PE exists as an additional PBP only in some cyanobacterial species, but exists in all red algae. The basic PE structure is a (aP )6 hexamer in cyanobacteria and a (aP)6y in red algae: the unique chromophore-bearing 30kDa y subunit is found inserted within the hexameric disk of red- algal PE. The first PE structures to be determined were those of Porphyridium sordidum bPE [52] and Porphyridium cruen-tum bPE-organisms that differ in the number of PE/PUB chromophors bound to the (aP) monomer and to the y subunit. Unfortunately, the coordinates of these structures were not deposited in the PDB. A number of years later, four additional PE structures were determined and their coordinates deposited in the PDB. These structures are all red algal PE that contain both singly and doubly linked cofactors, which has a noticeable effect on their conformation and absorption. All proteins prior to crystallization had the internal y subunit, except for the bPE structure; the presence of the protein in crystal was identified by SDS-PAGE of solubilized crystals. However, except for a very small number of residues, the y subunit structure could not be visualized in the electron density. In the [1B8D] structure, three residues of the y subunit were built into electron density within the (aP)6 disk [53], thus providing evidence for the general position of this subunit. The identified residues were located in the vicinity of the PE chromophores. It was proposed that the reason for the absence of the y subunit in the electron density was due to the threefold crystallographic averaging applied during structure determination )52, 53], although heterogeneity in the position of this subunit cannot be discounted. Another possibility is that crystal packing forces on the PE disks change the affinity toward the y-subunit to a degree that allows it to bind in a less specific manner, thereby lowering its apparent occupancy in the crystal structure.

The absorption of PE is blue) shifted compared to PC; some organisms take advantage of this difference to change their absorption cross-section by a mechanism known as complimentary chromatic adaptation (CCA) [54]. In this process, cells that contain phycobilisome rods with PC grown under red light modify the expression of PBP encoding genes, as a result of a shift to green light. The newly expressed genes encode for variants of PC, PE, and for the appropriate linker proteins. PE now becomes the terminal subunit on the newly assembled phycobili-some. A number of excellent reviews describe the mechanism of CCA in detail [41, 54, 55]. In normal sunlight, the phycobilisome contains intermediate levels of PC and PE, indicating that cells can respond correctly to the actual light quality, affording maximal energy transfer. Changes in light intensity, with or without additional changes in the light quality, have also been known to have an effect on both the number of phycobilisome and the length of the phycobilisome rods. These observations show that the phycobilisome is a dynamic complex, as far as composition, and requires the presence of additional accessory proteins in order to obtain its functional structure.

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