Updated on 2024/10/04

写真a

 
NAGATA Ryuhei
 
Organization
Graduate School of Bioagricultural Sciences Department of Applied Biosciences Assistant Professor
Graduate School
Graduate School of Bioagricultural Sciences
Undergraduate School
School of Agricultural Sciences Department of Applied Biosciences
Title
Assistant Professor

Degree 1

  1. 博士(理学) ( 2018.3   京都大学 ) 

Research Areas 1

  1. Life Science / Structural biochemistry

Research History 1

  1. Nagoya University   Graduate School of Bioagricultural Sciences Department of Applied Biosciences   Assistant Professor

    2024.10

 

Papers 4

  1. Substrate Recognition Mechanism of a Trichostatin A-Forming Hydroxyamidotransferase Reviewed

    Ryuhei Nagata, Makoto Nishiyama, Tomohisa Kuzuyama

    Biochemistry   Vol. 62 ( 12 ) page: 1833 - 1837   2023.5

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    Authorship:Lead author, Corresponding author   Publishing type:Research paper (scientific journal)   Publisher:American Chemical Society (ACS)  

    DOI: 10.1021/acs.biochem.3c00025

  2. Structural Basis for the Prenylation Reaction of Carbazole‐Containing Natural Products Catalyzed by Squalene Synthase‐like Enzymes Reviewed

    Ryuhei Nagata, Hironori Suemune, Masaya Kobayashi, Tetsuro Shinada, Kazuo Shin-ya, Makoto Nishiyama, Tomoya Hino, Yusuke Sato, Tomohisa Kuzuyama, Shingo Nagano

    Angewandte Chemie International Edition   Vol. 61 ( 20 ) page: e202117430   2022.3

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    Authorship:Lead author   Publishing type:Research paper (scientific journal)   Publisher:Wiley  

    DOI: 10.1002/anie.202117430

  3. Identification and enzymatic analysis of an archaeal ATP-dependent serine kinase from the hyperthermophilic archaeon Staphylothermus marinus Reviewed

    Yasunobu Mori, Hiroki Kawamura, Takaaki Sato, Takayuki Fujita, Ryuhei Nagata, Masahiro Fujihashi, Kunio Miki, Haruyuki Atomi

    Journal of Bacteriology   Vol. 203 ( 16 ) page: e00025-21   2021.7

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    Publishing type:Research paper (scientific journal)   Publisher:American Society for Microbiology  

    Serine kinase catalyzes the phosphorylation of free serine (Ser) to produce
    <italic>O</italic>
    -phosphoserine (Sep). An ADP-dependent Ser kinase in the hyperthermophilic archaeon
    <italic>Thermococcus kodakarensis</italic>
    (
    <italic>Tk</italic>
    -SerK) is involved in cysteine (Cys) biosynthesis and most likely Ser assimilation. An ATP-dependent Ser kinase in the mesophilic bacterium
    <italic>Staphylococcus aureus</italic>
    is involved in siderophore biosynthesis. Although proteins displaying various degrees of similarity with
    <italic>Tk</italic>
    -SerK are distributed in a wide range of organisms, it is unclear if they are actually Ser kinases. Here we examined proteins from Desulfurococcales species in Crenarchaeota that display moderate similarity with
    <italic>Tk</italic>
    -SerK from Euryarchaeota (42-45% identical).
    <italic>Tk</italic>
    -
    <italic>serK</italic>
    homologs from
    <italic>Staphylothermus marinus</italic>
    (Smar_0555),
    <italic>Desulfurococcus amylolyticus</italic>
    (DKAM_0858), and
    <italic>Desulfurococcus mucosus</italic>
    (Desmu_0904) were expressed in
    <italic>Escherichia coli</italic>
    . All three partially purified recombinant proteins exhibited Ser kinase activity utilizing ATP rather than ADP as a phosphate donor. Purified Smar_0555 protein displayed activity towards
    <sc>l</sc>
    -Ser, but not with other compounds including
    <sc>d</sc>
    -Ser,
    <sc>l</sc>
    -threonine and
    <sc>l</sc>
    -homoserine. The enzyme utilized ATP, UTP, GTP, CTP, and the inorganic polyphosphates triphosphate and tetraphosphate as the phosphate donor. Kinetic analysis indicated that the Smar_0555 protein preferred nucleoside 5’-triphosphates compared to triphosphate as a phosphate donor. Transcript levels and Ser kinase activity in
    <italic>S. marinus</italic>
    cells grown with or without serine suggested that the Smar_0555 gene is constitutively expressed. The genes encoding Ser kinases examined here form an operon with genes most likely responsible for the conversion between Sep and 3-phosphoglycerate of central sugar metabolism, suggesting that the ATP-dependent Ser kinases from Desulfurococcales play a role in the assimilation of Ser.




    <bold>IMPORTANCE</bold>




    Homologs of the ADP-dependent Ser kinase from the archaeon
    <italic>Thermococcus kodakarensis</italic>
    (
    <italic>Tk</italic>
    -SerK) include representatives from all three domains of life. The results of this study show that even homologs from the archaeal order Desulfurococcales, which are the most structurally related to the ADP-dependent Ser kinases from the Thermococcales, are Ser kinases that utilize ATP, and in at least some cases inorganic polyphosphates, as the phosphate donor. The differences in properties between the Desulfurococcales and Thermococcales enzymes raise the possibility that
    <italic>Tk</italic>
    -SerK homologs constitute a group of kinases that phosphorylate free serine with a wide range of phosphate donors.

    DOI: 10.1128/jb.00025-21

  4. Identification of a pyrophosphate-dependent kinase and its donor selectivity determinants Reviewed

    Ryuhei Nagata, Masahiro Fujihashi, Takaaki Sato, Haruyuki Atomi, Kunio Miki

    Nature Communications   Vol. 9   page: 1765   2018.5

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    Authorship:Lead author   Language:English   Publishing type:Research paper (scientific journal)   Publisher:Springer Science and Business Media LLC  

    DOI: 10.1038/s41467-018-04201-z

    Other Link: http://www.nature.com/articles/s41467-018-04201-z

MISC 2

  1. スクアレン合成酵素に似た酵素による芳香族化合物のプレニル化反応の仕組み Reviewed

    永田隆平, 葛山智久

    化学と生物   Vol. 61 ( 6 ) page: 260 - 262   2023.6

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    Authorship:Lead author  

  2. ATPでなくピロリン酸を利用する新規リン酸化酵素の基質認識機構 Reviewed

    永田隆平, 藤橋雅宏

    化学と生物   Vol. 56 ( 12 ) page: 779 - 780   2018.11

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    Authorship:Lead author, Corresponding author   Language:Japanese  

Research Project for Joint Research, Competitive Funding, etc. 4

  1. Seeking pyrophosphate-dependent protein kinase

    Grant number:22K14825  2022.4 - 2025.3

    Grants-in-Aid for Scientific Research  Grant-in-Aid for Early-Career Scientists

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    Authorship:Principal investigator 

    Grant amount:\3640000 ( Direct Cost: \2800000 、 Indirect Cost:\840000 )

  2. ポリケタイド合成酵素の基質受け渡し機構の解明を目指した高分解能構造解析

    2019.4 - 2022.3

    科学研究費助成事業  若手研究

    永田 隆平

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    Authorship:Principal investigator  Grant type:Competitive

  3. 医薬資源として有望なヒドロキサム酸を合成する酵素の機構解明と合理的改変法の確立

    2019.4 - 2022.3

    特別研究員奨励費 

    永田 隆平

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    Authorship:Principal investigator  Grant type:Competitive

  4. 酵素の工業利用のためにATP依存性のリン酸化酵素をピロリン酸依存性に改良する方法

    2016.4 - 2018.3

    特別研究員奨励費 

    永田 隆平

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    Authorship:Principal investigator  Grant type:Competitive

 

Teaching Experience (Off-campus) 2

  1. Biochemistry

    2022.7 The University of Tokyo)

  2. 専門化学実験II

    2020.5 - 2020.9 お茶の水女子大学理学部)

 

Academic Activities 2

  1. 第34回イソプレノイド研究会 座長

    Role(s):Panel moderator, session chair, etc.

    2024.9

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    Type:Academic society, research group, etc. 

  2. 日本農芸化学会2022年度大会 進行役

    Role(s):Panel moderator, session chair, etc.

    日本農芸化学会  2022.3

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    Type:Academic society, research group, etc.