Isolation, crystallization, crystal structure analysis and refinement of B-phycoerythrin from the red alga Porphyridium sordidum at 2.2 A resolution.

The light-harvesting pigment-protein complex B-phycoerythrin from the red alga Porphyridium sordidum has been isolated and crystallized. B-Phycoerythrin consists of three different subunits forming an (alpha beta)6 gamma aggregate. The three-dimensional structure of the (alpha beta)6 hexamer was solved by Patterson search techniques using the molecular model of C-phycocyanin from Fremyella diplosiphon. The asymmetric unit of the crystal cell (space group P3, with a = b = 111.2 A, c = 59.9 A, alpha = beta = 90 degrees, gamma = 120 degrees) contains two (alpha beta) monomers related by a local dyad. Three asymmetric units are arranged around the crystallographic 3-fold axis building an (alpha beta)6 hexamer, as in C-phycocyanin. The crystal structure has been refined by energy-restrained crystallographic refinement and model building. The conventional R-factor of the final model was 18.9% with data to 2.2 A resolution. The molecular structures of the alpha and beta-subunits resemble those of C-phycocyanin. Major changes in comparison to phycocyanin are caused by deletion or insertion of segments involved in protein-chromophore interactions. The singly linked phycoerythrobilin chromophores alpha-84, alpha-140a, beta-84 and beta-155 are each covalently bound to a cysteine by ring A. The doubly linked chromophore beta-50/beta-61 is attached at cysteine beta-50 through ring A and at cysteine beta-61 through ring D. B-Phycoerythrin contains additionally a 30 kDa gamma-subunit, which is presumably located in the central cavity of the hexamer. It is disordered, as a consequence of crystal and local symmetry averaging.