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17  structures 1444  species 2  interactions 1482  sequences 1  architecture

Family: Ycf9 (PF01737)

Summary: YCF9

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This is the Wikipedia entry entitled "Ycf9 protein domain". More...

Ycf9 protein domain Edit Wikipedia article

Ycf9 protein domain
PDB 2axt EBI.jpg
Crystal structure of Photosystem II from thermosynechococcus elongatus
Identifiers
Symbol Ycf9
Pfam PF01737
InterPro IPR002644

In molecular biology, the PsbZ (Ycf9) is a protein domain, which is low in molecular weight. It is a transmembrane protein and therefore is located in the thylakoid membrane of chloroplasts in cyanobacteria and plants. More specifically, it is located in Photosystem II (PSII) and in the light-harvesting complex II (LHCII). Ycf9 acts as a structural linker, that stabilises the PSII-LHCII supercomplexes. Moreover, the supercomplex fails to form in PsbZ-deficient mutants, providing further evidence to suggest Ycf9's role as a structural linker. This may be caused by a marked decrease in two LHCII antenna proteins, CP26 and CP29, found in PsbZ-deficient mutants, which result in structural changes, as well as functional modifications in PSII.[1]

Function

PSII is a multisubunit protein-pigment complex containing polypeptides bound to the photosynthetic membrane.[2][3] 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.[4] PsbZ may also be involved in photo-protective processes under sub-optimal growth conditions.

Photosynthesis

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.

References

  1. ^ Swiatek M, Kuras R, Sokolenko A, Higgs D, Olive J, Cinque G, Müller B, Eichacker LA, Stern DB, Bassi R, Herrmann RG, Wollman FA (June 2001). "The chloroplast gene ycf9 encodes a photosystem II (PSII) core subunit, PsbZ, that participates in PSII supramolecular architecture". Plant Cell 13 (6): 1347–67. doi:10.2307/3871300. PMC 135574. PMID 11402165. 
  2. ^ Kamiya N, Shen JR (January 2003). "Crystal structure of oxygen-evolving photosystem II from Thermosynechococcus vulcanus at 3.7-A resolution". Proc. Natl. Acad. Sci. U.S.A. 100 (1): 98–103. doi:10.1073/pnas.0135651100. PMC 140893. PMID 12518057. 
  3. ^ Raymond J, Blankenship RE (April 2004). "The evolutionary development of the protein complement of photosystem 2". Biochim. Biophys. Acta 1655 (1-3): 133–9. doi:10.1016/j.bbabio.2003.10.015. PMID 15100025. 
  4. ^ Shi LX, Schröder WP (February 2004). "The low molecular mass subunits of the photosynthetic supracomplex, photosystem II". Biochim. Biophys. Acta 1608 (2-3): 75–96. doi:10.1016/j.bbabio.2003.12.004. PMID 14871485. 

This article incorporates text from the public domain Pfam and InterPro IPR002644

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YCF9 Provide feedback

This family consists of the hypothetical protein product of the YCF9 gene from chloroplasts and cyanobacteria. These proteins have no known function.

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002644

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 PsbZ (Ycf9), which is a core low molecular weight transmembrane protein of photosystem II in thylakoid-containing chloroplasts of cyanobacteria and plants. It is thought to be located at the interface of PSII and LHCII (light-harvesting complex II) complexes, the latter containing the light-harvesting antenna. PsbZ appears to act as a structural factor, or linker, that stabilises the PSII-LHCII supercomplexes, which fail to form in PsbZ-deficient mutants. This may in part be due to the marked decrease in two LHCII antenna proteins, CP26 and CP29, found in PsbZ-deficient mutants, which result in structural changes, as well as functional modifications in PSII [PUBMED:11402165]. PsbZ may also be involved in photo-protective processes under sub-optimal growth conditions.

Gene Ontology

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Domain organisation

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Alignments

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(35)
Full
(1482)
Representative proteomes NCBI
(419)
Meta
(120)
RP15
(11)
RP35
(34)
RP55
(46)
RP75
(54)
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  Seed
(35)
Full
(1482)
Representative proteomes NCBI
(419)
Meta
(120)
RP15
(11)
RP35
(34)
RP55
(46)
RP75
(54)
Alignment:
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  Seed
(35)
Full
(1482)
Representative proteomes NCBI
(419)
Meta
(120)
RP15
(11)
RP35
(34)
RP55
(46)
RP75
(54)
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

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Curation and family details

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Curation View help on the curation process

Seed source: Pfam-B_2211 (release 4.1)
Previous IDs: YCF9;
Type: Family
Author: Bashton M, Bateman A
Number in seed: 35
Number in full: 1482
Average length of the domain: 57.60 aa
Average identity of full alignment: 81 %
Average coverage of the sequence by the domain: 94.87 %

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 20.9 20.9
Trusted cut-off 21.7 22.1
Noise cut-off 20.5 20.4
Model length: 59
Family (HMM) version: 12
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Species distribution

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Interactions

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

PSII Ycf9

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 Ycf9 domain has been found. There are 17 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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