Cyanobacterial photosystem II at 2.9-Å resolution and the role of quinones, lipids, channels and chloride

Photosystem II (PSII) catalyzes the first light-dependent step in photosynthesis. An improved structural model of a cyanobacterial PSII provides complete assignment of all subunits in the complex and reveals possible channels used for the transport of protons, oxygen and water to the thylakoid lumen. Photosystem II (PSII) is a large homodimeric protein–cofactor complex located in the photosynthetic thylakoid membrane that acts as light-driven water:plastoquinone oxidoreductase. The crystal structure of PSII from Thermosynechococcus elongatus at 2.9-Å resolution allowed the unambiguous assignment of all 20 protein subunits and complete modeling of all 35 chlorophyll a molecules and 12 carotenoid molecules, 25 integral lipids and 1 chloride ion per monomer. The presence of a third plastoquinone Q C and a second plastoquinone-transfer channel, which were not observed before, suggests mechanisms for plastoquinol-plastoquinone exchange, and we calculated other possible water or dioxygen and proton channels. Putative oxygen positions obtained from a Xenon derivative indicate a role for lipids in oxygen diffusion to the cytoplasmic side of PSII. The chloride position suggests a role in proton-transfer reactions because it is bound through a putative water molecule to the Mn 4 Ca cluster at a distance of 6.5 Å and is close to two possible proton channels.