Summary: Photosystem II protein
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This is the Wikipedia entry entitled "Photosystem II light harvesting protein". More...
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No Pfam abstract.
External database links
Transporter classification: | 3.E.2 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR000932
Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product.
PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane [PUBMED:12518057, PUBMED:15100025]. Within the core of the complex, the chlorophyll and beta-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection [PUBMED:14871485].
This entry represents the intrinsic antenna proteins CP43 (PsbC) and CP47 (PsbB) found in the reaction centre of PSII. These polypeptides bind to chlorophyll a and beta-carotene and pass the excitation energy on to the reaction centre [PUBMED:12163077]. This entry also includes the iron-stress induced chlorophyll-binding protein CP43' (IsiA), which evolved in cyanobacteria from a PSII protein to cope with light limitations and stress conditions. Under iron-deficient growth conditions, CP43' associates with PSI to form a complex that consists of a ring of 18 or more CP43' molecules around a PSI trimer, which significantly increases the light-harvesting system of PSI. IsiA can also provide photoprotection for PSII [PUBMED:15301529].
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Cellular component | membrane (GO:0016020) |
photosystem (GO:0009521) | |
Molecular function | chlorophyll binding (GO:0016168) |
Biological process | photosynthesis, light reaction (GO:0019684) |
photosynthetic electron transport chain (GO:0009767) |
Domain organisation
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Alignments
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Seed (16) |
Full (1506) |
Representative proteomes | UniProt (20232) |
NCBI (13122) |
Meta (840) |
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RP15 (56) |
RP35 (696) |
RP55 (1256) |
RP75 (1815) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
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Seed (16) |
Full (1506) |
Representative proteomes | UniProt (20232) |
NCBI (13122) |
Meta (840) |
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RP15 (56) |
RP35 (696) |
RP55 (1256) |
RP75 (1815) |
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Raw Stockholm | |||||||||
Gzipped |
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
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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.
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Curation and family details
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Curation
Seed source: | Pfam-B_182 (release 1.0) |
Previous IDs: | none |
Type: | Family |
Sequence Ontology: | SO:0100021 |
Author: |
Finn RD |
Number in seed: | 16 |
Number in full: | 1506 |
Average length of the domain: | 249.20 aa |
Average identity of full alignment: | 33 % |
Average coverage of the sequence by the domain: | 87.28 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model length: | 511 | ||||||||||||
Family (HMM) version: | 20 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Interactions
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 PSII domain has been found. There are 256 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 sequence.
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