Oxygen, Water, Proton and Quinone Channels in PSII

  • James Murray
  • James Barber


Using the crystal structure of Photosystem II (PSII) we have investigated the presence of channels for the entry of substrates, and exits of products, from catalytic sites within the complex. We identify three channels from the oxygen evolving centre, which we associate with possible water entry and the exit of proton and dioxygen. At the acceptor side, we examine the cavity adjacent to the QB site, and discuss its possible role as channel for plastoquinone/plastoquinol diffusion in and out of PSII.


photosystem II crystal structure substrate channels oxygen pathways structural bioinformatics 


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  1. Anderson JM (2001) Does functional photosystem II complex have an oxygen channel? FEBS Lett 488:1–4.PubMedCrossRefGoogle Scholar
  2. Barber J, Morris EP, da Fonseca PC (2003) Interaction of the allophycocyanin core complex with photosystem II. Photochem Photobiol Sci 2:536–541.PubMedCrossRefGoogle Scholar
  3. Delano WL (2002) The PyMol Molecular Graphics System. Delano Scientific, San Carlos, CA. Available from
  4. Ferreira KN, Iverson TM, Maghlaoui K, Barber J, Iwata S (2004) Architecture of the photosynthetic oxygen evolving center. Science 303:1831–1838.PubMedCrossRefGoogle Scholar
  5. Ishikita H, Saenger W, Loll B, Biesiadka J, Knapp E‐W (2006) Energetics of a possible proton exit pathway for water oxidation in photosystem II. Biochemistry 45:2063–2071.PubMedCrossRefGoogle Scholar
  6. Krivanek R, Kern J, Zouni A, Dau H, Haumann M (2007) Spare quinones in the QB cavity of crystallized photosystem II from Thermosynechococcus elongatus. Biochim Biophys Acta 1767:520–527.PubMedCrossRefGoogle Scholar
  7. Loll B, Kern J, Saenger W, Zouni A, Biesiadka J (2005) Towards complete cofactor arrangement in the 3.0 Å resolution structure of photosystem II. Nature 438:1040–1044.PubMedCrossRefGoogle Scholar
  8. Murray JW, Barber J (2006) Identification of a calciumbinding site in the PsbO protein of photosystem II. Biochemistry 45:4128–4130.PubMedCrossRefGoogle Scholar
  9. Murray JW, Barber J (2007) Structural characteristics of channels and pathways in photosystem II including the identification of an oxygen channel. J Struct Biol 159:228–37. doi:10.1016/j.jsb.2007.01.01.PubMedCrossRefGoogle Scholar
  10. Petřek M, Otyepka M, Banas P, Košinová P, Koca P, Damborský J (2006) CAVER: A new tool to explore routes from protein clefts, pockets and cavities. BMC Bioinformatics 7:316–324.PubMedCrossRefGoogle Scholar
  11. Svensson‐Ek M, Abramson J, Larsson G, Trnroth S, Brzezinksi P, Iwata S (2002) The X‐ray crystal structures of wild‐type and EQ(I‐286) mutant cytochrome c oxidases from Rhodobacter sphaeroides. J Mol Biol 321:329–339.PubMedCrossRefGoogle Scholar
  12. Word JM, Lovell SC, Richardson JS, Richardson DC (1999) Asparagine and glutamine: Using hydrogen atom contacts in the choice of side‐chain amide orientation. J Mol Biol 285:1735–1747.PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science + Business Media, B.V. 2008

Authors and Affiliations

  • James Murray
    • 1
  • James Barber
    • 1
  1. 1.Wolfson Laboratories, Division of Molecular Biosciences, Faculty of Natural SciencesImperial College LondonLondonUK

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