Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
6  structures 4  species 2  interactions 25  sequences 1  architecture

Family: Phycoerythr_ab (PF02972)

Summary: Phycoerythrin, alpha/beta chain

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Phycoerythrin". More...

Phycoerythrin Edit Wikipedia article

Phycoerythrin, alpha/beta chain
Identifiers
Symbol Phycoerythr_ab
Pfam PF02972
InterPro IPR004228
SCOP 1qgw
SUPERFAMILY 1qgw
The crystal structure of phycoerythrin 545 (PE545) from a unicellular cryptophyte Rhodomonas CS24 (PDB ID: 1XG0 [1][2]). Colors: chains - alpha-2, alpha-3, beta, beta (helixes, sheets are yellow), phycoerythrobilin, 15,16-dihydrobiliverdin (15,16-DHBV), 5-hydroxylysine, N-methyl asparagine, Mg2+, Cl-.

In molecular biology, phycoerythrin (PE), like all phycobiliproteins, is composed of a protein part covalently binding chromophores called phycobilins, and organised mostly in a hexameric structure of alpha and beta chains. In the phycoerythrin family, the phycobilins are: phycoerythrobilin, the typical phycoerythrin acceptor chromophore, and sometimes phycourobilin (marine organisms). Phycoerythrins are the phycobiliproteins that bind the highest number of phycobilins (up to six per alpha-beta subunit dimer).

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.)

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.

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. [3][4]

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.

Structural characteristics[edit]

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. [5]

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.

Crystal structures available in the Protein Data Bank [6] contain in one (αβ)2 or (αβγ)2 asymmetric unit of different phycoerythrins:

Phycoerythrobilin is the typical chromophore in phycoerythrin. It is similar to porphyrin of chlorophyll for example, but tetrapyrrole is linear, not closed into ring with metal ion in the middle.
The red algae Gracilaria contains R-phycoerythrin.
Chromophore or other
non-protein molecule
Phycoerythrin Chain
PE545 B-PE R-PE other types
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
1XF6
1QGW
3V57
3V58
1EYX
1LIA
1B8D
2VJH

The assumed biological molecule of phytoerythrin 545 (PE545) is (αβ)2 or rather 3β)(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 [7][8], however preparations from red algae yield also (αβ)6 hexamer [5]. 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 [9][10], 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) [11][5]. 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 [9][10][12][13].

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 are sample crystal structures of R- and B-phycoerythrin from Protein Data Bank:

The crystal structure of R-phycoerythrin from red algae Gracilaria chilensis (PDB ID: 1EYX [9][10]) - basic oligomer (αβγ)2 (so called asymmetric unit). It contains phycocyanobilin, biliverdine IX alpha, phycourobilin, N-methyl asparagine, SO42-. One fragment of γ chain is red, second one white because it is not considered as alpha helix despite identical aminoacid sequence.
The entire oligomer of R-phycoerythrin from Gracilaria chilensis (αβγ)6 (PDB ID: 1EYX [9][10]).
The crystal structure of B-phycoerythrin from red algae Porphyridium cruentum (PDB ID: 3V57 [7][8]). The asymmetric unit (αβ)2 on the left and assumed biological molecule (αβ)3. It contains phycoerythrobilin, N-methyl asparagine and SO42-.

Spectral characteristics[edit]

Fluorescent spectra of phycoerythrin
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. [3]

R-phycoerythrin variations[edit]

Excitation and emission profiles for r-phycoerythrin from two different algae. Common laser excitation wavelengths are also noted.

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.

References[edit]

  1. ^ 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. 
  2. ^ 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. 
  3. ^ a b 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. 
  4. ^ 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. 
  5. ^ a b c 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. 
  6. ^ "Protein Data Bank". RCSB Protein Data Bank (PDB). Retrieved 12 October 2012. 
  7. ^ a b 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. 
  8. ^ a b 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. 
  9. ^ a b c d 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. 
  10. ^ a b c d 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. 
  11. ^ 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. 
  12. ^ 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. 
  13. ^ 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. 

External links[edit]

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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.

Literature references

  1. 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].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

Loading domain graphics...

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

View options

We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(5)
Full
(25)
Representative proteomes NCBI
(31)
Meta
(0)
RP15
(0)
RP35
(0)
RP55
(0)
RP75
(0)
Jalview View  View          View   
HTML View  View             
PP/heatmap 1 View             
Pfam viewer View  View             

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(5)
Full
(25)
Representative proteomes NCBI
(31)
Meta
(0)
RP15
(0)
RP35
(0)
RP55
(0)
RP75
(0)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(5)
Full
(25)
Representative proteomes NCBI
(31)
Meta
(0)
RP15
(0)
RP35
(0)
RP55
(0)
RP75
(0)
Raw Stockholm Download   Download           Download    
Gzipped Download   Download           Download    

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Structural domain
Previous IDs: phycoerythr_ab;
Type: Family
Author: Griffiths-Jones SR
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 information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.5 22.5
Trusted cut-off 23.6 53.0
Noise cut-off 20.8 17.3
Model length: 57
Family (HMM) version: 9
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Show

This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

Loading sunburst data...

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

Interactions

There are 2 interactions for this family. More...

Phycoerythr_ab Phycobilisome

Structures

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.

Loading structure mapping...