start-ver=1.4
cd-journal=joma
no-vol=119
cd-vols=
no-issue=43
article-no=
start-page=e2122641119
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2022
dt-pub=20221017
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Structures and mechanisms of actin ATP hydrolysis
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=The major cytoskeleton protein actin undergoes cyclic transitions between the monomeric G-form and the filamentous F-form, which drive organelle transport and cell motility. This mechanical work is driven by the ATPase activity at the catalytic site in the F-form. For deeper understanding of the actin cellular functions, the reaction mechanism must be elucidated. Here, we show that a single actin molecule is trapped in the F-form by fragmin domain-1 binding and present their crystal structures in the ATP analog-, ADP-Pi-, and ADP-bound forms, at 1.15-? resolutions. The G-to-F conformational transition shifts the side chains of Gln137 and His161, which relocate four water molecules including W1 (attacking water) and W2 (helping water) to facilitate the hydrolysis. By applying quantum mechanics/molecular mechanics calculations to the structures, we have revealed a consistent and comprehensive reaction path of ATP hydrolysis by the F-form actin. The reaction path consists of four steps: 1) W1 and W2 rotations; 2) PG?O3B bond cleavage; 3) four concomitant events: W1?PO3? formation, OH? and proton cleavage, nucleophilic attack by the OH? against PG, and the abstracted proton transfer; and 4) proton relocation that stabilizes the ADP-Pi?bound F-form actin. The mechanism explains the slow rate of ATP hydrolysis by actin and the irreversibility of the hydrolysis reaction. While the catalytic strategy of actin ATP hydrolysis is essentially the same as those of motor proteins like myosin, the process after the hydrolysis is distinct and discussed in terms of Pi release, F-form destabilization, and global conformational changes.
en-copyright=
kn-copyright=

en-aut-name=KanematsuYusuke
en-aut-sei=Kanematsu
en-aut-mei=Yusuke
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=

en-aut-name=NaritaAkihiro
en-aut-sei=Narita
en-aut-mei=Akihiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=

en-aut-name=OdaToshiro
en-aut-sei=Oda
en-aut-mei=Toshiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=

en-aut-name=KoikeRyotaro
en-aut-sei=Koike
en-aut-mei=Ryotaro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=

en-aut-name=OtaMotonori
en-aut-sei=Ota
en-aut-mei=Motonori
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=5
ORCID=

en-aut-name=TakanoYu
en-aut-sei=Takano
en-aut-mei=Yu
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=6
ORCID=

en-aut-name=MoritsuguKei
en-aut-sei=Moritsugu
en-aut-mei=Kei
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=7
ORCID=

en-aut-name=FujiwaraIkuko
en-aut-sei=Fujiwara
en-aut-mei=Ikuko
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=8
ORCID=

en-aut-name=TanakaKotaro
en-aut-sei=Tanaka
en-aut-mei=Kotaro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=9
ORCID=

en-aut-name=KomatsuHideyuki
en-aut-sei=Komatsu
en-aut-mei=Hideyuki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=10
ORCID=

en-aut-name=NagaeTakayuki
en-aut-sei=Nagae
en-aut-mei=Takayuki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=11
ORCID=

en-aut-name=WatanabeNobuhisa
en-aut-sei=Watanabe
en-aut-mei=Nobuhisa
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=12
ORCID=

en-aut-name=IwasaMitsusada
en-aut-sei=Iwasa
en-aut-mei=Mitsusada
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=13
ORCID=

en-aut-name=Ma?daYuichiro
en-aut-sei=Ma?da
en-aut-mei=Yuichiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=14
ORCID=

en-aut-name=TakedaShuichi
en-aut-sei=Takeda
en-aut-mei=Shuichi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=15
ORCID=

affil-num=1
en-affil=Graduate School of Information Sciences, Hiroshima City University
kn-affil=

affil-num=2
en-affil=Structural Biology Research Center, Graduate School of Science, Nagoya University
kn-affil=

affil-num=3
en-affil=Faculty of Health and Welfare, Tokai Gakuin University
kn-affil=

affil-num=4
en-affil=Graduate School of Informatics, Nagoya University
kn-affil=

affil-num=5
en-affil=Graduate School of Informatics, Nagoya University
kn-affil=

affil-num=6
en-affil=Graduate School of Information Sciences, Hiroshima City University
kn-affil=

affil-num=7
en-affil=Graduate School of Medical Life Science, Yokohama City University
kn-affil=

affil-num=8
en-affil=Graduate School of Science, Osaka City University
kn-affil=

affil-num=9
en-affil=Structural Biology Research Center, Graduate School of Science, Nagoya University
kn-affil=

affil-num=10
en-affil=Department of Bioscience and Bioinformatics, Graduate School of Computer Science and Systems Engineering, Kyushu Institute of Technology
kn-affil=

affil-num=11
en-affil=Synchrotron Radiation Research Center, Nagoya University
kn-affil=

affil-num=12
en-affil=Synchrotron Radiation Research Center, Nagoya University
kn-affil=

affil-num=13
en-affil=Graduate School of Informatics, Nagoya University
kn-affil=

affil-num=14
en-affil=Research Institute for Interdisciplinary Science, Okayama University
kn-affil=

affil-num=15
en-affil=Research Institute for Interdisciplinary Science, Okayama University
kn-affil=
en-keyword=actin
kn-keyword=actin
en-keyword=ATP hydrolysis
kn-keyword=ATP hydrolysis
en-keyword=protein crystallography
kn-keyword=protein crystallography
en-keyword=QM
kn-keyword=QM
en-keyword=MM simulation
kn-keyword=MM simulation
END

start-ver=1.4
cd-journal=joma
no-vol=11
cd-vols=
no-issue=
article-no=
start-page=1105460
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2023
dt-pub=20230316
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Mutagenic analysis of actin reveals the mechanism of His161 flipping that triggers ATP hydrolysis
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=The dynamic assembly of actin is controlled by the hydrolysis of ATP, bound to the center of the molecule. Upon polymerization, actin undergoes a conformational change from the monomeric G-form to the fibrous F-form, which is associated with the flipping of the side chain of His161 toward ATP. His161 flipping from the gauche-minus to gauche-plus conformation leads to a rearrangement of the active site water molecules, including ATP attacking water (W1), into an orientation capable of hydrolysis. We previously showed that by using a human cardiac muscle a-actin expression system, mutations in the Pro-rich loop residues (A108G and P109A) and in a residue that was hydrogen-bonded to W1 (Q137A) affect the rate of polymerization and ATP hydrolysis. Here, we report the crystal structures of the three mutant actins bound to AMPPNP or ADP-P-i determined at a resolution of 1.35-1.55( )angstrom, which are stabilized in the F-form conformation with the aid of the fragmin F1 domain. In A108G, His161 remained non-flipped despite the global actin conformation adopting the F-form, demonstrating that the side chain of His161 is flipped to avoid a steric clash with the methyl group of A108. Because of the non-flipped His161, W1 was located away from ATP, similar to G-actin, which was accompanied by incomplete hydrolysis. In P109A, the absence of the bulky proline ring allowed His161 to be positioned near the Pro-rich loop, with a minor influence on ATPase activity. In Q137A, two water molecules replaced the side-chain oxygen and nitrogen of Gln137 almost exactly at their positions; consequently, the active site structure, including the W1 position, is essentially conserved. This seemingly contradictory observation to the reported low ATPase activity of the Q137A filament could be attributed to a high fluctuation of the active site water. Together, our results suggest that the elaborate structural design of the active site residues ensures the precise control of the ATPase activity of actin.
en-copyright=
kn-copyright=

en-aut-name=IwasaMitsusada
en-aut-sei=Iwasa
en-aut-mei=Mitsusada
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=

en-aut-name=TakedaShuichi
en-aut-sei=Takeda
en-aut-mei=Shuichi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=

en-aut-name=NaritaAkihiro
en-aut-sei=Narita
en-aut-mei=Akihiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=

en-aut-name=MaedaYuichiro
en-aut-sei=Maeda
en-aut-mei=Yuichiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=

en-aut-name=OdaToshiro
en-aut-sei=Oda
en-aut-mei=Toshiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=5
ORCID=

affil-num=1
en-affil=Graduate School of Informatics, Nagoya University
kn-affil=

affil-num=2
en-affil=Research Institute for Interdisciplinary Science (RIIS), Okayama University
kn-affil=

affil-num=3
en-affil=Structural Biology Research Center, Graduate School of Science, Nagoya University
kn-affil=

affil-num=4
en-affil=Research Institute for Interdisciplinary Science (RIIS), Okayama University
kn-affil=

affil-num=5
en-affil=Faculty of Health and Welfare, Tokai Gakuin University
kn-affil=
en-keyword=MD simulation
kn-keyword=MD simulation
en-keyword=actin
kn-keyword=actin
en-keyword=water dynamics
kn-keyword=water dynamics
en-keyword=ATP hydrolysis
kn-keyword=ATP hydrolysis
en-keyword=X-ray structure
kn-keyword=X-ray structure
en-keyword=baculovirus expression
kn-keyword=baculovirus expression
END

start-ver=1.4
cd-journal=joma
no-vol=5
cd-vols=
no-issue=1
article-no=
start-page=890
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2022
dt-pub=20220831
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Structural and biochemical evidence for the emergence of a calcium-regulated actin cytoskeleton prior to eukaryogenesis
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=Charting the emergence of eukaryotic traits is important for understanding the characteristics of organisms that contributed to eukaryogenesis. Asgard archaea and eukaryotes are the only organisms known to possess regulated actin cytoskeletons. Here, we determined that gelsolins (2DGels) from Lokiarchaeota (Loki) and Heimdallarchaeota (Heim) are capable of regulating eukaryotic actin dynamics in vitro and when expressed in eukaryotic cells. The actin filament severing and capping, and actin monomer sequestering, functionalities of 2DGels are strictly calcium controlled. We determined the X-ray structures of Heim and Loki 2DGels bound actin monomers. Each structure possesses common and distinct calcium-binding sites. Loki2DGel has an unusual WH2-like motif (LVDV) between its two gelsolin domains, in which the aspartic acid coordinates a calcium ion at the interface with actin. We conclude that the calcium-regulated actin cytoskeleton predates eukaryogenesis and emerged in the predecessors of the last common ancestor of Loki, Heim and Thorarchaeota. Calcium-regulated actin filament assembly predates eukaryogenesis and was present in the last common ancestor of Asgard archaea Loki, Heim, and Thorarchaeota.
en-copyright=
kn-copyright=

en-aut-name=AkilCaner
en-aut-sei=Akil
en-aut-mei=Caner
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=

en-aut-name=TranLinh T.
en-aut-sei=Tran
en-aut-mei=Linh T.
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=

en-aut-name=Orhant-PriouxMagali
en-aut-sei=Orhant-Prioux
en-aut-mei=Magali
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=

en-aut-name=BaskaranYohendran
en-aut-sei=Baskaran
en-aut-mei=Yohendran
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=

en-aut-name=SenjuYosuke
en-aut-sei=Senju
en-aut-mei=Yosuke
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=5
ORCID=

en-aut-name=TakedaShuichi
en-aut-sei=Takeda
en-aut-mei=Shuichi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=6
ORCID=

en-aut-name=ChotchuangPhatcharin
en-aut-sei=Chotchuang
en-aut-mei=Phatcharin
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=7
ORCID=

en-aut-name=MuengsaenDuangkamon
en-aut-sei=Muengsaen
en-aut-mei=Duangkamon
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=8
ORCID=

en-aut-name=SchulteAlbert
en-aut-sei=Schulte
en-aut-mei=Albert
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=9
ORCID=

en-aut-name=ManserEdward
en-aut-sei=Manser
en-aut-mei=Edward
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=10
ORCID=

en-aut-name=BlanchoinLaurent
en-aut-sei=Blanchoin
en-aut-mei=Laurent
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=11
ORCID=

en-aut-name=RobinsonRobert C.
en-aut-sei=Robinson
en-aut-mei=Robert C.
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=12
ORCID=

affil-num=1
en-affil=Research Institute for Interdisciplinary Science (RIIS), Okayama University
kn-affil=

affil-num=2
en-affil=Research Institute for Interdisciplinary Science (RIIS), Okayama University
kn-affil=

affil-num=3
en-affil=CytomorphoLab, Biosciences & Biotechnology Institute of Grenoble, Laboratoire de Physiologie Cellulaire & V?g?tale, Universit? Grenoble-Alpes/CEA/CNRS/INRA
kn-affil=

affil-num=4
en-affil=Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Biopolis
kn-affil=

affil-num=5
en-affil=Research Institute for Interdisciplinary Science (RIIS), Okayama University
kn-affil=

affil-num=6
en-affil=Research Institute for Interdisciplinary Science (RIIS), Okayama University
kn-affil=

affil-num=7
en-affil=School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC)
kn-affil=

affil-num=8
en-affil=School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC)
kn-affil=

affil-num=9
en-affil=School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC)
kn-affil=

affil-num=10
en-affil=Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Biopolis
kn-affil=

affil-num=11
en-affil=CytomorphoLab, Biosciences & Biotechnology Institute of Grenoble, Laboratoire de Physiologie Cellulaire & V?g?tale, Universit? Grenoble-Alpes/CEA/CNRS/INRA
kn-affil=

affil-num=12
en-affil=Research Institute for Interdisciplinary Science (RIIS), Okayama University
kn-affil=
END

start-ver=1.4
cd-journal=joma
no-vol=433
cd-vols=
no-issue=9
article-no=
start-page=166891
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2021
dt-pub=2021430
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Structural Insights into the Regulation of Actin Capping Protein by Twinfilin C-terminal Tail
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=Twinfilin is a conserved actin regulator that interacts with actin capping protein (CP) via C-terminus residues (TWtail) that exhibits sequence similarity with the CP interaction (CPI) motif of CARMIL. Here we report the crystal structure of TWtail in complex with CP. Our structure showed that although TWtail and CARMIL CPI bind CP to an overlapping surface via their middle regions, they exhibit different CP-binding modes at both termini. Consequently, TWtail and CARMIL CPI restrict the CP in distinct conformations of open and closed forms, respectively. Interestingly, V-1, which targets CP away from the TWtail binding site, also favors the open-form CP. Consistently, TWtail forms a stable ternary complex with CP and V-1, a striking contrast to CARMIL CPI, which rapidly dissociates V-1 from CP. Our results demonstrate that TWtail is a unique CP-binding motif that regulates CP in a manner distinct from CARMIL CPI.
en-copyright=
kn-copyright=

en-aut-name=TakedaShuichi
en-aut-sei=Takeda
en-aut-mei=Shuichi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=

en-aut-name=KoikeRyotaro
en-aut-sei=Koike
en-aut-mei=Ryotaro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=

en-aut-name=FujiwaraIkuko
en-aut-sei=Fujiwara
en-aut-mei=Ikuko
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=

en-aut-name=NaritaAkihiro
en-aut-sei=Narita
en-aut-mei=Akihiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=

en-aut-name=MiyataMakoto
en-aut-sei=Miyata
en-aut-mei=Makoto
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=5
ORCID=

en-aut-name=OtaMotonori
en-aut-sei=Ota
en-aut-mei=Motonori
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=6
ORCID=

en-aut-name=Ma?daYuichiro
en-aut-sei=Ma?da
en-aut-mei=Yuichiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=7
ORCID=

affil-num=1
en-affil=Research Institute for Interdisciplinary Science (RIIS), Okayama University
kn-affil=

affil-num=2
en-affil=Graduate School of Informatics, Nagoya University
kn-affil=

affil-num=3
en-affil=Graduate School of Science, Osaka City University
kn-affil=

affil-num=4
en-affil=Graduate School of Science, Nagoya University
kn-affil=

affil-num=5
en-affil=Graduate School of Science, Osaka City University
kn-affil=

affil-num=6
en-affil=Graduate School of Informatics, Nagoya University
kn-affil=

affil-num=7
en-affil=Graduate School of Informatics, Nagoya University
kn-affil=
en-keyword=Twinfilin
kn-keyword=Twinfilin
en-keyword= actin capping protein
kn-keyword= actin capping protein
en-keyword=actin dynamics
kn-keyword=actin dynamics
en-keyword=V-1
kn-keyword=V-1
en-keyword=crystal structure
kn-keyword=crystal structure
en-keyword=conformational flexibility
kn-keyword=conformational flexibility
END