Summary: Phycoerythrin, alpha/beta chain
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Phycoerythrin Edit Wikipedia article
|Phycoerythrin, alpha/beta chain|
Phycoerythrin (PE) is a red protein-pigment complex from the light-harvesting phycobiliprotein family, present in red algae and cryptophytes, accessory to the main chlorophyll pigments responsible for photosynthesis.
Like all phycobiliproteins, it is composed of a protein part covalently binding chromophores called phycobilins. In the phycoerythrin family, the most known phycobilins are: phycoerythrobilin, the typical phycoerythrin acceptor chromophore, and sometimes phycourobilin. Phycoerythrins are composed of (αβ) monomers, usually organised in a disk-shaped trimer (αβ)3 or hexamer (αβ)6 (second one is the functional unit of the antenna rods). These typical complexes contain also third type of subunit, the γ chain.
The phycobiliproteins that bind the highest number of phycobilins (up to ten per αβ monomer).
Phycobiliproteins are part of huge light harvesting antennae protein complexes called phycobilisomes. In red algae they are anchored to the stromal side of thylakoid membranes of chloroplasts, whereas in cryptophytes phycobilisomes are reduced and (phycobiliprotein 545 PE545 molecules here) are densely packed inside the lumen of thylakoides. 
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.
Phycoerythrins except phycoerythrin 545 (PE545) are composed of (αβ) monomers assembled into disc-shaped (αβ)6 hexamers or (αβ)3 trimers with 32 or 3 symmetry and enclosing central channel. In phycobilisomes (PBS) each trimer or hexamer contains at least one linker protein located in central channel. B-phycoerythrin (B-PE) and R-phycoerythrin (R-PE) from red algae in addition to α and β chains have third, γ subunit combining linker and light-harvesting functions, because bears chromophores. 
R-phycoerythrin is predominantly produced by red algae. The protein is made up of at least three different subunits and varies according to the species of algae that produces it. The subunit structure of the most common R-PE is (αβ)6γ. The α subunit has two phycoerythrobilins (PEB), the β subunit has 2 or 3 PEBs and one phycourobilin (PUB), while the different gamma subunits are reported to have 3 PEB and 2 PUB (γ1) or 1 or 2 PEB and 1 PUB (γ2). The molecular weight of R-PE is 250,000 Daltons.
|Chromophore or other
|Bilins||8||10||10||10||α and β|
|- Phycoerythrobilin (PEB)||6||10||0 or 8||8||β (PE545)
or α and β
|- 15,16-dihydrobiliverdin (DBV)||2||-||-||-||α (-3 and -2)|
|- Phycocyanobilin (CYC)||-||-||8 or 7 or 0||-||α and β|
|- Biliverdine IX alpha (BLA)||-||-||0 or 1||-||α|
|- Phycourobilin (PUB)||-||-||2||2||β|
|5-hydroxylysine (LYZ)||1 or 2||-||-||-||α (-3 or
-3 and -2)
|N-methyl asparagine (MEN)||2||2||0 or 2||2||β|
|Sulfate ion SO42- (SO4)||-||5 or 1||0 or 2||-||α or α and β|
|Chloride ion Cl- (CL)||1||-||-||-||β|
|Magnesium ion Mg2+ (MG)||2||-||-||-||α-3 and β|
|inspected PDB files||1XG0
The assumed biological molecule of phytoerythrin 545 (PE545) is (αβ)2 or rather (α3β)(α2β). The numbers 3 and 2 after α letters in second formula are part of chain names here, not their counts. The synonym cryptophytan name of α3 chain is α1 chain.
The largest assembly of B-phytoerythrin (B-PE) is (αβ)3 trimer , however preparations from red algae yield also (αβ)6 hexamer . In case of R-phytoerythrin (R-PE) the largest assumed biological molecule here is (αβγ)6, (αβγ)3(αβ)3 or (αβ)6 dependently on publication, for other phytoeritrin types (αβ)6. These γ chains from the Protein Data Bank are very small and consist only of 6 or 3 recognizable aminoacids , whereas described at the beginning of this section linker γ chain is large (for example 277 aminoacid long 33 kDa in case of γ33 from red algae Aglaothamnion neglectum) . This is because the electron density of the gamma-polypeptide is mostly averaged out by threefold crystallographic symmetry and only few aminoacids can be modeled .
Anyway for (αβγ)6, (αβ)6 or (αβγ)3(αβ)3 the values from the table should be simply multiplied by 3, (αβ)3 contain intermediate numbers of non-protein molecules.
In phycoerythrin PE545 above, one α chain (-2 or -3) binds 1 molecule of billin, in other examples 2 molecules, β chain always 3 molecules, that small γ chain no one.
Two molecules of N-methyl asparagine are bound to the chain β, one 5-hydroxylysine to α (-3 or -2), one Mg2+ to α-3 and β, one Cl- to β, 1-2 molecules of SO42- to α or β.
Below is sample crystal structure of R-phycoerythrin from Protein Data Bank:
Absorption peaks in the visible light spectrum are measured 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.)
|Absorption maximum||565 nm|
|Additional Absorption peak||498 nm|
|Emission maximum||573 nm|
|Extinction Coefficient (ε)||1.96 x 106 M−1cm−1|
|Quantum Yield (QY)||0.84|
|Brightness (ε x QY)||1.65 x 106 M−1cm−1|
PEB and DBV bilins in PE545 absorb in the green spectral region too, with maxima at 545 and 569 nm respectively. The fluorescence emission maximum is at 580 nm. 
As mentioned above, phycoerythrin can be found in a variety of algal species. As such, there can be variations in the efficiency of absorbance and emission of light required for facilitation of photosynthesis. This could be a result of where in the water column a specific alga resides and a consequent need for greater or less efficiency of the accessory pigments.
With advances in imaging and detection technology which can avoid rapid photobleaching, protein fluorophores have become a viable and powerful tool for researchers in fields such as microscopy, microarray analysis and Western blotting. In light of this, it may be beneficial for researchers to screen these variable R-phycoerythrins to determine which one is most appropriate for their particular application. Even a small increase in fluorescent efficiency could reduce background noise and lower the rate of false-negative results.
R-Phycoerythrin, or PE, 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.
R-Phycoerythrin and B-Phycoerythrin are among the brightest fluorescent dyes ever identified.
- Ficner R., Huber R. (1993). "Refined crystal structure of phycoerythrin from Porphyridium cruentum at 0.23-nm resolution and localization of the γ subunit.". Eur. J. Biochem. 218 (1): 103–106. doi:10.1111/j.1432-1033.1993.tb18356.x. PMID 8243457. Retrieved 13 October 2012.
- van der Weij-De Wit C. D., Doust A. B., van Stokkum I. H. M., Dekker J. P., Wilk K. E., Curmi P. M. G., Scholes G. D., van Grondelle R. (2006). "How Energy Funnels from the Phycoerythrin Antenna Complex to Photosystem I and Photosystem II in Cryptophyte Rhodomonas CS24 Cells.". J. Phys. Chem. B. 110: 25066–25073. doi:10.1021/jp061546w. PMID 17149931. Retrieved 13 October 2012.
- Christophe Six, Jean-Claude Thomas, Laurence Garczarek, Martin Ostrowski, Alexis Dufresne, Nicolas Blot, David J Scanlan and Frédéric Partensky (2007). "Diversity and evolution of phycobilisomes in marine Synechococcus spp.: a comparative genomics study". Genome Biology. 8:R259 (12). doi:10.1186/gb-2007-8-12-r259. Retrieved 16 April 2014.
- Glazer A. N. (1985). "Light Harvesting by Phycobilisomes.". Annual Review of Biophysics and Biophysical Chemistry 14: 47–77. doi:10.1146/annurev.bb.14.060185.000403. PMID 3924069. Retrieved 13 October 2012.
- Camara-Artigas, A. (2011-12-16). "Crystal Structure of the B-phycoerythrin from the red algae Porphyridium cruentum at pH8.". RCSB Protein Data Bank (PDB). doi:10.2210/pdb3v57/pdb. PDB ID: 3V57. Retrieved 12 October 2012.
- Camara-Artigas, A., Bacarizo, J., Andujar-Sanchez, M., Ortiz-Salmeron, E., Mesa-Valle, C., Cuadri, C., Martin-Garcia, J.M., Martinez-Rodriguez, S., Mazzuca-Sobczuk, T., Ibanez, M.J., Allen, J.P. (2012). "pH-dependent structural conformations of B-phycoerythrin from Porphyridium cruentum.". Febs J. 279: 3680–3691. doi:10.1111/j.1742-4658.2012.08730.x. PMID 22863205. PDB ID: 3V57. Retrieved 12 October 2012.
- "Protein Data Bank". RCSB Protein Data Bank (PDB). Retrieved 12 October 2012.
- Doust, A.B., Marai, C.N.J., Harrop, S.J., Wilk, K.E., Curmi, P.M.G., Scholes, G.D. (2004-09-16). "High resolution crystal structure of phycoerythrin 545 from the marine cryptophyte rhodomonas CS24.". RCSB Protein Data Bank (PDB). doi:10.2210/pdb1xg0/pdb. PDB ID: 1XG0. Retrieved 11 October 2012.
- Doust, A.B., Marai, C.N.J., Harrop, S.J., Wilk, K.E., Curmi, P.M.G., Scholes, G.D. (2004). "Developing a structure-function model for the cryptophyte phycoerythrin 545 using ultrahigh resolution crystallography and ultrafast laser spectroscopy.". J.Mol.Biol. 344: 135–153. doi:10.1016/j.jmb.2004.09.044. PMID 15504407. PDB ID: 1XG0. Retrieved 11 October 2012.
- Contreras-Martel, C., Legrand, P., Piras, C., Vernede, X., Martinez-Oyanedel, J., Bunster, M., Fontecilla-Camps, J.C. (2000-05-09). "Crystal structure of R-phycoerythrin at 2.2 angstroms.". RCSB Protein Data Bank (PDB). doi:10.2210/pdb1eyx/pdb. PDB ID: 1EYX. Retrieved 11 October 2012.
- Contreras-Martel, C., Martinez-Oyanedel, J., Bunster, M., Legrand, P., Piras, C., Vernede, X., Fontecilla-Camps, J.C. (2001). "Crystallization and 2.2 A resolution structure of R-phycoerythrin from Gracilaria chilensis: a case of perfect hemihedral twinning.". Acta Crystallogr.,Sect.D 57: 52–60. doi:10.1107/S0907444900015274. PMID 11134927. PDB ID: 1EYX. Retrieved 11 October 2012.
- Apt K. E., Hoffman N. E., Grossman A. R. (1993). "The γ Subunit of R-phycoerythrin and Its Possible Mode of Transport into the Plastiodf Red Algae.". J Biol Chem. 268 (22): 16208–16215. PMID 8344905. Retrieved 13 October 2012.
- Ritter, S., Hiller, R.G., Wrench, P.M., Welte, W., Diederichs, K. (1999-01-29). "Crystal structure of a phycourobilin-containing phycoerythrin.". RCSB Protein Data Bank (PDB). doi:10.2210/pdb1b8d/pdb. PDB ID: 1B8D. Retrieved 14 October 2012.
- Ritter, S., Hiller, R.G., Wrench, P.M., Welte, W., Diederichs, K. (1999). "Crystal structure of a phycourobilin-containing phycoerythrin at 1.90-A resolution.". J.Struct.Biol. 126: 86–97. doi:10.1006/jsbi.1999.4106. PMID 10388620. PDB ID: 1B8D. Retrieved 14 October 2012.
This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.
Phycoerythrin, alpha/beta chain Provide feedback
This family represents the non-globular alpha and beta chain components of phycoerythrin. The structure is a long beta-hairpin and a single alpha-helix.
Wilk KE, Harrop SJ, Jankova L, Edler D, Keenan G, Sharples F, Hiller RG, Curmi PM; , Proc Natl Acad Sci U S A 1999;96:8901-8906.: Evolution of a light-harvesting protein by addition of new subunits and rearrangement of conserved elements: crystal structure of a cryptophyte phycoerythrin at 1.63-A resolution. PUBMED:10430868 EPMC:10430868
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR004228
Cryptophytes are unicellular photosynthetic algae that use a lumenally located light-harvesting system, which is distinct from the phycobilisome structure found in cyanobacteria and red algae. One of the key components of this system is water-soluble phycoerythrin (PE) 545 whose expression is enhanced by low light levels [PUBMED:10430868]. Phycoerythrin (PE) 545 is a heterodimeric of alpha(1)alpha(2)betabeta subunits. Each alpha subunit carries a covalently linked 15,16-dihydrobiliverdin chromophore that probably acts as the final energy acceptor. The architecture of the heterodimer suggests that PE 545 may dock to an acceptor protein via a deep cleft and that energy may be transferred via this intermediary protein to the reaction centre [PUBMED:10430868].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Cellular component||phycobilisome (GO:0030089)|
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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|Seed source:||Structural domain|
|Number in seed:||5|
|Number in full:||25|
|Average length of the domain:||56.60 aa|
|Average identity of full alignment:||54 %|
|Average coverage of the sequence by the domain:||46.87 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||9|
|Download:||download the raw HMM for this family|
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How the sunburst is generated
The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.
In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:
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Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.
Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".
Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
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For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.
The tree shows the occurrence of this domain across different species. More...
We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.
Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.
If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.
For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.
Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.
We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
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There are 2 interactions for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Phycoerythr_ab domain has been found. There are 6 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.
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