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Protonation/deprotonation-driven switch for the redox stability of low-potential [4Fe-4S] ferredoxin

View ORCID ProfileKei Wada, Kenji Kobayashi, Iori Era, Yusuke Isobe, Taigo Kamimura, Masaki Marukawa, Takayuki Nagae, Kazuki Honjo, Noriko Kaseda, Yumiko Motoyama, Kengo Inoue, Masakazu Sugishima, Katsuhiro Kusaka, Naomine Yano, Keiichi Fukuyama, Masaki Mishima, Yasutaka Kitagawa, Masaki Unno
doi: https://doi.org/10.1101/2024.09.12.612615
Kei Wada
1Department of Medical Sciences, University of Miyazaki, Kiyotake, Miyazaki 889-1692, Japan,
2Frontier Science Research Center, University of Miyazaki, Kiyotake, Miyazaki 889-1692, Japan,
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Kenji Kobayashi
3Graduate School of Science and Engineering, Ibaraki University, Hitachi, Ibaraki 316-8511, Japan
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Iori Era
4Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
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Yusuke Isobe
3Graduate School of Science and Engineering, Ibaraki University, Hitachi, Ibaraki 316-8511, Japan
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Taigo Kamimura
4Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
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Masaki Marukawa
1Department of Medical Sciences, University of Miyazaki, Kiyotake, Miyazaki 889-1692, Japan,
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Takayuki Nagae
5Department of Molecular Biophysics, Tokyo University of Pharmacy and Life Sciences, Tokyo 192-0392, Japan
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Kazuki Honjo
4Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
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Noriko Kaseda
1Department of Medical Sciences, University of Miyazaki, Kiyotake, Miyazaki 889-1692, Japan,
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Yumiko Motoyama
1Department of Medical Sciences, University of Miyazaki, Kiyotake, Miyazaki 889-1692, Japan,
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Kengo Inoue
6Department of Biochemistry and Applied Biosciences, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan
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Masakazu Sugishima
7Department of Medical Biochemistry, Kurume University School of Medicine, Kurume, Fukuoka 830-0011, Japan
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Katsuhiro Kusaka
8Comprehensive Research Organization for Science and Society (CROSS) Neutron Science and Technology Center, Naka Ibaraki 319-1106, Japan
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Naomine Yano
9Structural Biology Division, Japan Synchrotron Radiation Research Institute, Hyogo679-5198, Japan, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
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Keiichi Fukuyama
10Research and Education Center for Atomic Sciences Ibaraki University, Naka Ibaraki 319-1106, Japan
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Masaki Mishima
5Department of Molecular Biophysics, Tokyo University of Pharmacy and Life Sciences, Tokyo 192-0392, Japan
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Yasutaka Kitagawa
4Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
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  • For correspondence: [email protected] [email protected] [email protected]
Masaki Unno
3Graduate School of Science and Engineering, Ibaraki University, Hitachi, Ibaraki 316-8511, Japan
10Research and Education Center for Atomic Sciences Ibaraki University, Naka Ibaraki 319-1106, Japan
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  • For correspondence: [email protected] [email protected] [email protected]
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Abstract

Ferredoxin is a small iron-sulfur protein and acts as an electron carrier. Low-potential ferredoxins harbor [4Fe-4S] cluster(s), which play(s) a crucial role as the redox center. Low-potential ferredoxins are able to cover a wide range of redox potentials (–700 to –200 mV); however, the mechanisms underlying the factors which control the redox potential are still enigmatic. Here, we determined the neutron structure of ferredoxin from Bacillus thermoproteolyticus, and experimentally revealed the exact hydrogen-bonding network involving the [4Fe-4S] cluster. The density functional theory calculations based on the hydrogen-bonding network revealed that protonation states of the sidechain of Asp64 close to the [4Fe-4S] cluster critically affected the stability of the reduced state in the cluster. These findings provide the first identification of the intrinsic control factor of redox potential for the [4Fe-4S] cluster in low-potential ferredoxins.

Competing Interest Statement

The authors have declared no competing interest.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted September 14, 2024.
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Protonation/deprotonation-driven switch for the redox stability of low-potential [4Fe-4S] ferredoxin
Kei Wada, Kenji Kobayashi, Iori Era, Yusuke Isobe, Taigo Kamimura, Masaki Marukawa, Takayuki Nagae, Kazuki Honjo, Noriko Kaseda, Yumiko Motoyama, Kengo Inoue, Masakazu Sugishima, Katsuhiro Kusaka, Naomine Yano, Keiichi Fukuyama, Masaki Mishima, Yasutaka Kitagawa, Masaki Unno
bioRxiv 2024.09.12.612615; doi: https://doi.org/10.1101/2024.09.12.612615
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Protonation/deprotonation-driven switch for the redox stability of low-potential [4Fe-4S] ferredoxin
Kei Wada, Kenji Kobayashi, Iori Era, Yusuke Isobe, Taigo Kamimura, Masaki Marukawa, Takayuki Nagae, Kazuki Honjo, Noriko Kaseda, Yumiko Motoyama, Kengo Inoue, Masakazu Sugishima, Katsuhiro Kusaka, Naomine Yano, Keiichi Fukuyama, Masaki Mishima, Yasutaka Kitagawa, Masaki Unno
bioRxiv 2024.09.12.612615; doi: https://doi.org/10.1101/2024.09.12.612615

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