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Young ID, Ibrahim M, Chatterjee R, Gul S, Fuller F, Koroidov S, Brewster AS, Tran R, Alonso-Mori R, Kroll T, Michels-Clark T, Laksmono H, Sierra RG, Stan CA, Hussein R, Zhang M, Douthit L, Kubin M, de Lichtenberg C, Long Vo P, Nilsson H, Cheah MH, Shevela D, Saracini C, Bean MA, Seuffert I, Sokaras D, Weng TC, Pastor E, Weninger C, Fransson T, Lassalle L, Bräuer P, Aller P, Docker PT, Andi B, Orville AM, Glownia JM, Nelson S, Sikorski M, Zhu D, Hunter MS, Lane TJ, Aquila A, Koglin JE, Robinson J, Liang M, Boutet S, Lyubimov AY, Uervirojnangkoorn M, Moriarty NW, Liebschner D, Afonine PV, Waterman DG, Evans G, Wernet P, Dobbek H, Weis WI, Brunger AT, Zwart PH, Adams PD, Zouni A, Messinger J, Bergmann U, Sauter NK, Kern J, Yachandra VK, Yano J. Structure of photosystem II and substrate binding at room temperature. Nature 2016; 540:453-457. [PMID: 27871088 DOI: 10.1038/nature20161] [Citation(s) in RCA: 257] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 10/14/2016] [Indexed: 12/16/2022]
Abstract
Light-induced oxidation of water by photosystem II (PS II) in plants, algae and cyanobacteria has generated most of the dioxygen in the atmosphere. PS II, a membrane-bound multi-subunit pigment protein complex, couples the one-electron photochemistry at the reaction centre with the four-electron redox chemistry of water oxidation at the Mn4CaO5 cluster in the oxygen-evolving complex (OEC). Under illumination, the OEC cycles through five intermediate S-states (S0 to S4), in which S1 is the dark-stable state and S3 is the last semi-stable state before O-O bond formation and O2 evolution. A detailed understanding of the O-O bond formation mechanism remains a challenge, and will require elucidation of both the structures of the OEC in the different S-states and the binding of the two substrate waters to the catalytic site. Here we report the use of femtosecond pulses from an X-ray free electron laser (XFEL) to obtain damage-free, room temperature structures of dark-adapted (S1), two-flash illuminated (2F; S3-enriched), and ammonia-bound two-flash illuminated (2F-NH3; S3-enriched) PS II. Although the recent 1.95 Å resolution structure of PS II at cryogenic temperature using an XFEL provided a damage-free view of the S1 state, measurements at room temperature are required to study the structural landscape of proteins under functional conditions, and also for in situ advancement of the S-states. To investigate the water-binding site(s), ammonia, a water analogue, has been used as a marker, as it binds to the Mn4CaO5 cluster in the S2 and S3 states. Since the ammonia-bound OEC is active, the ammonia-binding Mn site is not a substrate water site. This approach, together with a comparison of the native dark and 2F states, is used to discriminate between proposed O-O bond formation mechanisms.
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Affiliation(s)
- Iris D Young
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Mohamed Ibrahim
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany
| | - Ruchira Chatterjee
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Sheraz Gul
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Franklin Fuller
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Sergey Koroidov
- Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, SE 90187 Umeå, Sweden
| | - Aaron S Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Rosalie Tran
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | - Thomas Kroll
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.,SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Tara Michels-Clark
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Hartawan Laksmono
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Raymond G Sierra
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.,Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Claudiu A Stan
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Rana Hussein
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany
| | - Miao Zhang
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany
| | - Lacey Douthit
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Markus Kubin
- Institute for Methods and Instrumentation on Synchrotron Radiation Research, Helmholtz Zentrum, 14109 Berlin, Germany
| | - Casper de Lichtenberg
- Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, SE 90187 Umeå, Sweden
| | - Pham Long Vo
- Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, SE 90187 Umeå, Sweden
| | - Håkan Nilsson
- Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, SE 90187 Umeå, Sweden
| | - Mun Hon Cheah
- Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, SE 90187 Umeå, Sweden
| | - Dmitriy Shevela
- Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, SE 90187 Umeå, Sweden
| | - Claudio Saracini
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Mackenzie A Bean
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ina Seuffert
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany
| | | | - Tsu-Chien Weng
- SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Ernest Pastor
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Clemens Weninger
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Thomas Fransson
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Louise Lassalle
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Philipp Bräuer
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.,Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Pierre Aller
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Peter T Docker
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Babak Andi
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Allen M Orville
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - James M Glownia
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Silke Nelson
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Marcin Sikorski
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Diling Zhu
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Mark S Hunter
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Thomas J Lane
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Andy Aquila
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Jason E Koglin
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Joseph Robinson
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Mengning Liang
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Sébastien Boutet
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Artem Y Lyubimov
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
| | | | - Nigel W Moriarty
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Dorothee Liebschner
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Pavel V Afonine
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - David G Waterman
- STFC Rutherford Appleton Laboratory, Didcot, OX11 0QX, UK and CCP4, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
| | - Gwyndaf Evans
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Philippe Wernet
- Institute for Methods and Instrumentation on Synchrotron Radiation Research, Helmholtz Zentrum, 14109 Berlin, Germany
| | - Holger Dobbek
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany
| | - William I Weis
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA.,Department of Photon Science, Stanford University, Stanford, CA 94305.,Department of Structural Biology, Stanford University, Stanford, CA 94305
| | - Axel T Brunger
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA.,Department of Photon Science, Stanford University, Stanford, CA 94305
| | - Petrus H Zwart
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Paul D Adams
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,Department of Bioengineering, University of California Berkeley, Berkeley, CA 94720
| | - Athina Zouni
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany
| | - Johannes Messinger
- Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, SE 90187 Umeå, Sweden.,Department of Chemistry, Molecular Biomimetics, Ångström Laboratory, Uppsala University, SE 75237 Uppsala, Sweden
| | - Uwe Bergmann
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Nicholas K Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Vittal K Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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