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Safari C, Ghosh S, Andersson R, Johannesson J, Båth P, Uwangue O, Dahl P, Zoric D, Sandelin E, Vallejos A, Nango E, Tanaka R, Bosman R, Börjesson P, Dunevall E, Hammarin G, Ortolani G, Panman M, Tanaka T, Yamashita A, Arima T, Sugahara M, Suzuki M, Masuda T, Takeda H, Yamagiwa R, Oda K, Fukuda M, Tosha T, Naitow H, Owada S, Tono K, Nureki O, Iwata S, Neutze R, Brändén G. Time-resolved serial crystallography to track the dynamics of carbon monoxide in the active site of cytochrome c oxidase. Sci Adv 2023; 9:eadh4179. [PMID: 38064560 PMCID: PMC10708180 DOI: 10.1126/sciadv.adh4179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 11/09/2023] [Indexed: 12/18/2023]
Abstract
Cytochrome c oxidase (CcO) is part of the respiratory chain and contributes to the electrochemical membrane gradient in mitochondria as well as in many bacteria, as it uses the energy released in the reduction of oxygen to pump protons across an energy-transducing biological membrane. Here, we use time-resolved serial femtosecond crystallography to study the structural response of the active site upon flash photolysis of carbon monoxide (CO) from the reduced heme a3 of ba3-type CcO. In contrast with the aa3-type enzyme, our data show how CO is stabilized on CuB through interactions with a transiently ordered water molecule. These results offer a structural explanation for the extended lifetime of the CuB-CO complex in ba3-type CcO and, by extension, the extremely high oxygen affinity of the enzyme.
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Affiliation(s)
- Cecilia Safari
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Swagatha Ghosh
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Rebecka Andersson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Jonatan Johannesson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Petra Båth
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Owens Uwangue
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Peter Dahl
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Doris Zoric
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Emil Sandelin
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Adams Vallejos
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Eriko Nango
- RIKEN SPring-8 Center, 1-1-1 Kuoto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Rie Tanaka
- RIKEN SPring-8 Center, 1-1-1 Kuoto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Robert Bosman
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Per Börjesson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Elin Dunevall
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Greger Hammarin
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Giorgia Ortolani
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Matthijs Panman
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Tomoyuki Tanaka
- RIKEN SPring-8 Center, 1-1-1 Kuoto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Ayumi Yamashita
- RIKEN SPring-8 Center, 1-1-1 Kuoto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Toshi Arima
- RIKEN SPring-8 Center, 1-1-1 Kuoto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Michihiro Sugahara
- RIKEN SPring-8 Center, 1-1-1 Kuoto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Mamoru Suzuki
- Laboratory of Supramolecular Crystallography, Research Center for Structural and Functional Proteomics, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Tetsuya Masuda
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Japan
| | - Hanae Takeda
- RIKEN SPring-8 Center, 1-1-1 Kuoto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo 678-1297, Japan
| | - Raika Yamagiwa
- RIKEN SPring-8 Center, 1-1-1 Kuoto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo 678-1297, Japan
| | - Kazumasa Oda
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Masahiro Fukuda
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Takehiko Tosha
- RIKEN SPring-8 Center, 1-1-1 Kuoto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Hisashi Naitow
- RIKEN SPring-8 Center, 1-1-1 Kuoto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Shigeki Owada
- RIKEN SPring-8 Center, 1-1-1 Kuoto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Kensuke Tono
- RIKEN SPring-8 Center, 1-1-1 Kuoto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - So Iwata
- RIKEN SPring-8 Center, 1-1-1 Kuoto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Richard Neutze
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Gisela Brändén
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
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Yamagiwa R, Kurahashi T, Takeda M, Adachi M, Nakamura H, Arai H, Shiro Y, Sawai H, Tosha T. Pseudomonas aeruginosa overexpression system of nitric oxide reductase for in vivo and in vitro mutational analyses. Biochim Biophys Acta Bioenerg 2018; 1859:333-341. [PMID: 29499184 DOI: 10.1016/j.bbabio.2018.02.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 02/18/2018] [Accepted: 02/24/2018] [Indexed: 11/30/2022]
Abstract
Membrane-integrated nitric oxide reductase (NOR) reduces nitric oxide (NO) to nitrous oxide (N2O) with protons and electrons. This process is essential for the elimination of the cytotoxic NO that is produced from nitrite (NO2-) during microbial denitrification. A structure-guided mutagenesis of NOR is required to elucidate the mechanism for NOR-catalyzed NO reduction. We have already solved the crystal structure of cytochrome c-dependent NOR (cNOR) from Pseudomonas aeruginosa. In this study, we then constructed its expression system using cNOR-gene deficient and wild-type strains for further functional study. Characterizing the variants of the five conserved Glu residues located around the heme/non-heme iron active center allowed us to establish how the anaerobic growth rate of cNOR-deficient strains expressing cNOR variants correlates with the in vitro enzymatic activity of the variants. Since bacterial strains require active cNOR to eliminate cytotoxic NO and to survive under denitrification conditions, the anaerobic growth rate of a strain with a cNOR variant is a good indicator of NO decomposition capability of the variants and a marker for the screening of functionally important residues without protein purification. Using this in vivo screening system, we examined the residues lining the putative proton transfer pathways for NO reduction in cNOR, and found that the catalytic protons are likely transferred through the Glu57 located at the periplasmic protein surface. The homologous cNOR expression system developed here is an invaluable tool for facile identification of crucial residues in vivo, and for further in vitro functional and structural studies.
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Affiliation(s)
- Raika Yamagiwa
- Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan; RIKEN SPring-8 Center, Kouto, Sayo, Hyogo 679-5148, Japan
| | - Takuya Kurahashi
- Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan
| | - Mariko Takeda
- Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan
| | - Mayuho Adachi
- Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan
| | - Hiro Nakamura
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Hiroyuki Arai
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo 113-8657, Japan
| | - Yoshitsugu Shiro
- Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan; RIKEN SPring-8 Center, Kouto, Sayo, Hyogo 679-5148, Japan
| | - Hitomi Sawai
- Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan; RIKEN SPring-8 Center, Kouto, Sayo, Hyogo 679-5148, Japan.
| | - Takehiko Tosha
- RIKEN SPring-8 Center, Kouto, Sayo, Hyogo 679-5148, Japan.
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4
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Tosha T, Nomura T, Nishida T, Saeki N, Okubayashi K, Yamagiwa R, Sugahara M, Nakane T, Yamashita K, Hirata K, Ueno G, Kimura T, Hisano T, Muramoto K, Sawai H, Takeda H, Mizohata E, Yamashita A, Kanematsu Y, Takano Y, Nango E, Tanaka R, Nureki O, Shoji O, Ikemoto Y, Murakami H, Owada S, Tono K, Yabashi M, Yamamoto M, Ago H, Iwata S, Sugimoto H, Shiro Y, Kubo M. Capturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate. Nat Commun 2017; 8:1585. [PMID: 29147002 PMCID: PMC5691058 DOI: 10.1038/s41467-017-01702-1] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 10/07/2017] [Indexed: 12/21/2022] Open
Abstract
Time-resolved serial femtosecond crystallography using an X-ray free electron laser (XFEL) in conjunction with a photosensitive caged-compound offers a crystallographic method to track enzymatic reactions. Here we demonstrate the application of this method using fungal NO reductase, a heme-containing enzyme, at room temperature. Twenty milliseconds after caged-NO photolysis, we identify a NO-bound form of the enzyme, which is an initial intermediate with a slightly bent Fe-N-O coordination geometry at a resolution of 2.1 Å. The NO geometry is compatible with those analyzed by XFEL-based cryo-crystallography and QM/MM calculations, indicating that we obtain an intact Fe3+-NO coordination structure that is free of X-ray radiation damage. The slightly bent NO geometry is appropriate to prevent immediate NO dissociation and thus accept H- from NADH. The combination of using XFEL and a caged-compound is a powerful tool for determining functional enzyme structures during catalytic reactions at the atomic level.
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Affiliation(s)
- Takehiko Tosha
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan
| | - Takashi Nomura
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan
| | - Takuma Nishida
- Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamighori, Akoh, Hyogo, 678-1297, Japan
| | - Naoya Saeki
- Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamighori, Akoh, Hyogo, 678-1297, Japan
| | - Kouta Okubayashi
- Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamighori, Akoh, Hyogo, 678-1297, Japan
| | - Raika Yamagiwa
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan.,Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamighori, Akoh, Hyogo, 678-1297, Japan
| | | | - Takanori Nakane
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
| | | | - Kunio Hirata
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan.,Japan Science and Technology Agency, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | - Go Ueno
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan
| | - Tetsunari Kimura
- Department of Chemistry, Graduate School of Science, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe, 657-8501, Japan
| | - Tamao Hisano
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan
| | - Kazumasa Muramoto
- Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamighori, Akoh, Hyogo, 678-1297, Japan
| | - Hitomi Sawai
- Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamighori, Akoh, Hyogo, 678-1297, Japan
| | - Hanae Takeda
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan.,Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamighori, Akoh, Hyogo, 678-1297, Japan
| | - Eiichi Mizohata
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Ayumi Yamashita
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan
| | - Yusuke Kanematsu
- Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Asa-Minami-ku, Hiroshima, 731-3194, Japan
| | - Yu Takano
- Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Asa-Minami-ku, Hiroshima, 731-3194, Japan
| | - Eriko Nango
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan.,Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Rie Tanaka
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
| | - Osami Shoji
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan.,Japan Science and Technology Agency, CREST, 5 Sanbancho, Chiyoda-ku, Tokyo, 102-0075, Japan
| | - Yuka Ikemoto
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo, 679-5198, Japan
| | - Hironori Murakami
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo, 679-5198, Japan
| | - Shigeki Owada
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan
| | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo, 679-5198, Japan
| | - Makina Yabashi
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan
| | - Masaki Yamamoto
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan
| | - Hideo Ago
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan
| | - So Iwata
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan.,Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Hiroshi Sugimoto
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan. .,Japan Science and Technology Agency, CREST, 5 Sanbancho, Chiyoda-ku, Tokyo, 102-0075, Japan.
| | - Yoshitsugu Shiro
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan. .,Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamighori, Akoh, Hyogo, 678-1297, Japan.
| | - Minoru Kubo
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan. .,Japan Science and Technology Agency, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan.
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