut-mei=Yasufumi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=9
ORCID=
en-aut-name=YonekuraShinichiro
en-aut-sei=Yonekura
en-aut-mei=Shinichiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=10
ORCID=
en-aut-name=YuLong-Jiang
en-aut-sei=Yu
en-aut-mei=Long-Jiang
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=11
ORCID=
en-aut-name=MurakamiHironori
en-aut-sei=Murakami
en-aut-mei=Hironori
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=12
ORCID=
en-aut-name=NomuraTakashi
en-aut-sei=Nomura
en-aut-mei=Takashi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=13
ORCID=
en-aut-name=KimuraTetsunari
en-aut-sei=Kimura
en-aut-mei=Tetsunari
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=14
ORCID=
en-aut-name=KuboMinoru
en-aut-sei=Kubo
en-aut-mei=Minoru
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=15
ORCID=
en-aut-name=BabaSeiki
en-aut-sei=Baba
en-aut-mei=Seiki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=16
ORCID=
en-aut-name=KumasakaTakashi
en-aut-sei=Kumasaka
en-aut-mei=Takashi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=17
ORCID=
en-aut-name=TonoKensuke
en-aut-sei=Tono
en-aut-mei=Kensuke
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=18
ORCID=
en-aut-name=YabashiMakina
en-aut-sei=Yabashi
en-aut-mei=Makina
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=19
ORCID=
en-aut-name=IsobeHiroshi
en-aut-sei=Isobe
en-aut-mei=Hiroshi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=20
ORCID=
en-aut-name=YamaguchiKizashi
en-aut-sei=Yamaguchi
en-aut-mei=Kizashi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=21
ORCID=
en-aut-name=YamamotoMasaki
en-aut-sei=Yamamoto
en-aut-mei=Masaki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=22
ORCID=
en-aut-name=AgoHideo
en-aut-sei=Ago
en-aut-mei=Hideo
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=23
ORCID=
en-aut-name=ShenJian-Ren
en-aut-sei=Shen
en-aut-mei=Jian-Ren
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=24
ORCID=
affil-num=1
en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=2
en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=3
en-affil=RIKEN SPring-8 Center
kn-affil=
affil-num=4
en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=5
en-affil=RIKEN SPring-8 Center
kn-affil=
affil-num=6
en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=7
en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=8
en-affil=RIKEN SPring-8 Center
kn-affil=
affil-num=9
en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=10
en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=11
en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=12
en-affil=Japan Synchrotron Radiation Research Institute
kn-affil=
affil-num=13
en-affil=RIKEN SPring-8 Center
kn-affil=
affil-num=14
en-affil=Department of Chemistry, Graduate School of Science, Kobe University
kn-affil=
affil-num=15
en-affil=RIKEN SPring-8 Center
kn-affil=
affil-num=16
en-affil=Japan Synchrotron Radiation Research Institute
kn-affil=
affil-num=17
en-affil=Japan Synchrotron Radiation Research Institute
kn-affil=
affil-num=18
en-affil=RIKEN SPring-8 Center
kn-affil=
affil-num=19
en-affil=RIKEN SPring-8 Center
kn-affil=
affil-num=20
en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=21
en-affil=The Institute for Scientific and Industrial Research, Osaka University
kn-affil=
affil-num=22
en-affil=RIKEN SPring-8 Center
kn-affil=
affil-num=23
en-affil=RIKEN SPring-8 Center
kn-affil=
affil-num=24
en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
END
start-ver=1.4
cd-journal=joma
no-vol=292
cd-vols=
no-issue=23
article-no=
start-page=9599
end-page=9612
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2017
dt-pub=201706
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Crystal structure and redox properties of a novel cyanobacterial heme protein with a His/Cys heme axial ligation and a Per-Arnt-Sim (PAS)-like domain
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract= Photosystem II catalyzes light-induced water oxidation leading to the generation of dioxygen indispensable for sustaining aerobic life on Earth. The Photosystem II reaction center is composed of D1 and D2 proteins encoded by psbA and psbD genes, respectively. In cyanobacteria, different psbA genes are present in the genome. The thermophilic cyanobacterium Thermosynechococcus elongatus contains three psbA genes: psbA1, psbA2, and psbA3, and a new c-type heme protein, Tll0287, was found to be expressed in a strain expressing the psbA2 gene only, but the structure and function of Tll0287 are unknown. Here we solved the crystal structure of Tll0287 at a 2.0 Å resolution. The overall structure of Tll0287 was found to be similar to some kinases and sensor proteins with a Per-Arnt-Sim-like domain rather than to other c-type cytochromes. The fifth and sixth axial ligands for the heme were Cys and His, instead of the His/Met or His/His ligand pairs observed for most of the c-type hemes. The redox potential, E½, of Tll0287 was -255 ± 20 mV versus normal hydrogen electrode at pH values above 7.5. Below this pH value, the E½ increased by ≈57 mV/pH unit at 15 °C, suggesting the involvement of a protonatable group with a pKred = 7.2 ± 0.3. Possible functions of Tll0287 as a redox sensor under microaerobic conditions or a cytochrome subunit of an H2S-oxidizing system are discussed in view of the environmental conditions in which psbA2 is expressed, as well as phylogenetic analysis, structural, and sequence homologies.
en-copyright=
kn-copyright=
en-aut-name=MotomuraTaiki
en-aut-sei=Motomura
en-aut-mei=Taiki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=
en-aut-name=SugaMichihiro
en-aut-sei=Suga
en-aut-mei=Michihiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=
en-aut-name=HienerwadelRainer
en-aut-sei=Hienerwadel
en-aut-mei=Rainer
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=
en-aut-name=NakagawaAkiko
en-aut-sei=Nakagawa
en-aut-mei=Akiko
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=
en-aut-name=LaiThanh-Lan
en-aut-sei=Lai
en-aut-mei=Thanh-Lan
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=5
ORCID=
en-aut-name=NitschkeWolfgang
en-aut-sei=Nitschke
en-aut-mei=Wolfgang
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=6
ORCID=
en-aut-name=KumaTakahiro
en-aut-sei=Kuma
en-aut-mei=Takahiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=7
ORCID=
en-aut-name=SugiuraMiwa
en-aut-sei=Sugiura
en-aut-mei=Miwa
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=8
ORCID=
en-aut-name=BoussacAlain
en-aut-sei=Boussac
en-aut-mei=Alain
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=9
ORCID=
en-aut-name=ShenJian-Ren
en-aut-sei=Shen
en-aut-mei=Jian-Ren
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=10
ORCID=
affil-num=1
en-affil=the Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=2
en-affil=the Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=3
en-affil= the Laboratoire de Génétique et Biophysique des Plantes, UMR 7265, CNRS-CEA-Aix-Marseille Université, Faculté des Sciences de Luminy
kn-affil=
affil-num=4
en-affil= the Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=5
en-affil= iBiTec-S
kn-affil=
affil-num=6
en-affil= the Laboratoire de Bioénergétique et Ingénierie des Protéines
kn-affil=
affil-num=7
en-affil= the Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=8
en-affil=the Proteo-Science Research Center, Ehime University
kn-affil=
affil-num=9
en-affil=iBiTec-S
kn-affil=
affil-num=10
en-affil= the Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
en-keyword=D1 protein
kn-keyword=D1 protein
en-keyword=His-Cys heme axial coordination
kn-keyword=His-Cys heme axial coordination
en-keyword=PAS domain
kn-keyword=PAS domain
en-keyword=PAS-like domain
kn-keyword=PAS-like domain
en-keyword=Tll0287
kn-keyword=Tll0287
en-keyword=X-ray crystallography
kn-keyword=X-ray crystallography
en-keyword=cytochrome
kn-keyword=cytochrome
en-keyword=heme
kn-keyword=heme
en-keyword=photosynthesis
kn-keyword=photosynthesis
en-keyword=photosystem II
kn-keyword=photosystem II
END
start-ver=1.4
cd-journal=joma
no-vol=39
cd-vols=
no-issue=
article-no=
start-page=46
end-page=53
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2016
dt-pub=201608
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Structure and energy transfer pathways of the plant photosystem I-LHCI supercomplex
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=Photosystem I (PSI) is one of the two photosystems in oxygenic photosynthesis, and absorbs light energy to generate reducing power for the reduction of NADP+ to NADPH with a quantum efficiency close to 100%. The plant PSI core forms a supercomplex with light-harvesting complex I (LHCI) with a total molecular weight of over 600 kDa. Recent X-ray structure analysis of the PSI-LHCI membrane-protein supercomplex has revealed detailed arrangement of the light-harvesting pigments and other cofactors especially within LHCI. Here we introduce the overall structure of the PSI-LHCI supercomplex, and then focus on the excited energy transfer (EET) pathways from LHCI to the PSI core and photoprotection mechanisms based on the structure obtained.
en-copyright=
kn-copyright=
en-aut-name=SugaMichihiro
en-aut-sei=Suga
en-aut-mei=Michihiro
kn-aut-name=菅倫寛
kn-aut-sei=菅
kn-aut-mei=倫寛
aut-affil-num=1
ORCID=
en-aut-name=QinXiaochun
en-aut-sei=Qin
en-aut-mei=Xiaochun
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=
en-aut-name=KuangTingyun
en-aut-sei=Kuang
en-aut-mei=Tingyun
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=
en-aut-name=ShenJian-Ren
en-aut-sei=Shen
en-aut-mei=Jian-Ren
kn-aut-name=沈建仁
kn-aut-sei=沈
kn-aut-mei=建仁
aut-affil-num=4
ORCID=
affil-num=1
en-affil=Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University
kn-affil=岡山大学異分野基礎科学研究所
affil-num=2
en-affil=Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University
kn-affil=岡山大学異分野基礎科学研究所
affil-num=3
en-affil=Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences
kn-affil=
affil-num=4
en-affil=Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University
kn-affil=岡山大学異分野基礎科学研究所
END