skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: An improved crystal structure of C-phycoerythrin from the marine cyanobacterium Phormidium sp. A09DM

Abstract

C-Phycoerythrin (PE) from Phormidium sp. A09DM has been crystallized using different conditions and its structure determined to atomic resolution (1.14 Å). In order for the pigment present, phycoerythrobilin (PEB), to function as an efficient light-harvesting molecule it must be held rigidly (Kupka and Scheer in Biochim Biophys Acta 1777:94–103, 2008) and, moreover, the different PEB molecules in PE must be arranged, relative to each other, so as to promote efficient energy transfer between them. This improved structure has allowed us to define in great detail the structure of the PEBs and their binding sites. These precise structural details will facilitate theoretical calculations of each PEB’s spectroscopic properties. It was possible, however, to suggest a model for which chromophores contribute to the different regions of absorption spectrum and propose a tentative scheme for energy transfer. We show that some subtle differences in one of these PEB binding sites in two of the 12 subunits are caused by crystal contacts between neighboring hexamers in the crystal lattice. This explains some of the differences seen in previous lower resolution structures determined at two different pH values (Kumar et al. in Photosyn Res 129:17–28, 2016).

Authors:
 [1];  [2];  [2];  [1];  [2]
  1. Sardar Patel University, Anand (India)
  2. Univ. of Glasgow, Scotland (United Kingdom)
Publication Date:
Research Org.:
Energy Frontier Research Centers (EFRC) (United States). Photosynthetic Antenna Research Center (PARC)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)
OSTI Identifier:
1469862
Grant/Contract Number:  
SC0001035
Resource Type:
Accepted Manuscript
Journal Name:
Photosynthesis Research
Additional Journal Information:
Journal Volume: 135; Journal Issue: 1-3; Related Information: PARC partners with Washington University in St. Louis (lead); University of California, Riverside; University of Glasgow, UK; Los Alamos National Laboratory; University of New Mexico; New Mexico Corsortium; North Carolina State University; Northwestern University; Oak Ridge National Laboratory; University of Pennsylvania; Sandia National Laboratories; University of Sheffield, UK; Journal ID: ISSN 0166-8595
Publisher:
Springer
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Photosynthesis; Cyanobacteria; Phycobilisomes; Phycoerythrin; PEB chromophores; Atomic resolution crystal structure

Citation Formats

Sonani, Ravi R., Roszak, Aleksander W., Ortmann de Percin Northumberland, Claire, Madamwar, Datta, and Cogdell, Richard J. An improved crystal structure of C-phycoerythrin from the marine cyanobacterium Phormidium sp. A09DM. United States: N. p., 2017. Web. doi:10.1007/s11120-017-0443-2.
Sonani, Ravi R., Roszak, Aleksander W., Ortmann de Percin Northumberland, Claire, Madamwar, Datta, & Cogdell, Richard J. An improved crystal structure of C-phycoerythrin from the marine cyanobacterium Phormidium sp. A09DM. United States. doi:10.1007/s11120-017-0443-2.
Sonani, Ravi R., Roszak, Aleksander W., Ortmann de Percin Northumberland, Claire, Madamwar, Datta, and Cogdell, Richard J. Sat . "An improved crystal structure of C-phycoerythrin from the marine cyanobacterium Phormidium sp. A09DM". United States. doi:10.1007/s11120-017-0443-2. https://www.osti.gov/servlets/purl/1469862.
@article{osti_1469862,
title = {An improved crystal structure of C-phycoerythrin from the marine cyanobacterium Phormidium sp. A09DM},
author = {Sonani, Ravi R. and Roszak, Aleksander W. and Ortmann de Percin Northumberland, Claire and Madamwar, Datta and Cogdell, Richard J.},
abstractNote = {C-Phycoerythrin (PE) from Phormidium sp. A09DM has been crystallized using different conditions and its structure determined to atomic resolution (1.14 Å). In order for the pigment present, phycoerythrobilin (PEB), to function as an efficient light-harvesting molecule it must be held rigidly (Kupka and Scheer in Biochim Biophys Acta 1777:94–103, 2008) and, moreover, the different PEB molecules in PE must be arranged, relative to each other, so as to promote efficient energy transfer between them. This improved structure has allowed us to define in great detail the structure of the PEBs and their binding sites. These precise structural details will facilitate theoretical calculations of each PEB’s spectroscopic properties. It was possible, however, to suggest a model for which chromophores contribute to the different regions of absorption spectrum and propose a tentative scheme for energy transfer. We show that some subtle differences in one of these PEB binding sites in two of the 12 subunits are caused by crystal contacts between neighboring hexamers in the crystal lattice. This explains some of the differences seen in previous lower resolution structures determined at two different pH values (Kumar et al. in Photosyn Res 129:17–28, 2016).},
doi = {10.1007/s11120-017-0443-2},
journal = {Photosynthesis Research},
number = 1-3,
volume = 135,
place = {United States},
year = {2017},
month = {9}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Save / Share:

Works referenced in this record:

Linking Crystallographic Model and Data Quality
journal, May 2012


Crystal structure analysis of C-phycoerythrin from marine cyanobacterium Phormidium sp. A09DM
journal, April 2016


How good are my data and what is the resolution?
journal, June 2013

  • Evans, Philip R.; Murshudov, Garib N.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 69, Issue 7
  • DOI: 10.1107/S0907444913000061

Presenting your structures: the CCP 4 mg molecular-graphics software
journal, March 2011

  • McNicholas, S.; Potterton, E.; Wilson, K. S.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4
  • DOI: 10.1107/S0907444911007281

Photosynthetic Light-Harvesting Is Tuned by the Heterogeneous Polarizable Environment of the Protein
journal, March 2011

  • Curutchet, Carles; Kongsted, Jacob; Muñoz-Losa, Aurora
  • Journal of the American Chemical Society, Vol. 133, Issue 9
  • DOI: 10.1021/ja110053y

Overview of the CCP 4 suite and current developments
journal, March 2011

  • Winn, Martyn D.; Ballard, Charles C.; Cowtan, Kevin D.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4
  • DOI: 10.1107/S0907444910045749

xia2 : an expert system for macromolecular crystallography data reduction
journal, December 2009


Data processing and analysis with the autoPROC toolbox
journal, March 2011

  • Vonrhein, Clemens; Flensburg, Claus; Keller, Peter
  • Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4
  • DOI: 10.1107/S0907444911007773

pH-dependent structural conformations of B-phycoerythrin from Porphyridium cruentum
journal, September 2012


Developing a Structure–Function Model for the Cryptophyte Phycoerythrin 545 Using Ultrahigh Resolution Crystallography and Ultrafast Laser Spectroscopy
journal, November 2004

  • Doust, Alexander B.; Marai, Christopher N. J.; Harrop, Stephen J.
  • Journal of Molecular Biology, Vol. 344, Issue 1
  • DOI: 10.1016/j.jmb.2004.09.044

Phormidium phycoerythrin forms hexamers in crystals: a crystallographic study
journal, July 2015

  • Sonani, Ravi Raghav; Sharma, Mahima; Gupta, Gagan Deep
  • Acta Crystallographica Section F Structural Biology Communications, Vol. 71, Issue 8
  • DOI: 10.1107/S2053230X15010134

Remarks about protein structure precision
journal, March 1999

  • Cruickshank, D. W. J.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 55, Issue 3
  • DOI: 10.1107/S0907444998012645

Features and development of Coot
journal, March 2010

  • Emsley, P.; Lohkamp, B.; Scott, W. G.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4
  • DOI: 10.1107/S0907444910007493

A Multistate Model for the Fluorescence Response of R-Phycoerythrin
journal, January 2006


XDS
journal, January 2010

  • Kabsch, Wolfgang
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2
  • DOI: 10.1107/S0907444909047337

LigPlot+: Multiple Ligand–Protein Interaction Diagrams for Drug Discovery
journal, October 2011

  • Laskowski, Roman A.; Swindells, Mark B.
  • Journal of Chemical Information and Modeling, Vol. 51, Issue 10
  • DOI: 10.1021/ci200227u

Energy Flow in the Cryptophyte PE545 Antenna Is Directed by Bilin Pigment Conformation
journal, October 2012

  • Curutchet, Carles; Novoderezhkin, Vladimir I.; Kongsted, Jacob
  • The Journal of Physical Chemistry B, Vol. 117, Issue 16
  • DOI: 10.1021/jp305033d

REFMAC 5 for the refinement of macromolecular crystal structures
journal, March 2011

  • Murshudov, Garib N.; Skubák, Pavol; Lebedev, Andrey A.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4
  • DOI: 10.1107/S0907444911001314

Unfolding of C-phycocyanin followed by loss of non-covalent chromophore–protein interactions
journal, January 2008


Quantum Chemical Studies of Light Harvesting
journal, March 2016


Structure validation by Cα geometry: ϕ,ψ and Cβ deviation
journal, January 2003

  • Lovell, Simon C.; Davis, Ian W.; Arendall, W. Bryan
  • Proteins: Structure, Function, and Bioinformatics, Vol. 50, Issue 3
  • DOI: 10.1002/prot.10286

Picosecond excitation energy transfer of allophycocyanin studied in solution and in crystals
journal, July 2017

  • Ranjbar Choubeh, Reza; Sonani, Ravi R.; Madamwar, Datta
  • Photosynthesis Research, Vol. 135, Issue 1-3
  • DOI: 10.1007/s11120-017-0417-4

Impact of Electronic Fluctuations and Their Description on the Exciton Dynamics in the Light-Harvesting Complex PE545
journal, February 2017

  • Aghtar, Mortaza; Kleinekathöfer, Ulrich; Curutchet, Carles
  • The Journal of Physical Chemistry B, Vol. 121, Issue 6
  • DOI: 10.1021/acs.jpcb.6b10772

An introduction to data reduction: space-group determination, scaling and intensity statistics
journal, March 2011

  • Evans, Philip R.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4
  • DOI: 10.1107/S090744491003982X