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Title: The room temperature crystal structure of a bacterial phytochrome determined by serial femtosecond crystallography

Abstract

Phytochromes are a family of photoreceptors that control light responses of plants, fungi and bacteria. A sequence of structural changes, which is not yet fully understood, leads to activation of an output domain. Time-resolved serial femtosecond crystallography (SFX) can potentially shine light on these conformational changes. Here we report the room temperature crystal structure of the chromophore-binding domains of the Deinococcus radiodurans phytochrome at 2.1 Å resolution. The structure was obtained by serial femtosecond X-ray crystallography from microcrystals at an X-ray free electron laser. We find overall good agreement compared to a crystal structure at 1.35 Å resolution derived from conventional crystallography at cryogenic temperatures, which we also report here. The thioether linkage between chromophore and protein is subject to positional ambiguity at the synchrotron, but is fully resolved with SFX. As a result, the study paves the way for time-resolved structural investigations of the phytochrome photocycle with time-resolved SFX.

Authors:
 [1];  [2];  [1];  [1];  [1];  [3];  [1];  [4];  [4];  [5];  [1];  [1];  [1];  [3];  [6];  [6];  [7];  [8];  [8];  [8] more »;  [8];  [4];  [6];  [9];  [10];  [6];  [9];  [9];  [9];  [10];  [11];  [3];  [3];  [12];  [8];  [1] « less
  1. Univ. of Gothenburg, Gothenburg (Sweden)
  2. Univ. of Gothenburg, Gothenburg (Sweden); Univ. of Jyvaskyla, Jyvaskyla (Finland); Univ. of Helsinki, Helsinki (Finland)
  3. Univ. of Jyvaskyla, Jyvaskyla (Finland)
  4. Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany)
  5. The Univ. of Tokyo, Tokyo (Japan)
  6. Arizona State Univ., Tempe, AZ (United States)
  7. LaTrobe Univ., Melbourne, VIC (Australia)
  8. Univ. of Wisconsin, Milwaukee, WI (United States)
  9. SLAC National Accelerator Lab., Menlo Park, CA (United States)
  10. RIKEN SPring-8 Center, Hyogo (Japan)
  11. Univ. of Chicago, Chicago, IL (United States); Argonne National Lab. (ANL), Argonne, IL (United States)
  12. Northern Illinois Univ., Chicago, IL (United States)
Publication Date:
Research Org.:
SLAC National Accelerator Lab., Menlo Park, CA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1348400
Grant/Contract Number:  
AC02-76SF00515
Resource Type:
Accepted Manuscript
Journal Name:
Scientific Reports
Additional Journal Information:
Journal Volume: 6; Journal Issue: 1; Journal ID: ISSN 2045-2322
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; chemical biology; proteins

Citation Formats

Edlund, Petra, Takala, Heikki, Claesson, Elin, Henry, Léocadie, Dods, Robert, Lehtivuori, Heli, Panman, Matthijs, Pande, Kanupriya, White, Thomas, Nakane, Takanori, Berntsson, Oskar, Gustavsson, Emil, Båth, Petra, Modi, Vaibhav, Roy-Chowdhury, Shatabdi, Zook, James, Berntsen, Peter, Pandey, Suraj, Poudyal, Ishwor, Tenboer, Jason, Kupitz, Christopher, Barty, Anton, Fromme, Petra, Koralek, Jake D., Tanaka, Tomoyuki, Spence, John, Liang, Mengning, Hunter, Mark S., Boutet, Sebastien, Nango, Eriko, Moffat, Keith, Groenhof, Gerrit, Ihalainen, Janne, Stojković, Emina A., Schmidt, Marius, and Westenhoff, Sebastian. The room temperature crystal structure of a bacterial phytochrome determined by serial femtosecond crystallography. United States: N. p., 2016. Web. doi:10.1038/srep35279.
Edlund, Petra, Takala, Heikki, Claesson, Elin, Henry, Léocadie, Dods, Robert, Lehtivuori, Heli, Panman, Matthijs, Pande, Kanupriya, White, Thomas, Nakane, Takanori, Berntsson, Oskar, Gustavsson, Emil, Båth, Petra, Modi, Vaibhav, Roy-Chowdhury, Shatabdi, Zook, James, Berntsen, Peter, Pandey, Suraj, Poudyal, Ishwor, Tenboer, Jason, Kupitz, Christopher, Barty, Anton, Fromme, Petra, Koralek, Jake D., Tanaka, Tomoyuki, Spence, John, Liang, Mengning, Hunter, Mark S., Boutet, Sebastien, Nango, Eriko, Moffat, Keith, Groenhof, Gerrit, Ihalainen, Janne, Stojković, Emina A., Schmidt, Marius, & Westenhoff, Sebastian. The room temperature crystal structure of a bacterial phytochrome determined by serial femtosecond crystallography. United States. doi:10.1038/srep35279.
Edlund, Petra, Takala, Heikki, Claesson, Elin, Henry, Léocadie, Dods, Robert, Lehtivuori, Heli, Panman, Matthijs, Pande, Kanupriya, White, Thomas, Nakane, Takanori, Berntsson, Oskar, Gustavsson, Emil, Båth, Petra, Modi, Vaibhav, Roy-Chowdhury, Shatabdi, Zook, James, Berntsen, Peter, Pandey, Suraj, Poudyal, Ishwor, Tenboer, Jason, Kupitz, Christopher, Barty, Anton, Fromme, Petra, Koralek, Jake D., Tanaka, Tomoyuki, Spence, John, Liang, Mengning, Hunter, Mark S., Boutet, Sebastien, Nango, Eriko, Moffat, Keith, Groenhof, Gerrit, Ihalainen, Janne, Stojković, Emina A., Schmidt, Marius, and Westenhoff, Sebastian. Wed . "The room temperature crystal structure of a bacterial phytochrome determined by serial femtosecond crystallography". United States. doi:10.1038/srep35279. https://www.osti.gov/servlets/purl/1348400.
@article{osti_1348400,
title = {The room temperature crystal structure of a bacterial phytochrome determined by serial femtosecond crystallography},
author = {Edlund, Petra and Takala, Heikki and Claesson, Elin and Henry, Léocadie and Dods, Robert and Lehtivuori, Heli and Panman, Matthijs and Pande, Kanupriya and White, Thomas and Nakane, Takanori and Berntsson, Oskar and Gustavsson, Emil and Båth, Petra and Modi, Vaibhav and Roy-Chowdhury, Shatabdi and Zook, James and Berntsen, Peter and Pandey, Suraj and Poudyal, Ishwor and Tenboer, Jason and Kupitz, Christopher and Barty, Anton and Fromme, Petra and Koralek, Jake D. and Tanaka, Tomoyuki and Spence, John and Liang, Mengning and Hunter, Mark S. and Boutet, Sebastien and Nango, Eriko and Moffat, Keith and Groenhof, Gerrit and Ihalainen, Janne and Stojković, Emina A. and Schmidt, Marius and Westenhoff, Sebastian},
abstractNote = {Phytochromes are a family of photoreceptors that control light responses of plants, fungi and bacteria. A sequence of structural changes, which is not yet fully understood, leads to activation of an output domain. Time-resolved serial femtosecond crystallography (SFX) can potentially shine light on these conformational changes. Here we report the room temperature crystal structure of the chromophore-binding domains of the Deinococcus radiodurans phytochrome at 2.1 Å resolution. The structure was obtained by serial femtosecond X-ray crystallography from microcrystals at an X-ray free electron laser. We find overall good agreement compared to a crystal structure at 1.35 Å resolution derived from conventional crystallography at cryogenic temperatures, which we also report here. The thioether linkage between chromophore and protein is subject to positional ambiguity at the synchrotron, but is fully resolved with SFX. As a result, the study paves the way for time-resolved structural investigations of the phytochrome photocycle with time-resolved SFX.},
doi = {10.1038/srep35279},
journal = {Scientific Reports},
number = 1,
volume = 6,
place = {United States},
year = {2016},
month = {10}
}

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