Summary: Photosynthesis system II assembly factor YCF48
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Photosynthesis system II assembly factor YCF48 Provide feedback
YCF48 is one of several assembly factors of the photosynthesis system II. The photosynthesis system II occurs in Cyanobacteria that are Gram-negative bacteria performing oxygenic photosynthesis. One of the three membranes surrounding these bacteria is the inner thylakoid membrane (TM) system that is localised within the cell and houses the large pigment-protein complexes of the photosynthetic electron transfer chain, i.e. Photosystem (PS) II, PSI, the cytochrome b6f complex, and the ATP synthase. YCF48 is necessary for efficient assembly and repair of the PSII [1]. YCF48 is found predominantly in the thykaloid membrane [2]. It is a BNR repeat protein.
Literature references
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Komenda J, Nickelsen J, Tichy M, Prasil O, Eichacker LA, Nixon PJ;, J Biol Chem. 2008;283:22390-22399.: The cyanobacterial homologue of HCF136/YCF48 is a component of an early photosystem II assembly complex and is important for both the efficient assembly and repair of photosystem II in Synechocystis sp. PCC 6803. PUBMED:18550538 EPMC:18550538
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Rengstl B, Oster U, Stengel A, Nickelsen J;, J Biol Chem. 2011;286:21944-21951.: An intermediate membrane subfraction in cyanobacteria is involved in an assembly network for Photosystem II biogenesis. PUBMED:21531723 EPMC:21531723
Internal database links
SCOOP: | BNR_2 Sortilin-Vps10 |
Similarity to PfamA using HHSearch: | Sortilin-Vps10 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR028203
This entry represents a domain found in the photosynthesis system II assembly factor YCF48/HCF136 and associated proteins.
The photosynthesis system II (PSII) is a multi-subunit pigment-protein complex responsible for water oxidation during oxygenic photosynthesis [PUBMED:18550538]. PSII can be found in the thylakoid membrane of chloroplasts and cyanobacteria. Its assembly is regulated by PSII assembly factors including Ycf48/Hcf136, Psb27 and Psb28. Ycf48/Hcf136 contains the BNR repeats and can be found predominantly in the thykaloid membrane. Ycf48/Hcf136 is required for assembly and repair of an early intermediate in PSII assembly that includes D2 (psbD) and cytochrome b559 [PUBMED:18550538, PUBMED:21531723]. This domain can also be found in some YCF48-like proteins that may not affect PSII activity.
Domain organisation
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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Pfam Clan
This family is a member of clan Sialidase (CL0434), which has the following description:
This superfamily includes sialidases enzymes. Several viruses use sialic acid as a cell surface receptor for host invasion. These viruses then have cell surface neuraminidase enzymes to cleave sialic acid from cell surface proteins allowing them to leave the host cell after replication. This superfamily are composed of six beta-sheets that form a six-fold beta-propeller structure. Many members of this superfamily contain BNR sequence motifs Pfam:PF02012.
The clan contains the following 16 members:
BNR BNR_2 BNR_3 BNR_4 BNR_6 End_beta_barrel End_beta_propel Fungal_lectin HN Mcl1_mid Neur Neuraminidase OLF Phytase PSII_BNR Sortilin-Vps10Alignments
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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...
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Seed (15) |
Full (2376) |
Representative proteomes | UniProt (15320) |
NCBI (20562) |
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RP15 (347) |
RP35 (1119) |
RP55 (2325) |
RP75 (4324) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
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Seed (15) |
Full (2376) |
Representative proteomes | UniProt (15320) |
NCBI (20562) |
Meta (365) |
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RP15 (347) |
RP35 (1119) |
RP55 (2325) |
RP75 (4324) |
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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.
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
Seed source: | Pfam-B_547 (release 26.0) |
Previous IDs: | PSII_YCF48; |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Coggill P |
Number in seed: | 15 |
Number in full: | 2376 |
Average length of the domain: | 146.30 aa |
Average identity of full alignment: | 21 % |
Average coverage of the sequence by the domain: | 50.97 % |
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 details: |
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Model length: | 304 | ||||||||||||
Family (HMM) version: | 7 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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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_BNR domain has been found. There are 11 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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