In the photosynthetic bacterial reaction centre (RC), light-induced electron transfer is coupled to the uptake of protons from the cytoplasm at the binding site of the secondary quinone (Q(B)). Recent crystal structures of RCs from Rhodopseudomonas (Rp.) viridis modified at the Q(B) site (Lancaster and Michel, Structure 5 (1997) 1339-1359) can provide models for intermediates in the reaction cycle of ubiquinone reduction to ubiquinol. The structures of these intermediates provide explanations for their relative binding affinities as required for proper enzymatic function of the Q(B) site. The structure of the RC complex with ubiquinone-2 refined at 2.45 Å resolution (Protein Data Bank (PDB) entry code 2PRC), constitutes the first crystallographically reliably defined binding site for quinones from the bioenergetically important quinone pool of biological, energy-transducing membranes. In the RC structure with a Q(B)-depleted Q(B) site (PDB entry code 3PRC), refined at 2.4 Å resolution, apparently five, possibly six, water molecules are bound instead of the ubiquinone head group, and a detergent molecule binds in the region of the isoprenoid tail. Using the structures 2PRC and 3PRC as a reference, the original data set (1PRC, Deisenhofer et al., J. Mol. Biol. 246 (1995) 429-457) was re-examined, resulting in the suggestion of a modified dominant Q(B)-binding position for the native ubiquinone-9, which differs from that determined for ubiquinone-2. The RC- complex with the inhibitor stigmatellin (PDB entry 4PRC), refined at 2.4 Å resolution, indicates that additional hydrogen bonds stabilise the binding of stigmatellin over that of ubiquinone-2. The binding pattern observed for the stigmatellin complex can be viewed as a model for the stabilisation of a monoprotonated reduced intermediate (Q(B)H or Q(B)H-). This indicates that the Q(B) site is not optimised for Q(B) binding, but for Q(B) reduction to the quinol.
Lancaster, C. R. D. (1998). Ubiquinone reduction and protonation in photosynthetic reaction centres from Rhodopseudomonas viridis: X-ray structures and their functional implications. In Biochimica et Biophysica Acta - Bioenergetics (Vol. 1365, pp. 143–150). https://doi.org/10.1016/S0005-2728(98)00054-1