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Date uploaded: April 21, 2023

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Structure of Bifidobacterial Enzyme at Room Temperature Observed by X-ray Free Electron Laser - Enzymatic Reaction Mechanism Suggested by Local Structural Changes

Press Release 20230410


A joint research group of Sou Iwata, Eriko Nango, and Kensuke Tono has determined the steric structure of the glycolytic enzyme of bifidobacteria at room temperature and found new insights into the reaction mechanism of the enzyme.

This research result indicates that obtaining a protein structure close to the physiological environment may provide more useful information for clarifying the enzyme reaction mechanism, and is expected to contribute to the advancement of the industrial use of enzymes through the design of various enzymes with higher functionality.

This time, the group succeeded in analyzing the room temperature structure of phosphoketolase, one of the glycolytic enzymes of bifidobacteria, by the continuous femtosecond crystallography (SFX) method at the X-ray free electron laser (XFEL) facility "SACLA". As a result, they found that the small loop-like structure located at the entrance of the active site of phosphoketolase is different from the conventional cryogenic structure. The discussion based on the characteristics of the structure in complex with inhibitors, which was conducted at the same time, provided new insights into the reaction mechanism of phosphoketolase. The phosphoketolase microcrystals needed for the analysis were obtained using a light-induced protein crystallization plate, and this crystallization method was also found to be effective in improving the efficiency of structural analysis at SACLA.

This research was published in the online edition of the scientific journal Acta Crystallographica Section D on March 28.

  • (The original press release is in Japanese)

    https://www.tohoku.ac.jp/japanese/2023/04/press20230410-01-enzyme.html http://www2.tagen.tohoku.ac.jp/lab/news_press/20230410/

    Publication details


    Ambient temperature structure of phosphoketolase from Bifidobacterium longum determined by serial femtosecond X-ray crystallography


    Kunio Nakata, Tatsuki Kashiwagi, Naoki Kunishima, Hisashi Naitow, Yoshinori Matsuura, Hiroshi Miyano, Toshimi Mizukoshi, Kensuke Tono, Makina Yabashi, Eriko Nango and So Iwata


    Acta Crystallographica Section D, 79, 290-303, 2023.




    Professor Eriko NANGO
    E-mail: eriko.nango.c4 [at]tohoku.ac.jp
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    E-mail: press.tagen [at]grp.tohoku.ac.jp
    Please replace [at] with "@" in the email address.