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
en-aut-sei=Kato
en-aut-mei=Koji
kn-aut-name=
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
en-aut-sei=Kubo
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=14
cd-vols=
no-issue=1
article-no=
start-page=8164
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2023
dt-pub=20231209
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Structural insights into photosystem II supercomplex and trimeric FCP antennae of a centric diatom Cyclotella meneghiniana
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=Diatoms are dominant marine algae and contribute around a quarter of global primary productivity, the success of which is largely attributed to their photosynthetic capacity aided by specific fucoxanthin chlorophyll-binding proteins (FCPs) to enhance the blue-green light absorption under water. We purified a photosystem II (PSII)-FCPII supercomplex and a trimeric FCP from Cyclotella meneghiniana (Cm) and solved their structures by cryo-electron microscopy (cryo-EM). The structures reveal detailed organizations of monomeric, dimeric and trimeric FCP antennae, as well as distinct assemblies of Lhcx6_1 and dimeric FCPII-H in PSII core. Each Cm-PSII-FCPII monomer contains an Lhcx6_1, an FCP heterodimer and other three FCP monomers, which form an efficient pigment network for harvesting energy. More diadinoxanthins and diatoxanthins are found in FCPs, which may function to quench excess energy. The trimeric FCP contains more chlorophylls c and fucoxanthins. These diversified FCPs and PSII-FCPII provide a structural basis for efficient light energy harvesting, transfer, and dissipation in C. meneghiniana.
en-copyright=
kn-copyright=
en-aut-name=ZhaoSonghao
en-aut-sei=Zhao
en-aut-mei=Songhao
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=
en-aut-name=ShenLili
en-aut-sei=Shen
en-aut-mei=Lili
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=
en-aut-name=LiXiaoyi
en-aut-sei=Li
en-aut-mei=Xiaoyi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=
en-aut-name=TaoQiushuang
en-aut-sei=Tao
en-aut-mei=Qiushuang
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=
en-aut-name=LiZhenhua
en-aut-sei=Li
en-aut-mei=Zhenhua
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=5
ORCID=
en-aut-name=XuCaizhe
en-aut-sei=Xu
en-aut-mei=Caizhe
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=6
ORCID=
en-aut-name=ZhouCuicui
en-aut-sei=Zhou
en-aut-mei=Cuicui
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=7
ORCID=
en-aut-name=YangYanyan
en-aut-sei=Yang
en-aut-mei=Yanyan
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=8
ORCID=
en-aut-name=SangMin
en-aut-sei=Sang
en-aut-mei=Min
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=9
ORCID=
en-aut-name=HanGuangye
en-aut-sei=Han
en-aut-mei=Guangye
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=KuangTingyun
en-aut-sei=Kuang
en-aut-mei=Tingyun
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=12
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=13
ORCID=
en-aut-name=WangWenda
en-aut-sei=Wang
en-aut-mei=Wenda
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=14
ORCID=
affil-num=1
en-affil=Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences
kn-affil=
affil-num=2
en-affil=Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences
kn-affil=
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=Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences
kn-affil=
affil-num=5
en-affil=Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences
kn-affil=
affil-num=6
en-affil=Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences
kn-affil=
affil-num=7
en-affil=Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences
kn-affil=
affil-num=8
en-affil=Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences
kn-affil=
affil-num=9
en-affil=China National Botanical Garden
kn-affil=
affil-num=10
en-affil=Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences
kn-affil=
affil-num=11
en-affil=Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences
kn-affil=
affil-num=12
en-affil=Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences
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=Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences
kn-affil=
END
start-ver=1.4
cd-journal=joma
no-vol=299
cd-vols=
no-issue=7
article-no=
start-page=104839
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2023
dt-pub=202307
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Structural insights into the action mechanisms of artificial electron acceptors in photosystem II
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=Photosystem II (PSII) utilizes light energy to split water, and the electrons extracted from water are transferred to QB, a plastoquinone molecule bound to the D1 subunit of PSII. Many artificial electron acceptors (AEAs) with molecular structures similar to that of plastoquinone can accept electrons from PSII. However, the molecular mechanism by which AEAs act on PSII is unclear. Here, we solved the crystal structure of PSII treated with three different AEAs, 2,5-dibromo-1,4-benzoquinone, 2,6dichloro-1,4-benzoquinone, and 2-phenyl-1,4-benzoquinone, at 1.95 to 2.10 angstrom resolution. Our results show that all AEAs substitute for QB and are bound to the QB-binding site (QB site) to receive electrons, but their binding strengths are different, resulting in differences in their efficiencies to accept electrons. The acceptor 2-phenyl-1,4-benzoquinone binds most weakly to the QB site and showed the highest oxygen-evolving activity, implying a reverse relationship between the binding strength and oxygen-evolving activity. In addition, a novel quinonebinding site, designated the QD site, was discovered, which is located in the vicinity of QB site and close to QC site, a binding site reported previously. This QD site is expected to play a role as a channel or a storage site for quinones to be transported to the QB site. These results provide the structural basis for elucidating the actions of AEAs and exchange mechanism of QB in PSII and also provide information for the design of more efficient electron acceptors.
en-copyright=
kn-copyright=
en-aut-name=KamadaShinji
en-aut-sei=Kamada
en-aut-mei=Shinji
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=ShenJian-Ren
en-aut-sei=Shen
en-aut-mei=Jian-Ren
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=
affil-num=1
en-affil=Faculty of Science, 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=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
en-keyword=Photosystem II
kn-keyword=Photosystem II
en-keyword=photosynthesis
kn-keyword=photosynthesis
en-keyword=electron transfer
kn-keyword=electron transfer
en-keyword=structural biology
kn-keyword=structural biology
en-keyword=crystal structure
kn-keyword=crystal structure
en-keyword=electron acceptor
kn-keyword=electron acceptor
END
start-ver=1.4
cd-journal=joma
no-vol=14
cd-vols=
no-issue=1
article-no=
start-page=920
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2023
dt-pub=20230217
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Structure of a monomeric photosystem I core associated with iron-stress-induced-A proteins from Anabaena sp. PCC 7120
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=Iron-stress-induced-A proteins (IsiAs) are expressed in cyanobacteria under iron-deficient conditions. The cyanobacterium Anabaena sp. PCC 7120 has four isiA genes; however, their binding property and functional roles in PSI are still missing. We analyzed a cryo-electron microscopy structure of a PSI-IsiA supercomplex isolated from Anabaena grown under an iron-deficient condition. The PSI-IsiA structure contains six IsiA subunits associated with the PsaA side of a PSI core monomer. Three of the six IsiA subunits were identified as IsiA1 and IsiA2. The PSI-IsiA structure lacks a PsaL subunit; instead, a C-terminal domain of IsiA2 occupies the position of PsaL, which inhibits the oligomerization of PSI, leading to the formation of a PSI monomer. Furthermore, excitation-energy transfer from IsiAs to PSI appeared with a time constant of 55 ps. These findings provide insights into both the molecular assembly of the Anabaena IsiA family and the functional roles of IsiAs.
en-copyright=
kn-copyright=
en-aut-name=NagaoRyo
en-aut-sei=Nagao
en-aut-mei=Ryo
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=
en-aut-name=KatoKoji
en-aut-sei=Kato
en-aut-mei=Koji
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=
en-aut-name=HamaguchiTasuku
en-aut-sei=Hamaguchi
en-aut-mei=Tasuku
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=
en-aut-name=UenoYoshifumi
en-aut-sei=Ueno
en-aut-mei=Yoshifumi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=
en-aut-name=TsuboshitaNaoki
en-aut-sei=Tsuboshita
en-aut-mei=Naoki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=5
ORCID=
en-aut-name=ShimizuShota
en-aut-sei=Shimizu
en-aut-mei=Shota
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=6
ORCID=
en-aut-name=FurutaniMiyu
en-aut-sei=Furutani
en-aut-mei=Miyu
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=7
ORCID=
en-aut-name=EhiraShigeki
en-aut-sei=Ehira
en-aut-mei=Shigeki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=8
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=9
ORCID=
en-aut-name=KawakamiKeisuke
en-aut-sei=Kawakami
en-aut-mei=Keisuke
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=10
ORCID=
en-aut-name=SuzukiTakehiro
en-aut-sei=Suzuki
en-aut-mei=Takehiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=11
ORCID=
en-aut-name=DohmaeNaoshi
en-aut-sei=Dohmae
en-aut-mei=Naoshi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=12
ORCID=
en-aut-name=AkimotoSeiji
en-aut-sei=Akimoto
en-aut-mei=Seiji
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=13
ORCID=
en-aut-name=YonekuraKoji
en-aut-sei=Yonekura
en-aut-mei=Koji
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=14
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=15
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=Biostructural Mechanism Laboratory, RIKEN SPring-8 Center
kn-affil=
affil-num=4
en-affil=Graduate School of Science, Kobe University
kn-affil=
affil-num=5
en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama 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=Graduate School of Science, Kobe University
kn-affil=
affil-num=8
en-affil=Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University
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=Biostructural Mechanism Laboratory, RIKEN SPring-8 Center
kn-affil=
affil-num=11
en-affil=Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science
kn-affil=
affil-num=12
en-affil=Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science
kn-affil=
affil-num=13
en-affil=Graduate School of Science, Kobe University
kn-affil=
affil-num=14
en-affil= Biostructural Mechanism Laboratory, RIKEN SPring-8 Center
kn-affil=
affil-num=15
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=126
cd-vols=
no-issue=38
article-no=
start-page=7212
end-page=7228
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2022
dt-pub=20220915
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Roles of the Flexible Primary Coordination Sphere of the Mn4CaOx Cluster: What Are the Immediate Decay Products of the S-3 State?
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=The primary coordination sphere of the multinuclear cofactor (Mn4CaOx) in the oxygen-evolving complex (OEC) of photosystem II is absolutely conserved to maintain its structure and function. Recent time-resolved serial femtosecond crystallography identified large reorganization of the primary coordination sphere in the S-2 to S-3 transition, which elicits a cascade of events involving Mn oxidation and water molecule binding to a putative catalytic Mn site. We examined how the crystallographic fields, created by transient conformational states of the OEC at various time points, affect the thermodynamics of various isomers of the Mn cluster using DFT calculations, with an aim of comprehending the functional roles of the flexible primary coordination sphere in the S-2 to S-3 transition and in the recovery of the S-2 state. The results show that the relative movements of surrounding residues change the size and shape of the cavity of the cluster and thereby affect the thermodynamics of various catalytic intermediates as well as the ability to capture a new water molecule at a coordinatively unsaturated site. The implication of these findings is that the protein dynamics may serve to gate the catalytic reaction efficiently by controlling the sequence of Mn oxidation/reduction and water binding/release. This interpretation is consistent with EPR experiments; g similar to 5 and g similar to 3 signals obtained after near-infrared (NIR) excitation of the S-3 state at 4 K and a g similar to 5 only signal produced after prolonged incubation of the S-3 state at 77 K can be best explained as originating from water-bound S-2 clusters (S-total = 7/2) under a S-3 ligand field, i.e., the immediate one-electron reduction products of the oxyl-oxo (S-total = 6) and hydroxo-oxo (S-total = 3) species in the S-3 state.
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=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=SuzukiTakayoshi
en-aut-sei=Suzuki
en-aut-mei=Takayoshi
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=Center for Computational Science, University of Tsukuba,
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=Institute for NanoScience Design, Osaka University
kn-affil=
END
start-ver=1.4
cd-journal=joma
no-vol=11
cd-vols=
no-issue=
article-no=
start-page=e73990
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2022
dt-pub=20220411
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Structural basis for the absence of low-energy chlorophylls in a photosystem I trimer from Gloeobacter violaceus
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=Photosystem I (PSI) is a multi-subunit pigment-protein complex that functions in light-harvesting and photochemical charge-separation reactions, followed by reduction of NADP to NADPH required for CO2 fixation in photosynthetic organisms. PSI from different photosynthetic organisms has a variety of chlorophylls (Chls), some of which are at lower-energy levels than its reaction center P700, a special pair of Chls, and are called low-energy Chls. However, the sites of low-energy Chls are still under debate. Here, we solved a 2.04-& ANGS; resolution structure of a PSI trimer by cryo-electron microscopy from a primordial cyanobacterium Gloeobacter violaceus PCC 7421, which has no low-energy Chls. The structure shows the absence of some subunits commonly found in other cyanobacteria, confirming the primordial nature of this cyanobacterium. Comparison with the known structures of PSI from other cyanobacteria and eukaryotic organisms reveals that one dimeric and one trimeric Chls are lacking in the Gloeobacter PSI. The dimeric and trimeric Chls are named Low1 and Low2, respectively. Low2 is missing in some cyanobacterial and eukaryotic PSIs, whereas Low1 is absent only in Gloeobacter. These findings provide insights into not only the identity of low-energy Chls in PSI, but also the evolutionary changes of low-energy Chls in oxyphototrophs.
en-copyright=
kn-copyright=
en-aut-name=KatoKoji
en-aut-sei=Kato
en-aut-mei=Koji
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=
en-aut-name=HamaguchiTasuku
en-aut-sei=Hamaguchi
en-aut-mei=Tasuku
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=
en-aut-name=NagaoRyo
en-aut-sei=Nagao
en-aut-mei=Ryo
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=
en-aut-name=KawakamiKeisuke
en-aut-sei=Kawakami
en-aut-mei=Keisuke
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=
en-aut-name=UenoYoshifumi
en-aut-sei=Ueno
en-aut-mei=Yoshifumi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=5
ORCID=
en-aut-name=SuzukiTakehiro
en-aut-sei=Suzuki
en-aut-mei=Takehiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=6
ORCID=
en-aut-name=UchidaHiroko
en-aut-sei=Uchida
en-aut-mei=Hiroko
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=7
ORCID=
en-aut-name=MurakamiAkio
en-aut-sei=Murakami
en-aut-mei=Akio
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=8
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=9
ORCID=
en-aut-name=YokonoMakio
en-aut-sei=Yokono
en-aut-mei=Makio
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=10
ORCID=
en-aut-name=AkimotoSeiji
en-aut-sei=Akimoto
en-aut-mei=Seiji
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=11
ORCID=
en-aut-name=DohmaeNaoshi
en-aut-sei=Dohmae
en-aut-mei=Naoshi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=12
ORCID=
en-aut-name=YonekuraKoji
en-aut-sei=Yonekura
en-aut-mei=Koji
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=13
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=14
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=Biostructural Mechanism Laboratory, RIKEN SPring-8 Center
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=Biostructural Mechanism Laboratory, RIKEN SPring-8 Center
kn-affil=
affil-num=5
en-affil=Graduate School of Science, Kobe University
kn-affil=
affil-num=6
en-affil=Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science
kn-affil=
affil-num=7
en-affil=Research Center for Inland Seas, Kobe University
kn-affil=
affil-num=8
en-affil=Graduate School of Science, Kobe University
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=Institute of Low Temperature Science, Hokkaido University
kn-affil=
affil-num=11
en-affil=Graduate School of Science, Kobe University
kn-affil=
affil-num=12
en-affil=Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science
kn-affil=
affil-num=13
en-affil=Biostructural Mechanism Laboratory, RIKEN SPring-8 Center
kn-affil=
affil-num=14
en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
en-keyword=photosystem I
kn-keyword=photosystem I
en-keyword=cryo-EM
kn-keyword=cryo-EM
en-keyword=low-energy Chl
kn-keyword=low-energy Chl
en-keyword=Gloeobacter
kn-keyword=Gloeobacter
en-keyword=Other
kn-keyword=Other
END
start-ver=1.4
cd-journal=joma
no-vol=13
cd-vols=
no-issue=1
article-no=
start-page=1764
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2022
dt-pub=20220401
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Structural basis for different types of hetero-tetrameric light-harvesting complexes in a diatom PSII-FCPII supercomplex
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=Fucoxanthin chlorophyll (Chl) a/c-binding proteins (FCPs) function as light harvesters in diatoms. The structure of a diatom photosystem II-FCPII (PSII-FCPII) supercomplex have been solved by cryo-electron microscopy (cryo-EM) previously; however, the FCPII subunits that constitute the FCPII tetramers and monomers are not identified individually due to their low resolutions. Here, we report a 2.5 angstrom resolution structure of the PSII-FCPII supercomplex using cryo-EM. Two types of tetrameric FCPs, S-tetramer, and M-tetramer, are identified as different types of hetero-tetrameric complexes. In addition, three FCP monomers, m1, m2, and m3, are assigned to different gene products of FCP. The present structure also identifies the positions of most Chls c and diadinoxanthins, which form a complicated pigment network. Excitation-energy transfer from FCPII to PSII is revealed by time-resolved fluorescence spectroscopy. These structural and spectroscopic findings provide insights into an assembly model of FCPII and its excitation-energy transfer and quenching processes. Fucoxanthin chlorophyll a/c-binding proteins (FCPs) harvest light energy in diatoms. The authors analyzed a structure of PSII-FCPII supercomplex at high resolution by cryo-EM, which identified each FCP subunit and pigment network in the supercomplex.
en-copyright=
kn-copyright=
en-aut-name=NagaoRyo
en-aut-sei=Nagao
en-aut-mei=Ryo
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=
en-aut-name=KatoKoji
en-aut-sei=Kato
en-aut-mei=Koji
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=
en-aut-name=KumazawaMinoru
en-aut-sei=Kumazawa
en-aut-mei=Minoru
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=
en-aut-name=IfukuKentaro
en-aut-sei=Ifuku
en-aut-mei=Kentaro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=
en-aut-name=YokonoMakio
en-aut-sei=Yokono
en-aut-mei=Makio
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=5
ORCID=
en-aut-name=SuzukiTakehiro
en-aut-sei=Suzuki
en-aut-mei=Takehiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=6
ORCID=
en-aut-name=DohmaeNaoshi
en-aut-sei=Dohmae
en-aut-mei=Naoshi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=7
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=8
ORCID=
en-aut-name=AkimotoSeiji
en-aut-sei=Akimoto
en-aut-mei=Seiji
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=9
ORCID=
en-aut-name=MiyazakiNaoyuki
en-aut-sei=Miyazaki
en-aut-mei=Naoyuki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=10
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=11
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=Graduate School of Biostudies, Kyoto University
kn-affil=
affil-num=4
en-affil=Graduate School of Agriculture, Kyoto University
kn-affil=
affil-num=5
en-affil=Institute of Low Temperature Science, Hokkaido University
kn-affil=
affil-num=6
en-affil=Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science
kn-affil=
affil-num=7
en-affil=Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science
kn-affil=
affil-num=8
en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=9
en-affil=Graduate School of Science, Kobe University
kn-affil=
affil-num=10
en-affil=Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba
kn-affil=
affil-num=11
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=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 earthfs 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 ?. 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=4
cd-vols=
no-issue=1
article-no=
start-page=382
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2021
dt-pub=20210322
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=High-resolution cryo-EM structure of photosystem II reveals damage from high-dose electron beams
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=Photosystem II (PSII) plays a key role in water-splitting and oxygen evolution. X-ray crystallography has revealed its atomic structure and some intermediate structures. However, these structures are in the crystalline state and its final state structure has not been solved. Here we analyzed the structure of PSII in solution at 1.95?? resolution by single-particle cryo-electron microscopy (cryo-EM). The structure obtained is similar to the crystal structure, but a PsbY subunit was visible in the cryo-EM structure, indicating that it represents its physiological state more closely. Electron beam damage was observed at a high-dose in the regions that were easily affected by redox states, and reducing the beam dosage by reducing frames from 50 to 2 yielded a similar resolution but reduced the damage remarkably. This study will serve as a good indicator for determining damage-free cryo-EM structures of not only PSII but also all biological samples, especially redox-active metalloproteins.
en-copyright=
kn-copyright=
en-aut-name=KatoKoji
en-aut-sei=Kato
en-aut-mei=Koji
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=
en-aut-name=MiyazakiNaoyuki
en-aut-sei=Miyazaki
en-aut-mei=Naoyuki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=
en-aut-name=HamaguchiTasuku
en-aut-sei=Hamaguchi
en-aut-mei=Tasuku
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=AkitaFusamichi
en-aut-sei=Akita
en-aut-mei=Fusamichi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=5
ORCID=
en-aut-name=YonekuraKoji
en-aut-sei=Yonekura
en-aut-mei=Koji
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=6
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=7
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=Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba
kn-affil=
affil-num=3
en-affil=Biostructural Mechanism Laboratory, 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=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=6
en-affil=Institute of Multidisciplinary Research for Advanced Materials, Tohoku 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=
END
start-ver=1.4
cd-journal=joma
no-vol=12
cd-vols=
no-issue=1
article-no=
start-page=1100
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2021
dt-pub=20210217
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Structure of photosystem I-LHCI-LHCII from the green alga Chlamydomonas reinhardtii in State 2
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=Photosystem I (PSI) and II (PSII) balance their light energy distribution absorbed by their light-harvesting complexes (LHCs) through state transition to maintain the maximum photosynthetic performance and to avoid photodamage. In state 2, a part of LHCII moves to PSI, forming a PSI-LHCI-LHCII supercomplex. The green alga Chlamydomonas reinhardtii exhibits state transition to a far larger extent than higher plants. Here we report the cryo-electron microscopy structure of a PSI-LHCI-LHCII supercomplex in state 2 from C. reinhardtii at 3.42?? resolution. The result reveals that the PSI-LHCI-LHCII of C. reinhardtii binds two LHCII trimers in addition to ten LHCI subunits. The PSI core subunits PsaO and PsaH, which were missed or not well-resolved in previous Cr-PSI-LHCI structures, are observed. The present results reveal the organization and assembly of PSI core subunits, LHCI and LHCII, pigment arrangement, and possible pathways of energy transfer from peripheral antennae to the PSI core.
en-copyright=
kn-copyright=
en-aut-name=HuangZihui
en-aut-sei=Huang
en-aut-mei=Zihui
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=
en-aut-name=ShenLiangliang
en-aut-sei=Shen
en-aut-mei=Liangliang
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=
en-aut-name=WangWenda
en-aut-sei=Wang
en-aut-mei=Wenda
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=
en-aut-name=MaoZhiyuan
en-aut-sei=Mao
en-aut-mei=Zhiyuan
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=
en-aut-name=YiXiaohan
en-aut-sei=Yi
en-aut-mei=Xiaohan
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=5
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=6
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=7
ORCID=
en-aut-name=ZhangXing
en-aut-sei=Zhang
en-aut-mei=Xing
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=8
ORCID=
en-aut-name=HanGuangye
en-aut-sei=Han
en-aut-mei=Guangye
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=9
ORCID=
affil-num=1
en-affil=Department of Biophysics, and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine
kn-affil=
affil-num=2
en-affil=Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences
kn-affil=
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=Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences
kn-affil=
affil-num=5
en-affil=Department of Biophysics, and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine
kn-affil=
affil-num=6
en-affil=Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences
kn-affil=
affil-num=7
en-affil=Institute for Interdisciplinary Science, and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=8
en-affil=Department of Biophysics, and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine
kn-affil=
affil-num=9
en-affil=Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences
kn-affil=
END
start-ver=1.4
cd-journal=joma
no-vol=7
cd-vols=
no-issue=1
article-no=
start-page=10
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2021
dt-pub=20210216
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Antenna arrangement and energy-transfer pathways of PSI-LHCI from the moss Physcomitrella patens
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=Plants harvest light energy utilized for photosynthesis by light-harvesting complex I and II (LHCI and LHCII) surrounding photosystem I and II (PSI and PSII), respectively. During the evolution of green plants, moss is at an evolutionarily intermediate position from aquatic photosynthetic organisms to land plants, being the first photosynthetic organisms that landed. Here, we report the structure of the PSI-LHCI supercomplex from the moss Physcomitrella patens (Pp) at 3.23 angstrom resolution solved by cryo-electron microscopy. Our structure revealed that four Lhca subunits are associated with the PSI core in an order of Lhca1-Lhca5-Lhca2-Lhca3. This number is much decreased from 8 to 10, the number of subunits in most green algal PSI-LHCI, but the same as those of land plants. Although Pp PSI-LHCI has a similar structure as PSI-LHCI of land plants, it has Lhca5, instead of Lhca4, in the second position of Lhca, and several differences were found in the arrangement of chlorophylls among green algal, moss, and land plant PSI-LHCI. One chlorophyll, PsaF-Chl 305, which is found in the moss PSI-LHCI, is located at the gap region between the two middle Lhca subunits and the PSI core, and therefore may make the excitation energy transfer from LHCI to the core more efficient than that of land plants. On the other hand, energy-transfer paths at the two side Lhca subunits are relatively conserved. These results provide a structural basis for unravelling the mechanisms of light-energy harvesting and transfer in the moss PSI-LHCI, as well as important clues on the changes of PSI-LHCI after landing.
en-copyright=
kn-copyright=
en-aut-name=YanQiujing
en-aut-sei=Yan
en-aut-mei=Qiujing
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=
en-aut-name=ZhaoLiang
en-aut-sei=Zhao
en-aut-mei=Liang
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=
en-aut-name=WangWenda
en-aut-sei=Wang
en-aut-mei=Wenda
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=
en-aut-name=PiXiong
en-aut-sei=Pi
en-aut-mei=Xiong
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=
en-aut-name=HanGuangye
en-aut-sei=Han
en-aut-mei=Guangye
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=5
ORCID=
en-aut-name=WangJie
en-aut-sei=Wang
en-aut-mei=Jie
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=6
ORCID=
en-aut-name=ChengLingpeng
en-aut-sei=Cheng
en-aut-mei=Lingpeng
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=7
ORCID=
en-aut-name=HeYi-Kun
en-aut-sei=He
en-aut-mei=Yi-Kun
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=8
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=9
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=10
ORCID=
en-aut-name=SuiSen-Fang
en-aut-sei=Sui
en-aut-mei=Sen-Fang
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=11
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=12
ORCID=
affil-num=1
en-affil=Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences
kn-affil=
affil-num=2
en-affil=State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University
kn-affil=
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=State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University
kn-affil=
affil-num=5
en-affil=Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences
kn-affil=
affil-num=6
en-affil=Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences
kn-affil=
affil-num=7
en-affil=State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University
kn-affil=
affil-num=8
en-affil=College of Life Sciences, Department of Chemistry, Capital Normal University,
kn-affil=
affil-num=9
en-affil=Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences
kn-affil=
affil-num=10
en-affil=School of Biological Science and Technology, University of Jinan
kn-affil=
affil-num=11
en-affil=State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University
kn-affil=
affil-num=12
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=405
cd-vols=
no-issue=
article-no=
start-page=112905
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2021
dt-pub=20210115
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Exploring reaction pathways for the structural rearrangements of the Mn cluster induced by water binding in the S3 state of the oxygen evolving complex of photosystem II
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=Photosynthetic oxidation of water to dioxygen is catalyzed by the Mn4CaO5 cluster in the protein-cofactor complex photosystem II. The light-driven catalytic cycle consists of four observable intermediates (S0, S1, S2, and S3) and one transient S4 state. Recently, using X-ray free-electron laser crystallography, two experimental groups independently observed incorporation of one additional oxygen into the cluster during the S2 to S3 transition, which is likely to represent a substrate. The present study implicates two competing reaction routes encountered during the structural rearrangement of the catalyst induced by the water binding and immediately preceding the formation of final stable forms in the S3 state. This mutually exclusive competition involves concerted versus stepwise conformational changes between two isomers, called open and closed cubane structures, which have different consequences on the immediate product in the S3 state. The concerted pathway involves a one-step conversion between two isomeric hydroxo forms without changes to the metal oxidation and total spin (Stotal?=?3) states. Alternatively, in the stepwise process, the bound waters are oxidized and transformed into an oxyl?oxo form in a higher spin (Stotal?=?6) state. Here, density functional calculations are used to characterize all relevant intermediates and transition structures and demonstrate that the stepwise pathway to the substrate activation is substantially favored over the concerted one, as evidenced by comparison of the activation barriers (11.1 and 20.9?kcal?mol?1, respectively). Only after formation of the oxyl?oxo precursor can the hydroxo species be generated; this occurs with a slow kinetics and an activation barrier of 17.8?kcal?mol?1. The overall thermodynamic driving force is likely to be controlled by the movements of two glutamate ligands, D1-Glu189 and CP43-Glu354, in the active site and ranges from very weak (+0.4?kcal mol?1) to very strong (?23.5?kcal?mol?1).
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=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=SuzukiTakayoshi
en-aut-sei=Suzuki
en-aut-mei=Takayoshi
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=Center for Computational Science, University of Tsukuba
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=Institute for NanoScience Design, Osaka University
kn-affil=
en-keyword=Photosynthesis
kn-keyword=Photosynthesis
en-keyword=Water oxidation
kn-keyword=Water oxidation
en-keyword=Photosystem II
kn-keyword=Photosystem II
en-keyword=Oxygen evolving complex
kn-keyword=Oxygen evolving complex
en-keyword=Mn4CaO6 cluster
kn-keyword=Mn4CaO6 cluster
en-keyword=Ligand environment
kn-keyword=Ligand environment
END
start-ver=1.4
cd-journal=joma
no-vol=11
cd-vols=
no-issue=1
article-no=
start-page=5081
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2020
dt-pub=20201008
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Structural basis for energy transfer in a huge diatom PSI-FCPI supercomplex
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=Diatom is an important group of marine algae and contributes to around 20% of the global photosynthetic carbon fixation. Photosystem I (PSI) of diatoms is associated with a large number of fucoxanthin-chlorophyll a/c proteins (FCPIs). We report the structure of PSI-FCPI from a diatom Chaetoceros gracilis at 2.38?? resolution by single-particle cryo-electron microscopy. PSI-FCPI is a monomeric supercomplex consisting of 12 core and 24 antenna subunits (FCPIs), and 326 chlorophylls a, 34 chlorophylls c, 102 fucoxanthins, 35 diadinoxanthins, 18 ΐ-carotenes and some electron transfer cofactors. Two subunits designated PsaR and PsaS were found in the core, whereas several subunits were lost. The large number of pigments constitute a unique and huge network ensuring efficient energy harvesting, transfer and dissipation. These results provide a firm structural basis for unraveling the mechanisms of light-energy harvesting, transfer and quenching in the diatom PSI-FCPI, and also important clues to evolutionary changes of PSI-LHCI.
en-copyright=
kn-copyright=
en-aut-name=XuCaizhe
en-aut-sei=Xu
en-aut-mei=Caizhe
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=
en-aut-name=PiXiong
en-aut-sei=Pi
en-aut-mei=Xiong
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=
en-aut-name=HuangYawen
en-aut-sei=Huang
en-aut-mei=Yawen
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=
en-aut-name=HanGuangye
en-aut-sei=Han
en-aut-mei=Guangye
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=
en-aut-name=ChenXiaobo
en-aut-sei=Chen
en-aut-mei=Xiaobo
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=5
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=6
ORCID=
en-aut-name=HuangGuoqiang
en-aut-sei=Huang
en-aut-mei=Guoqiang
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=7
ORCID=
en-aut-name=ZhaoSonghao
en-aut-sei=Zhao
en-aut-mei=Songhao
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=8
ORCID=
en-aut-name=YangYanyan
en-aut-sei=Yang
en-aut-mei=Yanyan
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=9
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=10
ORCID=
en-aut-name=WangWenda
en-aut-sei=Wang
en-aut-mei=Wenda
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=11
ORCID=
en-aut-name=SuiSen-Fang
en-aut-sei=Sui
en-aut-mei=Sen-Fang
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=12
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=13
ORCID=
affil-num=1
en-affil=Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, The Chinese Academy of Sciences
kn-affil=
affil-num=2
en-affil=State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University
kn-affil=
affil-num=3
en-affil=State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University
kn-affil=
affil-num=4
en-affil=Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, The Chinese Academy of Sciences
kn-affil=
affil-num=5
en-affil=Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, The Chinese Academy of Sciences
kn-affil=
affil-num=6
en-affil=School of Biological Science and Technology, University of Jinan
kn-affil=
affil-num=7
en-affil=State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University
kn-affil=
affil-num=8
en-affil=Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, The Chinese Academy of Sciences
kn-affil=
affil-num=9
en-affil=Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, The Chinese Academy of Sciences
kn-affil=
affil-num=10
en-affil=Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, The Chinese Academy of Sciences
kn-affil=
affil-num=11
en-affil=Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, The Chinese Academy of Sciences
kn-affil=
affil-num=12
en-affil=State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University
kn-affil=
affil-num=13
en-affil=Research Institute for Interdisciplinary Science, and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
en-keyword=Bioenergetics
kn-keyword=Bioenergetics
en-keyword=Cryoelectron microscopy
kn-keyword=Cryoelectron microscopy
en-keyword=Photosystem I
kn-keyword=Photosystem I
END
start-ver=1.4
cd-journal=joma
no-vol=1861
cd-vols=
no-issue=7
article-no=
start-page=148191
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2020
dt-pub=20200701
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Spectral tuning of light-harvesting complex II in the siphonous alga Bryopsis corticulans and its effect on energy transfer dynamics
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=Light-harvesting complex II (LHCII) from the marine green macroalga Bryopsis corticulans is spectroscopically characterized to understand the structural and functional changes resulting from adaptation to intertidal environment. LHCII is homologous to its counterpart in land plants but has a different carotenoid and chlorophyll (Chl) composition. This is reflected in the steady-state absorption, fluorescence, linear dichroism, circular dichroism and anisotropic circular dichroism spectra. Time-resolved fluorescence and two-dimensional electronic spectroscopy were used to investigate the consequences of this adaptive change in the pigment composition on the excited-state dynamics. The complex contains additional Chl b spectral forms ? absorbing at around 650 nm and 658 nm ? and lacks the red-most Chl a forms compared with higher-plant LHCII. Similar to plant LHCII, energy transfer between Chls occurs on timescales from under hundred fs (mainly from Chl b to Chl a) to several picoseconds (mainly between Chl a pools). However, the presence of long-lived, weakly coupled Chl b and Chl a states leads to slower exciton equilibration in LHCII from B. corticulans. The finding demonstrates a trade-off between the enhanced absorption of blue-green light and the excitation migration time. However, the adaptive change does not result in a significant drop in the overall photochemical efficiency of Photosystem II. These results show that LHCII is a robust adaptable system whose spectral properties can be tuned to the environment for optimal light harvesting.
en-copyright=
kn-copyright=
en-aut-name=AkhtarParveen
en-aut-sei=Akhtar
en-aut-mei=Parveen
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=
en-aut-name=NowakowskiPawe? J.
en-aut-sei=Nowakowski
en-aut-mei=Pawe? J.
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=
en-aut-name=WangWenda
en-aut-sei=Wang
en-aut-mei=Wenda
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=
en-aut-name=DoThanh Nhut
en-aut-sei=Do
en-aut-mei=Thanh Nhut
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=
en-aut-name=ZhaoSonghao
en-aut-sei=Zhao
en-aut-mei=Songhao
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=5
ORCID=
en-aut-name=SiligardiGiuliano
en-aut-sei=Siligardi
en-aut-mei=Giuliano
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=6
ORCID=
en-aut-name=GarabGy?z?
en-aut-sei=Garab
en-aut-mei=Gy?z?
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=
en-aut-name=TanHowe-Siang
en-aut-sei=Tan
en-aut-mei=Howe-Siang
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=9
ORCID=
en-aut-name=LambrevPetar H.
en-aut-sei=Lambrev
en-aut-mei=Petar H.
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=10
ORCID=
affil-num=1
en-affil=Biological Research Centre
kn-affil=
affil-num=2
en-affil=ivision of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University
kn-affil=
affil-num=3
en-affil=Photosynthesis Research Centre, Chinese Academy of Sciences
kn-affil=
affil-num=4
en-affil=Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University
kn-affil=
affil-num=5
en-affil=Photosynthesis Research Centre, Chinese Academy of Sciences
kn-affil=
affil-num=6
en-affil=Diamond Light Source Ltd., Harwell Science and Innovation Campus
kn-affil=
affil-num=7
en-affil=Biological Research Centre
kn-affil=
affil-num=8
en-affil=Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=9
en-affil=Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University
kn-affil=
affil-num=10
en-affil=Biological Research Centre
kn-affil=
en-keyword=Circular dichroism
kn-keyword=Circular dichroism
en-keyword=Light-harvesting complexes
kn-keyword=Light-harvesting complexes
en-keyword=Marine algae
kn-keyword=Marine algae
en-keyword=Photosynthesis
kn-keyword=Photosynthesis
en-keyword=Time-resolved spectroscopy
kn-keyword=Time-resolved spectroscopy
en-keyword=Two-dimensional spectroscopy
kn-keyword=Two-dimensional spectroscopy
END
start-ver=1.4
cd-journal=joma
no-vol=3
cd-vols=
no-issue=1
article-no=
start-page=232
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2020
dt-pub=20200511
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Structure of a cyanobacterial photosystem I surrounded by octadecameric IsiA antenna proteins
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=Iron-stress induced protein A (IsiA) is a chlorophyll-binding membrane-spanning protein in photosynthetic prokaryote cyanobacteria, and is associated with photosystem I (PSI) trimer cores, but its structural and functional significance in light harvesting remains unclear. Here we report a 2.7-angstrom resolution cryo-electron microscopic structure of a supercomplex between PSI core trimer and IsiA from a thermophilic cyanobacterium Thermosynechococcus vulcanus. The structure showed that 18 IsiA subunits form a closed ring surrounding a PSI trimer core. Detailed arrangement of pigments within the supercomplex, as well as molecular interactions between PSI and IsiA and among IsiAs, were resolved. Time-resolved fluorescence spectra of the PSI-IsiA supercomplex showed clear excitation-energy transfer from IsiA to PSI, strongly indicating that IsiA functions as an energy donor, but not an energy quencher, in the supercomplex. These structural and spectroscopic findings provide important insights into the excitation-energy-transfer and subunit assembly mechanisms in the PSI-IsiA supercomplex. Akita et al. present the latest approach to solve IsiA-PSI supercomplex molecular structure with increased resolution using cryo-EM and time-resolved fluorescence studies. With 2.7 angstrom resolution, they reveal molecular interactions between PSI and IsiA subunits and that IsiA functions as an energy donor in the supercomplex.
en-copyright=
kn-copyright=
en-aut-name=AkitaFusamichi
en-aut-sei=Akita
en-aut-mei=Fusamichi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=
en-aut-name=NagaoRyo
en-aut-sei=Nagao
en-aut-mei=Ryo
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=
en-aut-name=KatoKoji
en-aut-sei=Kato
en-aut-mei=Koji
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=YokonoMakio
en-aut-sei=Yokono
en-aut-mei=Makio
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=5
ORCID=
en-aut-name=UenoYoshifumi
en-aut-sei=Ueno
en-aut-mei=Yoshifumi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=6
ORCID=
en-aut-name=SuzukiTakehiro
en-aut-sei=Suzuki
en-aut-mei=Takehiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=7
ORCID=
en-aut-name=DohmaeNaoshi
en-aut-sei=Dohmae
en-aut-mei=Naoshi
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=AkimotoSeiji
en-aut-sei=Akimoto
en-aut-mei=Seiji
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=10
ORCID=
en-aut-name=MiyazakiNaoyuki
en-aut-sei=Miyazaki
en-aut-mei=Naoyuki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=11
ORCID=
affil-num=1
en-affil=Graduate School of Natural Science and Technology, 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=Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=5
en-affil=Nippon Flour Mills Co., Ltd., Innovation Center
kn-affil=
affil-num=6
en-affil=Graduate School of Science, Kobe University
kn-affil=
affil-num=7
en-affil=Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science
kn-affil=
affil-num=8
en-affil=Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science
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=Graduate School of Science, Kobe University
kn-affil=
affil-num=11
en-affil=Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba
kn-affil=
en-keyword=Cryoelectron microscopy
kn-keyword=Cryoelectron microscopy
en-keyword=Photosystem I
kn-keyword=Photosystem I
END
start-ver=1.4
cd-journal=joma
no-vol=11
cd-vols=
no-issue=1
article-no=
start-page=
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2020
dt-pub=20200518
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Structural basis for assembly and function of a diatom photosystem I-light-harvesting supercomplex
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=Photosynthetic light-harvesting complexes (LHCs) play a pivotal role in collecting solar energy for photochemical reactions in photosynthesis. One of the major LHCs are fucoxanthin chlorophyll a/c-binding proteins (FCPs) present in diatoms, a group of organisms having important contribution to the global carbon cycle. Here, we report a 2.40-angstrom resolution structure of the diatom photosystem I (PSI)-FCPI supercomplex by cryo-electron microscopy. The supercomplex is composed of 16 different FCPI subunits surrounding a monomeric PSI core. Each FCPI subunit showed different protein structures with different pigment contents and binding sites, and they form a complicated pigment-protein network together with the PSI core to harvest and transfer the light energy efficiently. In addition, two unique, previously unidentified subunits were found in the PSI core. The structure provides numerous insights into not only the light-harvesting strategy in diatom PSI-FCPI but also evolutionary dynamics of light harvesters among oxyphototrophs. One of the major photosynthetic light-harvesting complexes (LHCs) are fucoxanthin chlorophyll a/c-binding proteins (FCPs), which are present in diatoms, a major group of algae. Here, the authors present the cryo-EM structure of the photosystem I-FCP (PSI-FCPI) supercomplex isolated from the marine centric diatom Chaetoceros gracilis that contains 16 FCPI subunits surrounding the PSI core and discuss possible excitation energy transfer pathways.
en-copyright=
kn-copyright=
en-aut-name=NagaoRyo
en-aut-sei=Nagao
en-aut-mei=Ryo
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=
en-aut-name=KatoKoji
en-aut-sei=Kato
en-aut-mei=Koji
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=
en-aut-name=IfukuKentaro
en-aut-sei=Ifuku
en-aut-mei=Kentaro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=
en-aut-name=SuzukiTakehiro
en-aut-sei=Suzuki
en-aut-mei=Takehiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=
en-aut-name=KumazawaMinoru
en-aut-sei=Kumazawa
en-aut-mei=Minoru
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=5
ORCID=
en-aut-name=UchiyamaIkuo
en-aut-sei=Uchiyama
en-aut-mei=Ikuo
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=6
ORCID=
en-aut-name=KashinoYasuhiro
en-aut-sei=Kashino
en-aut-mei=Yasuhiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=7
ORCID=
en-aut-name=DohmaeNaoshi
en-aut-sei=Dohmae
en-aut-mei=Naoshi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=8
ORCID=
en-aut-name=AkimotoSeiji
en-aut-sei=Akimoto
en-aut-mei=Seiji
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=
en-aut-name=MiyazakiNaoyuki
en-aut-sei=Miyazaki
en-aut-mei=Naoyuki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=11
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=12
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=Graduate School of Biostudies, Kyoto University
kn-affil=
affil-num=4
en-affil=Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science
kn-affil=
affil-num=5
en-affil=Faculty of Agriculture, Kyoto University
kn-affil=
affil-num=6
en-affil=National Institute for Basic Biology, National Institutes of Natural Sciences
kn-affil=
affil-num=7
en-affil=Graduate School of Life Science, University of Hyogo
kn-affil=
affil-num=8
en-affil=Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science
kn-affil=
affil-num=9
en-affil=Graduate School of Science,Kobe 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=Institute for Protein Research, Osaka University
kn-affil=
affil-num=12
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=11
cd-vols=
no-issue=1
article-no=
start-page=238
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2020
dt-pub=20200113
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Structural basis for the adaptation and function of chlorophyll f in photosystem I
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=Chlorophylls (Chl) play pivotal roles in energy capture, transfer and charge separation in photosynthesis. Among Chls functioning in oxygenic photosynthesis, Chl f is the most red-shifted type first found in a cyanobacterium Halomicronema hongdechloris. The location and function of Chl f in photosystems are not clear. Here we analyzed the high-resolution structures of photosystem I (PSI) core from H. hongdechloris grown under white or far-red light by cryo-electron microscopy. The structure showed that, far-red PSI binds 83 Chl a and 7 Chl f, and Chl f are associated at the periphery of PSI but not in the electron transfer chain. The appearance of Chl f is well correlated with the expression of PSI genes induced under far-red light. These results indicate that Chl f functions to harvest the far-red light and enhance uphill energy transfer, and changes in the gene sequences are essential for the binding of Chl f.
en-copyright=
kn-copyright=
en-aut-name=KatoKoji
en-aut-sei=Kato
en-aut-mei=Koji
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=
en-aut-name=ShinodaToshiyuki
en-aut-sei=Shinoda
en-aut-mei=Toshiyuki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=
en-aut-name=NagaoRyo
en-aut-sei=Nagao
en-aut-mei=Ryo
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=
en-aut-name=AkimotoSeiji
en-aut-sei=Akimoto
en-aut-mei=Seiji
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=
en-aut-name=SuzukiTakehiro
en-aut-sei=Suzuki
en-aut-mei=Takehiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=5
ORCID=
en-aut-name=DohmaeNaoshi
en-aut-sei=Dohmae
en-aut-mei=Naoshi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=6
ORCID=
en-aut-name=ChenMin
en-aut-sei=Chen
en-aut-mei=Min
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=7
ORCID=
en-aut-name=AllakhverdievSuleyman I.
en-aut-sei=Allakhverdiev
en-aut-mei=Suleyman I.
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=AkitaFusamichi
en-aut-sei=Akita
en-aut-mei=Fusamichi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=10
ORCID=
en-aut-name=MiyazakiNaoyuki
en-aut-sei=Miyazaki
en-aut-mei=Naoyuki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=11
ORCID=
en-aut-name=TomoTatsuya
en-aut-sei=Tomo
en-aut-mei=Tatsuya
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=12
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=Faculty of Science, Tokyo University of Science
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=Graduate School of Science, Kobe University
kn-affil=
affil-num=5
en-affil=Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science
kn-affil=
affil-num=6
en-affil=Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science
kn-affil=
affil-num=7
en-affil=School of Life and Environmental Sciences, University of Sydney
kn-affil=
affil-num=8
en-affil=K.A. Timiryazev Institute of Plant Physiology RAS
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=Institute for Protein Research, Laboratory of Protein Synthesis and Expression, Osaka University
kn-affil=
affil-num=12
en-affil=Faculty of Science, Tokyo University of Science
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=543
cd-vols=
no-issue=7643
article-no=
start-page=131
end-page=135
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2017
dt-pub=201703
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Light-induced structural changes and the site of O=O bond formation in PSII caught by XFEL
en-subtitle=
kn-subtitle=
en-abstract=
kn-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?? 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?? using time-resolved serial femtosecond crystallography with an XFEL provided by the SPring-8 ?ngstr?m 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?? 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 Κ4-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?? between these two oxygen atoms. This provides a mechanism for the O=O bond formation consistent with that proposed previously
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=SugaharaMichihiro
en-aut-sei=Sugahara
en-aut-mei=Michihiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
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=4
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=5
ORCID=
en-aut-name=NakaneTakanori
en-aut-sei=Nakane
en-aut-mei=Takanori
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=6
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=7
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=8
ORCID=
en-aut-name=NakabayashiMakoto
en-aut-sei=Nakabayashi
en-aut-mei=Makoto
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=9
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=10
ORCID=
en-aut-name=NakanoTakamitsu
en-aut-sei=Nakano
en-aut-mei=Takamitsu
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=11
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=12
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=13
ORCID=
en-aut-name=InoueShigeyuki
en-aut-sei=Inoue
en-aut-mei=Shigeyuki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=14
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=15
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=16
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=17
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=18
ORCID=
en-aut-name=SakamotoTomohiro
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en-aut-mei=Tomohiro
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kn-aut-sei=
kn-aut-mei=
aut-affil-num=19
ORCID=
en-aut-name=MotomuraTaiki
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kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=20
ORCID=
en-aut-name=ChenJing-Hua
en-aut-sei=Chen
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kn-aut-sei=
kn-aut-mei=
aut-affil-num=21
ORCID=
en-aut-name=KatoYuki
en-aut-sei=Kato
en-aut-mei=Yuki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=22
ORCID=
en-aut-name=NoguchiTakumi
en-aut-sei=Noguchi
en-aut-mei=Takumi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=23
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=24
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=25
ORCID=
en-aut-name=KameshimaTakashi
en-aut-sei=Kameshima
en-aut-mei=Takashi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=26
ORCID=
en-aut-name=HatsuiTakaki
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en-aut-mei=Takaki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=27
ORCID=
en-aut-name=NangoEriko
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en-aut-mei=Eriko
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=28
ORCID=
en-aut-name=TanakaRie
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en-aut-mei=Rie
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=29
ORCID=
en-aut-name=NaitowHisashi
en-aut-sei=Naitow
en-aut-mei=Hisashi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=30
ORCID=
en-aut-name=MatsuuraYoshinori
en-aut-sei=Matsuura
en-aut-mei=Yoshinori
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=31
ORCID=
en-aut-name=YamashitaAyumi
en-aut-sei=Yamashita
en-aut-mei=Ayumi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=32
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=33
ORCID=
en-aut-name=NurekiOsamu
en-aut-sei=Nureki
en-aut-mei=Osamu
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=34
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=35
ORCID=
en-aut-name=IshikawaTetsuya
en-aut-sei=Ishikawa
en-aut-mei=Tetsuya
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=36
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=37
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=38
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=Japan Science and Technology Agency, PRESTO
kn-affil=
affil-num=5
en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=6
en-affil=Department of Biological Sciences, Graduate School of Science, The University of Tokyo
kn-affil=
affil-num=7
en-affil=RIKEN SPring-8 Center
kn-affil=
affil-num=8
en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
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=Institute for Protein Research, Osaka University
kn-affil=
affil-num=13
en-affil=Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University
kn-affil=
affil-num=14
en-affil=Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo
kn-affil=
affil-num=15
en-affil=Department of Chemistry, Graduate School of Science, Kobe University
kn-affil=
affil-num=16
en-affil=RIKEN SPring-8 Center
kn-affil=
affil-num=17
en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=18
en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=19
en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
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=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=22
en-affil=Division of Material Science, Graduate School of Science, Nagoya University
kn-affil=
affil-num=23
en-affil=Division of Material Science, Graduate School of Science, Nagoya University
kn-affil=
affil-num=24
en-affil=Japan Synchrotron Radiation Research Institute
kn-affil=
affil-num=25
en-affil=Japan Synchrotron Radiation Research Institute
kn-affil=
affil-num=26
en-affil=Japan Synchrotron Radiation Research Institute46
kn-affil=
affil-num=27
en-affil=RIKEN SPring-8 Center
kn-affil=
affil-num=28
en-affil=RIKEN SPring-8 Center
kn-affil=
affil-num=29
en-affil=RIKEN SPring-8 Center
kn-affil=
affil-num=30
en-affil=RIKEN SPring-8 Center
kn-affil=
affil-num=31
en-affil=RIKEN SPring-8 Center
kn-affil=
affil-num=32
en-affil=RIKEN SPring-8 Center
kn-affil=
affil-num=33
en-affil=RIKEN SPring-8 Center
kn-affil=
affil-num=34
en-affil=Department of Biological Sciences, Graduate School of Science, The University of Tokyo
kn-affil=
affil-num=35
en-affil=RIKEN SPring-8 Center
kn-affil=
affil-num=36
en-affil=RIKEN SPring-8 Center
kn-affil=
affil-num=37
en-affil=RIKEN SPring-8 Center
kn-affil=
affil-num=38
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=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=Ο°
kn-aut-sei=
kn-aut-mei=Ο°
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=Ύm
kn-aut-sei=Ύ
kn-aut-mei=m
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=ͺRεwΩͺμξbΘw€
affil-num=2
en-affil=Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University
kn-affil=ͺRεwΩͺμξbΘw€
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=ͺRεwΩͺμξbΘw€
END
start-ver=1.4
cd-journal=joma
no-vol=517
cd-vols=
no-issue=
article-no=
start-page=99
end-page=103
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2015
dt-pub=20150101
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Native structure of photosystem II at 1.95 ? resolution viewed by femtosecond X-ray pulses
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=Photosynthesis converts light energy into biologically useful chemical energy vital to life on Earth. The initial reaction of photosynthesis takes place in photosystem II (PSII), a 700-kilodalton homodimeric membrane protein complex which catalyses photo-oxidation of water into dioxygen through an S-state cycle of the oxygen evolving complex (OEC). The structure of PSII has been solved by X-ray diffraction (XRD) at 1.9-?ngstr?m (?) resolution, which revealed that the OEC is a Mn4CaO5-cluster coordinated by a well-defined protein environment1. However, extended X-ray absorption fine structure (EXAFS) studies showed that the manganese cations in the OEC are easily reduced by X-ray irradiation2, and slight differences were found in the Mn?Mn distances between the results of XRD1, EXAFS3?7 and theoretical studies8?14. Here we report a eradiation-damage-freef structure of PSII from Thermosynechococcus vulcanus in the S1 state at a resolution of 1.95 ? using femtosecond X-ray pulses of the SPring-8 ?ngstr?m compact free-electron laser (SACLA) and a huge number of large, highly isomorphous PSII crystals. Compared with the structure from XRD, the OEC in the X-ray free electron laser structure has Mn?Mn distances that are shorter by 0.1?0.2 ?. The valences of each manganese atom were tentatively assigned as Mn1D(III), Mn2C(IV), Mn3B(IV) and Mn4A(III), based on the average Mn?ligand distances and analysis of the Jahn?Teller axis on Mn(III). One of the oxo-bridged oxygens, O5, has significantly longer Mn?O distances in contrast to the other oxo-oxygen atoms, suggesting that it is a hydroxide ion instead of a normal oxygen dianion and therefore may serve as one of the substrate oxygen atoms. These findings provide a structural basis for the mechanism of oxygen evolution, and we expect that this structure will provide a blueprint for design of artificial catalysts for 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=HirataKunio
en-aut-sei=Hirata
en-aut-mei=Kunio
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
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=4
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=5
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=6
ORCID=
en-aut-name=ShimizuTetsuya
en-aut-sei=Shimizu
en-aut-mei=Tetsuya
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=7
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=8
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=9
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=10
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=11
ORCID=
affil-num=1
en-affil=
kn-affil=Photosynthesis Research Center, Graduate School of Natural Science and Technology, Okayama University
affil-num=2
en-affil=
kn-affil=Photosynthesis Research Center, Graduate School of Natural Science and Technology, Okayama University
affil-num=3
en-affil=
kn-affil=RIKEN SPring-8 Center
affil-num=4
en-affil=
kn-affil=RIKEN SPring-8 Center
affil-num=5
en-affil=
kn-affil=RIKEN SPring-8 Center
affil-num=6
en-affil=
kn-affil=Photosynthesis Research Center, Graduate School of Natural Science and Technology, Okayama University
affil-num=7
en-affil=
kn-affil=Photosynthesis Research Center, Graduate School of Natural Science and Technology, Okayama University
affil-num=8
en-affil=
kn-affil=RIKEN SPring-8 Center
affil-num=9
en-affil=
kn-affil=RIKEN SPring-8 Center
affil-num=10
en-affil=
kn-affil=RIKEN SPring-8 Center
affil-num=11
en-affil=
kn-affil=Photosynthesis Research Center, Graduate School of Natural Science and Technology, Okayama University
END
start-ver=1.4
cd-journal=joma
no-vol=1797
cd-vols=
no-issue=2
article-no=
start-page=278
end-page=284
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2010
dt-pub=201002
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Structural and functional studies on Ycf12 (Psb30) and PsbZ-deletion mutants from a thermophilic cyanobacterium
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=Ycf12 (Psb30) and PsbZ are two low molecular weight subunits of photosystem II (PSII), with one and two trans-membrane helices, respectively. In order to study the functions of these two subunits from a structural point of view, we constructed deletion mutants lacking either Ycf12 or PsbZ from Thermosynechococcus elongatus, and purified, crystallized and analyzed the structure of PSII dimer from the two mutants. Our results showed that Ycf12 is located in the periphery of PSII, close to PsbK, PsbZ and PsbJ, and corresponded to the unassigned helix X1 reported previously, in agreement with the recent structure at 2.9 ? resolution (A. Guskov, J. Kern, A. Gabdulkhakov, M. Broser, A. Zouni, W. Saenger, Cyanobacterial photosystem II at 2.9 ? resolution: role of quinones, lipids, channels and chloride, Nat. Struct. Mol. Biol. 16 (2009) 334?342). On the other hand, crystals of PsbZ-deleted PSII showed a remarkably different unit cell constants from those of wild-type PSII, indicating a role of PsbZ in the interactions between PSII dimers within the crystal. This is the first example for a different arrangement of PSII dimers within the cyanobacterial PSII crystals. PSII dimers had a lower oxygen-evolving activity from both mutants than that from the wild type. In consistent with this, the relative content of PSII in the thylakoid membranes was lower in the two mutants than that in the wild type. These results suggested that deletion of both subunits affected the PSII activity, thereby destabilized PSII, leading to a decrease in the PSII content in vivo. While PsbZ was present in PSII purified from the Ycf12-deletion mutant, Ycf12 was present in crude PSII but absent in the finally purified PSII from the PsbZ-deletion mutant, indicating a preferential, stabilizing role of PsbZ for the binding of Ycf12 to PSII. These results were discussed in terms of the PSII crystal structure currently available
en-copyright=
kn-copyright=
en-aut-name=TakasakaKenji
en-aut-sei=Takasaka
en-aut-mei=Kenji
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
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=2
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=3
ORCID=
en-aut-name=KawakamiKeisuke
en-aut-sei=Kawakami
en-aut-mei=Keisuke
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=
en-aut-name=OhmoriYukari
en-aut-sei=Ohmori
en-aut-mei=Yukari
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=TakahashiYuichiro
en-aut-sei=Takahashi
en-aut-mei=Yuichiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=7
ORCID=
en-aut-name=KamiyaNobuo
en-aut-sei=Kamiya
en-aut-mei=Nobuo
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=
affil-num=1
en-affil=
kn-affil=Division of Bioscience, Graduate School of Natural Science and Technology/Faculty of Science; Okayama University
affil-num=2
en-affil=
kn-affil=Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science
affil-num=3
en-affil=
kn-affil=Department of Chemistry, Graduate School of Science, Osaka City University
affil-num=4
en-affil=
kn-affil=Division of Bioscience, Graduate School of Natural Science and Technology/Faculty of Science; Okayama University
affil-num=5
en-affil=
kn-affil=Division of Bioscience, Graduate School of Natural Science and Technology/Faculty of Science; Okayama University
affil-num=6
en-affil=
kn-affil=Department of Life Sciences (Biology), Graduate School of Arts and Science, The University of Tokyo
affil-num=7
en-affil=
kn-affil=Division of Bioscience, Graduate School of Natural Science and Technology/Faculty of Science; Okayama University
affil-num=8
en-affil=
kn-affil=Department of Chemistry, Graduate School of Science, Osaka City University
affil-num=9
en-affil=
kn-affil=Division of Bioscience, Graduate School of Natural Science and Technology/Faculty of Science; Okayama University
en-keyword=Photosystem II
kn-keyword=Photosystem II
en-keyword=Mutant
kn-keyword=Mutant
en-keyword=Crystal structure
kn-keyword=Crystal structure
en-keyword=Ycf12
kn-keyword=Ycf12
en-keyword=PsbZ
kn-keyword=PsbZ
en-keyword=Oxygen evolution
kn-keyword=Oxygen evolution
END
start-ver=1.4
cd-journal=joma
no-vol=684
cd-vols=
no-issue=
article-no=
start-page=41
end-page=51
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2011
dt-pub=2011
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Purification and Crystallization of Oxygen-Evolving Photosystem II Core Complex from Thermophilic Cyanobacteria
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=This chapter describes the purification and crystallization of oxygen-evolving photosystem II core dimer complex from a thermophilic cyanobacterium Thermosynechococcus vulcanus. Procedures used for purification of photosystem II from the cyanobacterium involves cultivation of cells, isolation of thylakoid membranes, purification of crude and pure photosystem II core complexes by detergent solubilization, followed by differential centrifugation and column chromatography. The purified core dimer particles were successfully used for crystallization, and the methods and conditions used for crystallization are presented. These purification and crystallization procedures can be applied for another thermophilic cyanobacterium T. elongatus.
en-copyright=
kn-copyright=
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=1
ORCID=
en-aut-name=KawakamiKeisuke
en-aut-sei=Kawakami
en-aut-mei=Keisuke
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=
en-aut-name=KoikeHiroyuki
en-aut-sei=Koike
en-aut-mei=Hiroyuki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=
affil-num=1
en-affil=
kn-affil=Graduate School of Natural Science and Technology, Okayama University
affil-num=2
en-affil=
kn-affil=Graduate School of Natural Science and Technology, Okayama University
affil-num=3
en-affil=
kn-affil=Department of Biosciences, Faculty of Science and Engineering, Chuo University
en-keyword=Photosystem II
kn-keyword=Photosystem II
en-keyword=Oxygen evolution
kn-keyword=Oxygen evolution
en-keyword=Crystallization
kn-keyword=Crystallization
en-keyword=Membrane proteins
kn-keyword=Membrane proteins
en-keyword=Ion-exchange chromatography
kn-keyword=Ion-exchange chromatography
END
start-ver=1.4
cd-journal=joma
no-vol=285
cd-vols=
no-issue=38
article-no=
start-page=29191
end-page=29199
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2010
dt-pub=20100917
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Binding and Functional Properties of Five Extrinsic Proteins in Oxygen-evolving Photosystem II from a Marine Centric Diatom, Chaetoceros gracilis
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=Oxygen-evolving photosystem II (PSII) isolated from a marine centric diatom, Chaetoceros gracilis, contains a novel extrinsic protein (Psb31) in addition to four red algal type extrinsic proteins of PsbO, PsbQ, PsbV, and PsbU. In this study, the five extrinsic proteins were purified from alkaline Tris extracts of the diatom PSII by anion and cation exchange chromatographic columns at different pH values. Reconstitution experiments in various combinations with the purified extrinsic proteins showed that PsbO, PsbQ, and Psb31 rebound directly to PSII in the absence of other extrinsic proteins, indicating that these extrinsic proteins have their own binding sites in PSII intrinsic proteins. On the other hand, PsbV and PsbU scarcely rebound to PSII alone, and their effective bindings required the presence of all of the other extrinsic proteins. Interestingly, PSII reconstituted with Psb31 alone considerably restored the oxygen evolving activity in the absence of PsbO, indicating that Psb31 serves as a substitute in part for PsbO in supporting oxygen evolution. A significant difference found between PSIIs reconstituted with Psb31 and with PsbO is that the oxygen evolving activity of the former is scarcely stimulated by Cl? and Ca2+ ions but that of the latter is largely stimulated by these ions, although rebinding of PsbV and PsbU activated oxygen evolution in the absence of Cl? and Ca2+ ions in both the former and latter PSIIs. Based on these results, we proposed a model for the association of the five extrinsic proteins with intrinsic proteins in diatom PSII and compared it with those in PSIIs from the other organisms.
en-copyright=
kn-copyright=
en-aut-name=NagaoRyo
en-aut-sei=Nagao
en-aut-mei=Ryo
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=
en-aut-name=MoriguchiAkira
en-aut-sei=Moriguchi
en-aut-mei=Akira
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=
en-aut-name=TomoTatsuya
en-aut-sei=Tomo
en-aut-mei=Tatsuya
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=
en-aut-name=NiikuraAyako
en-aut-sei=Niikura
en-aut-mei=Ayako
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=
en-aut-name=NakajimaSaori
en-aut-sei=Nakajima
en-aut-mei=Saori
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=5
ORCID=
en-aut-name=SuzukiTakehiro
en-aut-sei=Suzuki
en-aut-mei=Takehiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=6
ORCID=
en-aut-name=OkumuraAkinori
en-aut-sei=Okumura
en-aut-mei=Akinori
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=7
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=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=IkeuchiMasahiko
en-aut-sei=Ikeuchi
en-aut-mei=Masahiko
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=10
ORCID=
en-aut-name=EnamiIsao
en-aut-sei=Enami
en-aut-mei=Isao
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=11
ORCID=
affil-num=1
en-affil=
kn-affil=Department of Life Sciences (Biology), Graduate School of Art and Sciences, University of Tokyo
affil-num=2
en-affil=
kn-affil=Department of Biology, Faculty of Science, Tokyo University of Science
affil-num=3
en-affil=
kn-affil=Department of Biology, Faculty of Science, Tokyo University of Science
affil-num=4
en-affil=
kn-affil=Division of Biosciences, Graduate School of Natural Science and Technology, Okayama University
affil-num=5
en-affil=
kn-affil=Department of Biology, Faculty of Science, Tokyo University of Science
affil-num=6
en-affil=
kn-affil=Biomolecular Characterization Team, Discovery Research Institute, RIKEN
affil-num=7
en-affil=
kn-affil=Department of Integrated Sciences in Physics and Biology, College of Humanities and Sciences, Nihon University
affil-num=8
en-affil=
kn-affil=Department of Life Sciences (Biology), Graduate School of Art and Sciences, University of Tokyo
affil-num=9
en-affil=
kn-affil=Division of Biosciences, Graduate School of Natural Science and Technology, Okayama University
affil-num=10
en-affil=
kn-affil=Department of Life Sciences (Biology), Graduate School of Art and Sciences, University of Tokyo
affil-num=11
en-affil=
kn-affil=Department of Biology, Faculty of Science, Tokyo University of Science
END
start-ver=1.4
cd-journal=joma
no-vol=13
cd-vols=
no-issue=
article-no=
start-page=373
end-page=389
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2010
dt-pub=2010
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Mechanisms of Acido-Tolerance and Characteristics of Photosystems in an Acidophilic and Thermophilic Red Alga, Cyanidium Caldarium
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=In this chapter, we describe the mechanisms of acido-tolerance in an acidophilic- and thermophilic red alga, Cyanidium caldarium. In spite of the extremely acidic environments it inhabits, the intracellular pH of Cyanidium cells is kept neutral by pumping out the protons previously leaked into the cells according to the steep pH gradient. The H+ pump is driven by the plasma membrane ATPase, utilizing intracellular ATP produced by both oxidative phosphorylation and cyclic photophosphorylation via photosystem I. We also describe the characteristics and function of the two photosystems, Photosystem I (PSI) and II (PSII), in Cyanidium caldarium in comparison with those of cyanobacteria, other eukaryotic algae, and higher plants, based on the crystal structures of the two complexes reported so far.
en-copyright=
kn-copyright=
en-aut-name=EnamiIsao
en-aut-sei=Enami
en-aut-mei=Isao
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=
en-aut-name=AdachiHideyuki
en-aut-sei=Adachi
en-aut-mei=Hideyuki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
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=3
ORCID=
affil-num=1
en-affil=
kn-affil=Department of Biology, Faculty of Science, Tokyo University of Science
affil-num=2
en-affil=
kn-affil=Division of Bioscience, Graduate School of Natural Science and Technology, Okayama University
affil-num=3
en-affil=
kn-affil=Division of Bioscience, Graduate School of Natural Science and Technology, Okayama University
END
start-ver=1.4
cd-journal=joma
no-vol=473
cd-vols=
no-issue=7345
article-no=
start-page=55
end-page=60
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2011
dt-pub=20110505
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Crystal structure of oxygen-evolving photosystem II at a resolution of 1.9??
en-subtitle=
kn-subtitle=
en-abstract=
kn-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.
en-copyright=
kn-copyright=
en-aut-name=UmenaYasufumi
en-aut-sei=Umena
en-aut-mei=Yasufumi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=
en-aut-name=KawakamiKeisuke
en-aut-sei=Kawakami
en-aut-mei=Keisuke
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
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=3
ORCID=
en-aut-name=KamiyaNobuo
en-aut-sei=Kamiya
en-aut-mei=Nobuo
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=
affil-num=1
en-affil=
kn-affil=Department of Chemistry, Graduate School of Science, Osaka City University
affil-num=2
en-affil=
kn-affil=Division of Bioscience, Graduate School of Natural Science and Technology/Faculty of Science; Okayama University
affil-num=3
en-affil=
kn-affil=Division of Bioscience, Graduate School of Natural Science and Technology/Faculty of Science; Okayama University
affil-num=4
en-affil=
kn-affil=Department of Chemistry, Graduate School of Science, Osaka City University
END
start-ver=1.4
cd-journal=joma
no-vol=104
cd-vols=
no-issue=1-2
article-no=
start-page=9
end-page=18
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2011
dt-pub=2011
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Structure of the catalytic, inorganic core of oxygen-evolving photosystem II at 1.9 ? resolution
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=The catalytic center for photosynthetic water-splitting consists of 4 Mn atoms and 1 Ca atom and is located near the lumenal surface of photosystem II. So far the structure of the Mn(4)Ca-cluster has been studied by a variety of techniques including X-ray spectroscopy and diffraction, and various structural models have been proposed. However, its exact structure is still unknown due to the limited resolution of crystal structures of PSII achieved so far, as well as possible radiation damages that might have occurred. Very recently, we have succeeded in solving the structure of photosystem II at 1.9 angstrom. which yielded a detailed picture of the Mn(4)CaO(5)-cluster for the first time. In the high resolution structure, the Mn(4)CaO(5)-cluster is arranged in a distorted chair form, with a cubane-like structure formed by 3 Mn and 1 Ca, 4 oxygen atoms as the distorted base of the chair, and 1 Mn and 1 oxygen atom outside of the cubane as the back of the chair. In addition, four water molecules were associated with the cluster, among which, two are associated with the terminal Mn atom and two are associated with the Ca atom. Some of these water molecules may therefore serve as the substrates for water-splitting. The high resolution structure of the catalytic center provided a solid basis for elucidation of the mechanism of photosynthetic water splitting. We review here the structural features of the Mn(4)CaO(5)-cluster analyzed at 1.9 angstrom resolution, and compare them with the structures reported previously.
en-copyright=
kn-copyright=
en-aut-name=KawakamiKeisuke
en-aut-sei=Kawakami
en-aut-mei=Keisuke
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
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=2
ORCID=
en-aut-name=KamiyaNobuo
en-aut-sei=Kamiya
en-aut-mei=Nobuo
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=
affil-num=1
en-affil=
kn-affil=Department of Chemistry, Graduate School of Science, and The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University
affil-num=2
en-affil=
kn-affil=Department of Chemistry, Graduate School of Science, and The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University
affil-num=3
en-affil=
kn-affil=Department of Chemistry, Graduate School of Science, and The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University
affil-num=4
en-affil=
kn-affil=Division of Bioscience, Graduate School of Natural Science and Technology/Faculty of Science, Okayama University
en-keyword=Crystal structure
kn-keyword=Crystal structure
en-keyword=Membrane protein structure
kn-keyword=Membrane protein structure
en-keyword=Oxygen-evolving complex
kn-keyword=Oxygen-evolving complex
en-keyword=Photosystem II
kn-keyword=Photosystem II
en-keyword=Water-oxidation
kn-keyword=Water-oxidation
END
start-ver=1.4
cd-journal=joma
no-vol=1807
cd-vols=
no-issue=3
article-no=
start-page=319
end-page=325
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2011
dt-pub=201103
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Roles of PsbI and PsbM in photosystem II dimer formation and stability studied by deletion mutagenesis and X-ray crystallography
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=PsbM and PsbI are two low molecular weight subunits of photosystem II (PSII), with PsbM being located in the center, and PsbI in the periphery, of the PSII dimer. In order to study the functions of these two subunits from a structural point of view, we crystallized and analyzed the crystal structure of PSII dimers from two mutants lacking either PsbM or PsbI. Our results confirmed the location of these two subunits in the current crystal structure, as well as their absence in the respective mutants. The relative contents of PSII dimers were found to be decreased in both mutants, with a concomitant increase in the amount of PSII monomers, suggesting a destabilization of PSII dimers in both of the mutants. On the other hand, the accumulation level of the overall PSII complexes in the two mutants was similar to that in the wild-type strain. Treatment of purified PSII dimers with lauryldimethylamine N-oxide at an elevated temperature preferentially disintegrated the dimers from the PsbM deletion mutant into monomers and CP43-less monomers, whereas no significant degradation of the dimers was observed from the PsbI deletion mutant. These results indicate that although both PsbM and PsbI are required for the efficient formation and stability of PSII dimers in vivo, they have different roles, namely, PsbM is required directly for the formation of dimers and its absence led to the instability of the dimers accumulated. On the other hand, PsbI is required in the assembly process of PSII dimers in vivo; once the dimers are formed, PsbI was no longer required for its stability.
en-copyright=
kn-copyright=
en-aut-name=KawakamiKeisuke
en-aut-sei=Kawakami
en-aut-mei=Keisuke
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
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=2
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=3
ORCID=
en-aut-name=KawabataYousuke
en-aut-sei=Kawabata
en-aut-mei=Yousuke
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
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=5
ORCID=
en-aut-name=KamiyaNobuo
en-aut-sei=Kamiya
en-aut-mei=Nobuo
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=6
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=7
ORCID=
affil-num=1
en-affil=
kn-affil=Division of Bioscience, Graduate School of Natural Science and Technology/Faculty of Science, Okayama University
affil-num=2
en-affil=
kn-affil=Department of Chemistry, Graduate School of Science, Osaka City University
affil-num=3
en-affil=
kn-affil=Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science
affil-num=4
en-affil=
kn-affil=Division of Bioscience, Graduate School of Natural Science and Technology/Faculty of Science, Okayama University
affil-num=5
en-affil=
kn-affil=Department of Life Sciences (Biology), Graduate School of Arts and Science, The University of Tokyo
affil-num=6
en-affil=
kn-affil=Department of Chemistry, Graduate School of Science, Osaka City University
affil-num=7
en-affil=
kn-affil=Division of Bioscience, Graduate School of Natural Science and Technology/Faculty of Science, Okayama University
en-keyword=Photosystem II
kn-keyword=Photosystem II
en-keyword=Mutant
kn-keyword=Mutant
en-keyword=Crystal structure
kn-keyword=Crystal structure
en-keyword=PsbM
kn-keyword=PsbM
en-keyword=PsbI
kn-keyword=PsbI
en-keyword=Oxygen evolution
kn-keyword=Oxygen evolution
END