Like all phycobiliproteins, phycoerythrin is composed of a protein part, organised in a hexameric structure of alpha and beta chains, covalently binding chromophores called phycobilins. In the phycoerythrin family, the phycobilins are: phycoerythrobilin, the typical phycoerythrin acceptor chromophore, and sometimes phycourobilin (marine organisms). Phycoerythrins are the phycobiliproteins which bind the highest number of phycobilins (up to six per alpha-beta subunit dimer).
In deep-ocean-dwelling red algae, there is a paradox in the rules of photosynthesis. Though the algae appears pink, red or black, the accessory pigments "trick" the eye into seeing these colors though they are not really there. Phycoerythrin absorbs red and purple wavelengths and reflects green, however the color of other algae in the ocean can pick up the reflected colors easier than the human eye, so the algae appears red.
Absorption peaks in the visible light spectrum are at 495 and 545/566 nm, depending on the chromophores bound and the considered organism. A strong emission peak exists at 575 ± 10 nm. (i.e., phycoerythrin absorbs slightly blue-green/yellowish light and emits slightly orange-yellow light.)
Phycoerythrin is an accessory pigment to the main chlorophyll pigments responsible for photosynthesis. The light energy is captured by phycoerythrin and is then passed on to the reaction centre chlorophyll pair, most of the time via the phycobiliproteins phycocyanin and allophycocyanin.
R-Phycoerythrin is useful in the laboratory as a fluorescence-based indicator for the presence of cyanobacteria and for labeling antibodies in a technique called immunofluorescence, among other applications. There are also other types of phycoerythrins, such as B-Phycoerythrin, which has slightly different spectral properties. B-Phycoerythrin absorbs strongly at about 545 nm (slightly yellowish green) and emits strongly at 572 nm (yellow) instead and could be better suited for some instruments. B-Phycoerythrin may also be less "sticky" than R-Phycoerythrin and contributes less to background signal due to non-specific binding in certain applications.