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Title: Crystal structure of CO-bound cytochrome c oxidase determined by serial femtosecond X-ray crystallography at room temperature

Here, cytochrome c oxidase (C cO), the terminal enzyme in the electron transfer chain, translocates protons across the inner mitochondrial membrane by harnessing the free energy generated by the reduction of oxygen to water. Several redox-coupled proton translocation mechanisms have been proposed, but they lack confirmation, in part from the absence of reliable structural information due to radiation damage artifacts caused by the intense synchrotron radiation. Here we report the room temperature, neutral pH (6.8), damage-free structure of bovine C cO (bC cO) in the carbon monoxide (CO)-bound state at a resolution of 2.3 Å, obtained by serial femtosecond X-ray crystallography (SFX) with an X-ray free electron laser. As a comparison, an equivalent structure was obtained at a resolution of 1.95 Å, from data collected at a synchrotron light source. In the SFX structure, the CO is coordinated to the heme a3 iron atom, with a bent Fe–C–O angle of ~142°. In contrast, in the synchrotron structure, the Fe–CO bond is cleaved; CO relocates to a new site near Cu B, which, in turn, moves closer to the heme a 3 iron by ~0.38 Å. Structural comparison reveals that ligand binding to the heme a 3 iron in the SFXmore » structure is associated with an allosteric structural transition, involving partial unwinding of the helix-X between heme a and a 3, thereby establishing a communication linkage between the two heme groups, setting the stage for proton translocation during the ensuing redox chemistry.« less
Authors:
 [1] ;  [2] ;  [3] ;  [4] ;  [2] ;  [2] ;  [2] ;  [5] ;  [6] ;  [6] ;  [6] ;  [2] ;  [2] ;  [1] ;  [1]
  1. Albert Einstein College of Medicine, Bronx, NY (United States)
  2. Arizona State Univ., Tempe, AZ (United States)
  3. Albert Einstein College of Medicine, Bronx, NY (United States); Institute of Materials Structure Science, Ibaraki (Japan)
  4. Arizona State Univ., Tempe, AZ (United States); National Cancer Institute, Frederick, MD (United States)
  5. State Univ. of New York at Buffalo, Buffalo, NY (United States)
  6. SLAC National Accelerator Lab., Menlo Park, CA (United States)
Publication Date:
Grant/Contract Number:
AC02-76SF00515; GM098799; GM115773; GM095583; CHE-1404929; ABI-1565180; STC-1231306
Type:
Accepted Manuscript
Journal Name:
Proceedings of the National Academy of Sciences of the United States of America
Additional Journal Information:
Journal Volume: 114; Journal Issue: 30; Journal ID: ISSN 0027-8424
Publisher:
National Academy of Sciences, Washington, DC (United States)
Research Org:
SLAC National Accelerator Lab., Menlo Park, CA (United States)
Sponsoring Org:
USDOE
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; bioenergetics; X-ray free electron laser; crystallography; cytochrome c oxidase; serial femtosecond crystallography
OSTI Identifier:
1390295

Ishigami, Izumi, Zatsepin, Nadia A., Hikita, Masahide, Conrad, Chelsie E., Nelson, Garrett, Coe, Jesse D., Basu, Shibom, Grant, Thomas D., Seaberg, Matthew H., Sierra, Raymond G., Hunter, Mark S., Fromme, Petra, Fromme, Raimund, Yeh, Syun -Ru, and Rousseau, Denis L.. Crystal structure of CO-bound cytochrome c oxidase determined by serial femtosecond X-ray crystallography at room temperature. United States: N. p., Web. doi:10.1073/pnas.1705628114.
Ishigami, Izumi, Zatsepin, Nadia A., Hikita, Masahide, Conrad, Chelsie E., Nelson, Garrett, Coe, Jesse D., Basu, Shibom, Grant, Thomas D., Seaberg, Matthew H., Sierra, Raymond G., Hunter, Mark S., Fromme, Petra, Fromme, Raimund, Yeh, Syun -Ru, & Rousseau, Denis L.. Crystal structure of CO-bound cytochrome c oxidase determined by serial femtosecond X-ray crystallography at room temperature. United States. doi:10.1073/pnas.1705628114.
Ishigami, Izumi, Zatsepin, Nadia A., Hikita, Masahide, Conrad, Chelsie E., Nelson, Garrett, Coe, Jesse D., Basu, Shibom, Grant, Thomas D., Seaberg, Matthew H., Sierra, Raymond G., Hunter, Mark S., Fromme, Petra, Fromme, Raimund, Yeh, Syun -Ru, and Rousseau, Denis L.. 2017. "Crystal structure of CO-bound cytochrome c oxidase determined by serial femtosecond X-ray crystallography at room temperature". United States. doi:10.1073/pnas.1705628114. https://www.osti.gov/servlets/purl/1390295.
@article{osti_1390295,
title = {Crystal structure of CO-bound cytochrome c oxidase determined by serial femtosecond X-ray crystallography at room temperature},
author = {Ishigami, Izumi and Zatsepin, Nadia A. and Hikita, Masahide and Conrad, Chelsie E. and Nelson, Garrett and Coe, Jesse D. and Basu, Shibom and Grant, Thomas D. and Seaberg, Matthew H. and Sierra, Raymond G. and Hunter, Mark S. and Fromme, Petra and Fromme, Raimund and Yeh, Syun -Ru and Rousseau, Denis L.},
abstractNote = {Here, cytochrome c oxidase (CcO), the terminal enzyme in the electron transfer chain, translocates protons across the inner mitochondrial membrane by harnessing the free energy generated by the reduction of oxygen to water. Several redox-coupled proton translocation mechanisms have been proposed, but they lack confirmation, in part from the absence of reliable structural information due to radiation damage artifacts caused by the intense synchrotron radiation. Here we report the room temperature, neutral pH (6.8), damage-free structure of bovine CcO (bCcO) in the carbon monoxide (CO)-bound state at a resolution of 2.3 Å, obtained by serial femtosecond X-ray crystallography (SFX) with an X-ray free electron laser. As a comparison, an equivalent structure was obtained at a resolution of 1.95 Å, from data collected at a synchrotron light source. In the SFX structure, the CO is coordinated to the heme a3 iron atom, with a bent Fe–C–O angle of ~142°. In contrast, in the synchrotron structure, the Fe–CO bond is cleaved; CO relocates to a new site near CuB, which, in turn, moves closer to the heme a3 iron by ~0.38 Å. Structural comparison reveals that ligand binding to the heme a3 iron in the SFX structure is associated with an allosteric structural transition, involving partial unwinding of the helix-X between heme a and a3, thereby establishing a communication linkage between the two heme groups, setting the stage for proton translocation during the ensuing redox chemistry.},
doi = {10.1073/pnas.1705628114},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
number = 30,
volume = 114,
place = {United States},
year = {2017},
month = {7}
}

Works referenced in this record:

Femtosecond X-ray protein nanocrystallography
journal, February 2011
  • Chapman, Henry N.; Fromme, Petra; Barty, Anton
  • Nature, Vol. 470, Issue 7332, p. 73-77
  • DOI: 10.1038/nature09750