Summary: Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits

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Wikipedia: Cytochrome b559
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Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits

Structure of Photosystem II from Thermosynechococcus elongatus.^[1]

Identifiers

Symbol

Cytochrom_B559

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit

Structure of oxygen-evolving photosystem II from Thermosynechococcus vulcanus.^[2]

Identifiers

Symbol

Cytochrom_B559a

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

Cytochrome b559 is an important component of Photosystem II.

PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane.^[3]^[4] 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 chlorophylls in 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) provides electrons to re-reduce the PSII reaction center and oxidizes 2 water molecules to recover its reduced initial state. It 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.^[5]

Cytochrome b559, which forms part of the reaction centre core of PSII is a heterodimer composed of one alpha subunit (PsbE), one beta (PsbF) subunit, and a heme cofactor. Two histidine residues from each subunit coordinate the haem. Although cytochrome b559 is a redox-active protein, it is unlikely to be involved in the primary electron transport in PSII due to its very slow photo-oxidation and photo-reduction kinetics. Instead, cytochrome b559 could participate in a secondary electron transport pathway that helps protect PSII from photo-damage. Cytochrome b559 is essential for PSII assembly.^[6]

This domain occurs in both the alpha and beta subunits of cytochrome B559. In the alpha sbunit it occurs together with a lumenal domain (IPR013082), while in the beta subunit it occurs on its own.

Cytochrome b559 can exist in three forms, each with a characteristic redox potential, These forms are very low potential (VLP), â¤ zero mV; low potential (LP) at 60 mV; and high potential (HP) at 370 mV. There is also an intermediate potential (IP) form that has a redox potential at pH 6.5-7.0 that ranges from 170 to 240 mV. In oxygen evolving reaction centers, more than half of the cyt b559 is in the HP form. In manganese depleted non oxygen evolving photosystem II reaction centers, cyt b559 is usually in the LP form.^[7]

[edit] References

^ Loll B, Kern J, Saenger W, Zouni A, Biesiadka J (December 2005). "Towards complete cofactor arrangement in the 3.0 A resolution structure of photosystem II". Nature 438 (7070): 1040â4. doi:10.1038/nature04224. PMID 16355230.
^ 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): 98â103. doi:10.1073/pnas.0135651100. PMC 140893. PMID 12518057. //www.ncbi.nlm.nih.gov/pmc/articles/PMC140893/.
^ Kamiya N, Shen JR (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): 98â103. doi:10.1073/pnas.0135651100. PMC 140893. PMID 12518057. //www.ncbi.nlm.nih.gov/pmc/articles/PMC140893/.
^ Blankenship RE, Raymond J (2004). "The evolutionary development of the protein complement of photosystem 2". Biochim. Biophys. Acta 1655 (1-3): 133â139. doi:10.1016/j.bbabio.2003.10.015. PMID 15100025.
^ Schroder WP, Shi LX (2004). "The low molecular mass subunits of the photosynthetic supracomplex, photosystem II". Biochim. Biophys. Acta 1608 (2-3): 75â96. doi:10.1016/j.bbabio.2003.12.004. PMID 14871485.
^ Burda K, Kruk J, Borgstadt R, Stanek J, StrzaBka K, Schmid GH, Kruse O (2003). "MÃ¶ssbauer studies of the non-heme iron and cytochrome b559 in a Chlamydomonas reinhardtii PSI- mutant and their interactions with alpha-tocopherol quinone". FEBS Lett. 535 (1-3): 159â165. doi:10.1016/S0014-5793(02)03895-4. PMID 12560096.
^ Mizusawa N, Yamashita T, Miyao M (1999). "Restoration of the high-potential form of cytochrome b559 of photosystem II occurs via a two-step mechanism under illumination in the presence of manganese ions". BBA 1410 (3): 273â286. doi:10.1016/S0005-2728(99)00005-5. PMID 10082793.

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Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits Provide feedback

No Pfam abstract.

External database links

PANDIT:	PF00283
PROSITE:	PDOC00464
Pseudofam:	PF00283
SYSTERS:	Cytochrom_B559

This tab holds annotation information from the InterPro database.

InterPro entry IPR013081

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].

Cytochrome b559, which forms part of the reaction centre core of PSII is a heterodimer composed of one alpha subunit (PsbE), one beta (PsbF) subunit, and a haem cofactor. Two histidine residues from each subunit coordinate the haem. Although cytochrome b559 is a redox-active protein, it is unlikely to be involved in the primary electron transport in PSII due to its very slow photo-oxidation and photo-reduction kinetics. Instead, cytochrome b559 could participate in a secondary electron transport pathway that helps protect PSII from photo-damage. Cytochrome b559 is essential for PSII assembly [PUBMED:12560096].

This domain occurs in both the alpha and beta subunits of cytochrome B559. In the alpha sbunit it occurs together with a lumenal domain (INTERPRO), while in the beta subunit it occurs on its own.

Gene Ontology

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

Cellular component	photosystem II (GO:0009523)
	integral to membrane (GO:0016021)
	plastid (GO:0009536)
	thylakoid (GO:0009579)
Molecular function	metal ion binding (GO:0046872)
Biological process	photosynthesis (GO:0015979)

Domain organisation

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

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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...

There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.

Alignment types

We make a range of alignments for each Pfam-A family:

seed: the curated alignment from which the HMM for the family is built
full: the alignment generated by searching the sequence database using the HMM
RP15/RP35/RP55/RP75: Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
NCBI: alignment generated by searching the NCBI sequence database using the family HMM
meta: alignment generated by searching the metagenomics sequence database using the family HMM

Viewing

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Pfam viewer: an HTML-based viewer that uses DAS to retrieve alignment fragments on request

Reformatting

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You can also change the order in which sequences are listed in the alignment, change how insertions are represented, alter the characters that are used to represent gaps in sequences and, finally, choose whether to download the alignment or to view it in your browser directly.

Downloading

You may find that large alignments cause problems for the viewers and the reformatting tool, so we also provide all alignments in Stockholm format. You can download either the plain text alignment, or a gzipped version of it.

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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.

	Seed (8)	Full (2001)	Representative proteomes				NCBI (639)	Meta (147)
	Seed (8)	Full (2001)	RP15 (28)	RP35 (71)	RP55 (99)	RP75 (112)	NCBI (639)	Meta (147)
Jalview	View	View	View	View	View	View	View	View
HTML	View	View	View	View	View	View
PP/heatmap	₁	View	View	View	View	View
Pfam viewer	View	View

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

Key: available, not generated, — not available.

Format an alignment

	Seed (8)	Full (2001)	Representative proteomes				NCBI (639)	Meta (147)
	Seed (8)	Full (2001)	RP15 (28)	RP35 (71)	RP55 (99)	RP75 (112)	NCBI (639)	Meta (147)
Alignment:
Format:
Order:	Tree Alphabetical
Sequence:	Inserts lower case All upper case
Gaps:
Download/view:	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 (8)	Full (2001)	Representative proteomes				NCBI (639)	Meta (147)
	Seed (8)	Full (2001)	RP15 (28)	RP35 (71)	RP55 (99)	RP75 (112)	NCBI (639)	Meta (147)
Raw Stockholm	Download	Download	Download	Download	Download	Download	Download	Download
Gzipped	Download	Download	Download	Download	Download	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

Seed source:

Prosite

Previous IDs:

cytochr_b559;

Type:

Family

Author:

Finn RD

Number in seed:

8

Number in full:

2001

Average length of the domain:

28.50 aa

Average identity of full alignment:

55 %

Average coverage of the sequence by the domain:

47.05 %

HMM information

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	29.5	29.5
Trusted cut-off	30.7	30.3
Noise cut-off	29.4	29.4

Model length:

29

Family (HMM) version:

14

Download:

download the raw HMM for this family

Species distribution

Sunburst
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How the sunburst is generated

The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.

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Unmapped species names

The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.

So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".

Sub-species

Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.

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For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.

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Interactive tree

For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.

We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.

Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.

We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.

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Interactions

There are 6 interactions for this family. More...

Cytochrom_B559 PsbJ PsbX Photo_RC Cytochrom_B559a PsbH

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 Cytochrom_B559 domain has been found. There are 42 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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Archea	Eukaryota
Bacteria	Other sequences
Viruses	Unclassified
Viroids	Unclassified sequence

Family: Cytochrom_B559 (PF00283)

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