Crystal structure of allophycocyanin from red algae Porphyra yezoensis at 2.2-Å resolution

The crystal structure of allophycocyanin from red algae Porphyra yezoensis (APC-PY) at 2.2-Angstrom resolution has been determined by the molecular replacement method. The crystal belongs to space group R32 with cell parameters a = b = 105.3 Angstrom, c = 189.4 Angstrom, alpha = beta = 90 degrees, gamma = 120 degrees, After several cycles of refinement using program X-PLOR and model building based on the electron density map, the crystallographic R-factor converged to 19.3% (R-free factor is 26.9%) in the range of 10.0 to 2.2 Angstrom The r.m.s. deviations of bond length and angles are 0.015 Angstrom and 2.9 degrees, respectively. In the crystal, two APC-PY trimers associate face to face into a hexamer, The assembly of two trimers within the hexamer is similar to that of C-phycocyanin (C-PC) and R-phycoerythrin (R-PE) hexamers, but the assembly tightness of the two trimers to the hexamer is not so high as that in C-PC and R-PE hexamers, The chromophore-protein interactions and possible pathway of energy transfer were discussed. Phycocyanobilin 1 alpha 84 of APC-PY forms 5 hydrogen bonds with 3 residues in subunit 2 beta of another monomer, In R-PE and C-PC, chromophore 1 alpha 84 only forms 1 hydrogen bond with 2 beta 77 residue in subunit 2 beta. This result may support and explain great spectrum difference exists between APC trimer and monomer.