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We report on the unexpected structural changes caused by substitution of acidic amino acids in the Q_B binding pocket of the bacterial photosynthetic reaction center by alanines. The mutations targeted key residues L212Glu and L213Asp of this transmembrane protein−cofactor complex. The amino acid substitutions in the L212Ala-L213Ala mutant reaction center (“AA”) were known to affect the delivery of protons after the light-induced generation of Q_B^-, which renders the AA strain incapable of photosynthetic growth. The AA structure not only revealed side chain rearrangements but also showed movement of the main chain segments that are contiguous with the mutation sites. The alanine substitutions caused an expansion of the cavity rather than its collapse. In addition, Q_B is found mainly in the binding site that is proximal to the iron−ligand complex (closest to Q_A) as opposed to its distal binding site (furthest from …