Ubiquinone binding, ubiquinone exclusion, and detailed cofactor conformation in a mutant bacterial reaction center

The X-ray crystal structure of a Rhodobacter sphaeroides reaction center wi th the mutation Ala M260 to Trp (AM260W) has been determined. Diffraction d ata were collected that were 97.6% complete between 30.0 and 2.1 Angstrom r esolution. The electron density maps confirm the conclusions of a previous spectroscopic study, that the Q(A) ubiquinone is absent from the AM260W rea ction center (Ridge, J. P., van Brederode, M. E., Goodwin, M. G., van Grond elle, R., and Jones, M. R. (1999) Photosynthesis Res. 59, 9-26). Exclusion of the Q(A) ubiquinone caused by the AM260W mutation is accompanied by a ch ange in the packing of amino acids in the vicinity of the Q(A) Site that fo rm part of a loop that connects the DE and E helices of the M subunit. This repacking minimizes the volume of the cavity that results from the exclusi on of the Q(A) ubiquinone, and further space is taken up by a feature in th e electron density maps that has been modeled as a chloride ion. An unexpec ted finding is that the occupancy of the Q(B) Site by ubiquinone appears to be high in the AM260W crystals, and as a result the position of the Q(B) u biquinone is well-defined. The high quality of the electron density maps al so reveals more precise information on the detailed conformation of the rea ction center carotenoid, and we discuss the possibility of a bonding intera ction between the methoxy group of the carotenoid and residue Trp M75. The conformation of the 2-acetyl carbonyl group in each of the reaction center bacteriochlorins is also discussed.