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0  structures 112  species 0  interactions 176  sequences 4  architectures

Family: PsbY (PF06298)

Summary: Photosystem II protein Y (PsbY)

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Photosystem II protein Y (PsbY) Provide feedback

This family consists of several bacterial and plant photosystem II protein Y (PsbY) sequences. PsbY is a manganese-binding protein that has an L-arginine metabolising enzyme activity [1].

Literature references

  1. Gau AE, Thole HH, Sokolenko A, Altschmied L, Hermann RG, Pistorius EK; , Mol Gen Genet 1998;260:56-68.: PsbY, a novel manganese-binding, low-molecular-mass protein associated with photosystem II. PUBMED:9829828 EPMC:9829828


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR009388

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 10 kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection [PUBMED:14871485].

This family represents the low molecular weight transmembrane protein PsbY found in PSII. In higher plants, two related PsbY proteins exist, PsbY-1 and PsbY-2, which appear to function as a heterodimer. In spinach and Arabidopsis, these two proteins arise from a single-copy nuclear gene that is processed in the chloroplast. By contrast, prokaryotic and organellar chromosomes encode a single PsbY protein, as found in cyanobacteria and red algae, indicating a duplication event in the evolution of higher plants [PUBMED:15042356]. PsbY has two low manganese-dependent activities: a catalase-like activity and an L-arginine metabolising activity that converts L-arginine into ornithine and urea [PUBMED:9829828]. In addition, a redox-active group is thought to be present in the protein. In cyanobacteria, PsbY deletion mutants have a slightly impaired PSII that is less capable of coping with low levels of calcium ions than the wild-type.

Gene Ontology

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Domain organisation

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Alignments

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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.

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(22)
Full
(176)
Representative proteomes NCBI
(159)
Meta
(18)
RP15
(16)
RP35
(49)
RP55
(63)
RP75
(72)
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  Seed
(22)
Full
(176)
Representative proteomes NCBI
(159)
Meta
(18)
RP15
(16)
RP35
(49)
RP55
(63)
RP75
(72)
Alignment:
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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
(22)
Full
(176)
Representative proteomes NCBI
(159)
Meta
(18)
RP15
(16)
RP35
(49)
RP55
(63)
RP75
(72)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
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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.

Pfam alignments:

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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

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: Pfam-B_12212 (release 9.0)
Previous IDs: none
Type: Family
Author: Moxon SJ
Number in seed: 22
Number in full: 176
Average length of the domain: 35.00 aa
Average identity of full alignment: 45 %
Average coverage of the sequence by the domain: 49.48 %

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 20.4 20.4
Trusted cut-off 23.3 20.9
Noise cut-off 20.0 20.3
Model length: 36
Family (HMM) version: 6
Download: download the raw HMM for this family

Species distribution

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