Cyanobacterial Photosystem II at 3.2 Å resolution – the plastoquinone binding pockets


Photosystem II from thylakoid membranes of the thermophilic cyanobacterium Thermosynechococcus elongatus was solubilized with n-β-dodecylmaltoside and purified using anion exchange chromatography. Molecular weight, pigment stoichiometry and subunit composition were assayed using various techniques. The holocomplex is dimeric with a molecular mass of 756 ± 18 kDa and functionally fully active. Crystals obtained from these samples showed significantly improved quality leading to a 3D structure at 3.2 Å resolution. Several loop regions of the principal protein subunits are now defined that were not interpretable at lower (3.8 Å) resolution, thus resulting in a more complete model. The head groups of the cofactors of the electron transfer chain and of the antennae have been modeled, coordinating and hydrogen bonding amino acids identified and the nature of the binding pockets derived. The orientations of these cofactors resemble those of the reaction centre from anoxygenic purple bacteria. For the two plastoquinones, electron density was only found for the head group of Q A and none for Q B indicating low or even no occupancy of this site in the crystal structure. Both binding pockets and problems related to the Q B site are discussed here and compared to the situation in the purple bacterial reaction centre.

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atom absorption spectroscopy





Chl a:

Chlorophyll a




dynamic light scattering


gel permeation chromatography


matrix assisted laser desorption ionisation time of flight mass spetrometry


purple bacterial reaction centre


Pheophytin a


plastoquinone 9



Q A :

primary quinone

Q B :

secondary quinone


reverse phase chromatography


thin layer chromatography




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Correspondence to Klaus-Dieter Irrgang or Jacek Biesiadka.

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Kern, J., Loll, B., Zouni, A. et al. Cyanobacterial Photosystem II at 3.2 Å resolution – the plastoquinone binding pockets. Photosynth Res 84, 153–159 (2005).

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  • crystal structure
  • Photosystem II
  • plastoquinone 9
  • quinone binding sites
  • Thermosynechococcus elongatus