Summary: Cytochrome B6-F complex Fe-S subunit

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Wikipedia: Rieske protein
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Rieske protein Edit Wikipedia article

Mitochondrial cytochrome bc1 complex. (PDB 1bcc)

Identifiers

Symbol

Rieske

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

Cytochrome B6-F complex Fe-S subunit, alpha helical transmembrane domain

crystal structure of cytochrome b6f complex from m.laminosus

Identifiers

Symbol

CytB6-F_Fe-S

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

Rieske proteins are iron-sulfur protein (ISP) components of cytochrome bc₁ complexes and cytochrome b₆f complexes which were first discovered and isolated by John S. Rieske and co-workers in 1964.^[1] It is a unique [2Fe-2S] cluster in that one of the two Fe atoms is coordinated by two histidine residues rather than two cysteine residues. They have since been found in plants, animals, and bacteria with widely ranging electron reduction potentials from -150 to +400 mV.^[2]

[edit] Biological function (in oxidative phosphorylation systems)

Ubiquinol-cytochrome-c reductase (also known as bc1 complex or complex III) is an enzyme complex of bacterial and mitochondrial oxidative phosphorylation systems. It catalyses the oxidoreduction of the mobile redox components ubiquinol and cytochrome c, generating an electrochemical potential, which is linked to ATP synthesis.^[3]^[4]

The complex consists of three subunits in most bacteria, and nine in mitochondria: both bacterial and mitochondrial complexes contain cytochrome b and cytochrome c1 subunits, and an iron-sulphur 'Rieske' subunit, which contains a high potential 2Fe-2S cluster.^[5] The mitochondrial form also includes six other subunits that do not possess redox centres. Plastoquinone-plastocyanin reductase (b6f complex), present in cyanobacteria and the chloroplasts of plants, catalyses the oxidoreduction of plastoquinol and cytochrome f. This complex, which is functionally similar to ubiquinol-cytochrome c reductase, comprises cytochrome b6, cytochrome f and Rieske subunits.^[6]

The Rieske subunit acts by binding either a ubiquinol or plastoquinol anion, transferring an electron to the 2Fe-2S cluster, then releasing the electron to the cytochrome c or cytochrome f haem iron.^[3]^[6] The reduction of the Rieske center increases the affinity of the subunit by several orders of magnitude, stabilizing the semiquinone radical at the Q(P) site.^[7] The Rieske domain has a [2Fe-2S] centre. Two conserved cysteines coordinate one Fe ion while the other Fe ion is coordinated by two conserved histidines. The 2Fe-2S cluster is bound in the highly conserved C-terminal region of the Rieske subunit.

[edit] Rieske protein family

The homologues of the Rieske proteins include ISP components of cytochrome b₆f complex, aromatic-ring-hydroxylating dioxygenases (phthalate dioxygenase, benzene, naphthalene and toluene 1,2-dioxygenases) and arsenite oxidase (EC 1.20.98.1). Comparison of amino acid sequences has revealed the following consensus sequence:

Cys-Xaa-His-(Xaa)_15â17-Cys-Xaa-Xaa-His

Rieske iron-sulfur center

[edit] 3D structure

The crystal structures of a number of Rieske proteins are known. The overall fold, comprising two subdomains, is dominated by antiparallel Î²-structure and contains variable numbers of Î±-helices. The smaller "cluster-binding" subdomains in mitochondrial and chloroplast proteins are virtually identical, whereas the large subdomains are substantially different in spite of a common folding topology. The [Fe₂S₂] cluster-binding subdomains have the topology of an incomplete antiparallel Î²-barrel. One iron atom of the Rieske [Fe₂S₂] cluster in the domain is coordinated by two cysteine residues and the other is coordinated by two histidine residues through the N^Î´ atoms. The ligands coordinating the cluster originate from two loops; each loop contributes one Cys and one His.

[edit] Subfamilies

[edit] Human proteins containing this domain

AIFM3; RFESD; UQCRFS1;

[edit] References

^ Rieske JS, Maclennan DH, Coleman, R (1964). "Isolation and properties of an iron-protein from the (reduced coenzyme Q)-cytochrome C reductase complex of the respiratory chain". Biochem. Biophys. Res. Commun. 15 (4): 338â344. doi:10.1016/0006-291X(64)90171-8.
^ Brown, E.N. and Friemann, R. and Karlsson, A. and Parales, J.V. and Couture, M.M. and Eltis, L.D. and Ramaswamy, S. (2008). "Determining Rieske cluster reduction potentials". J.Biol.Inorg.Chem. 13 (8): 1301â1313. doi:10.1007/s00775-008-0413-4. PMID 18719951.
^ ^a ^b Harnisch U, Weiss H, Sebald W (May 1985). "The primary structure of the iron-sulfur subunit of ubiquinol-cytochrome c reductase from Neurospora, determined by cDNA and gene sequencing". Eur. J. Biochem. 149 (1): 95â9. doi:10.1111/j.1432-1033.1985.tb08898.x. PMID 2986972.
^ Gabellini N, Sebald W (February 1986). "Nucleotide sequence and transcription of the fbc operon from Rhodopseudomonas sphaeroides. Evaluation of the deduced amino acid sequences of the FeS protein, cytochrome b and cytochrome c1". Eur. J. Biochem. 154 (3): 569â79. doi:10.1111/j.1432-1033.1986.tb09437.x. PMID 3004982.
^ Kurowski B, Ludwig B (October 1987). "The genes of the Paracoccus denitrificans bc1 complex. Nucleotide sequence and homologies between bacterial and mitochondrial subunits". J. Biol. Chem. 262 (28): 13805â11. PMID 2820981.
^ ^a ^b MadueÃ±o F, Napier JA, Cejudo FJ, Gray JC (October 1992). "Import and processing of the precursor of the Rieske FeS protein of tobacco chloroplasts". Plant Mol. Biol. 20 (2): 289â99. doi:10.1007/BF00014496. PMID 1391772.
^ Link TA (July 1997). "The role of the 'Rieske' iron sulfur protein in the hydroquinone oxidation (Q(P)) site of the cytochrome bc1 complex. The 'proton-gated affinity change' mechanism". FEBS Lett. 412 (2): 257â64. doi:10.1016/S0014-5793(97)00772-2. PMID 9256231.

[edit] Further reading

Iwata S, Saynovits M, Link TA, Michel H (May 1996). "Structure of a water soluble fragment of the 'Rieske' iron-sulfur protein of the bovine heart mitochondrial cytochrome bc1 complex determined by MAD phasing at 1.5 A resolution". Structure 4 (5): 567â79. doi:10.1016/S0969-2126(96)00062-7. PMID 8736555.
Huang JT, Struck F, Matzinger DF, Levings CS (December 1991). "Functional analysis in yeast of cDNA coding for the mitochondrial Rieske iron-sulfur protein of higher plants". Proc. Natl. Acad. Sci. U.S.A. 88 (23): 10716â20. doi:10.1073/pnas.88.23.10716. PMC 53001. PMID 1961737. //www.ncbi.nlm.nih.gov/pmc/articles/PMC53001/.
Brandt U, Yu L, Yu CA, Trumpower BL (April 1993). "The mitochondrial targeting presequence of the Rieske iron-sulfur protein is processed in a single step after insertion into the cytochrome bc1 complex in mammals and retained as a subunit in the complex". J. Biol. Chem. 268 (12): 8387â90. PMID 8386158.
Ferraro, D.J., Gakhar, L. and Ramaswamy, S. (2005). "Rieske business: structure-function of Rieske non-heme oxygenases". Biochem. Biophys. Res. Commun. 338 (1): 175â190. doi:10.1016/j.bbrc.2005.08.222. PMID 16168954.
Mason, J.R. and Cammack, R. (1992). "The electron-transport proteins of hydroxylating bacterial dioxygenases". Annu. Rev. Microbiol. 46: 277â305. doi:10.1146/annurev.mi.46.100192.001425. PMID 1444257.
Schmidt, C.L. (2004). "Rieske iron-sulfur proteins from extremophilic organisms". J. Bioenerg. Biomembr. 36 (1): 107â113. doi:10.1023/B:JOBB.0000019602.96578.78. PMID 15168614.
Schneider, D. and Schmidt, C.L. (2005). "Multiple Rieske proteins in prokaryotes: where and why?". Biochim. Biophys. Acta 1710 (1): 1â12. doi:10.1016/j.bbabio.2005.09.003. PMID 16271700.
Brown, E.N. and Friemann, R. and Karlsson, A. and Parales, J.V. and Couture, M.M. and Eltis, L.D. and Ramaswamy, S. (2008). "Determining Rieske cluster reduction potentials". J.Biol.Inorg.Chem. 13 (8): 1301â1313. doi:10.1007/s00775-008-0413-4. PMID 18719951.

[edit] External links

PDB 1RIE - X-ray structure of Rieske protein (water-soluble fragment) of the bovine mitochondrial cytochrome bc₁ complex
PDB 1RFS - X-ray structure of Rieske protein (water-soluble fragment) of the spinach chloroplast cytochrome b₆ fcomplex
PDB 1FQT - X-ray structure of Rieske-type ferredoxin associated with biphenyl dioxygenase from Burkholderia cepacia
PDB 1G8J - X-ray structure of Rieske subunit of arsenite oxidase from Alcaligenes faecalis
PDB 2I7F - X-ray structure of the Sphingomonas yanoikuyae B1 Rieske ferredoxin
PDB 2QPZ - X-ray structure of the Pseudomonas Naphthalene 1,2-dioxygenase Rieske ferredoxin
IPR005806 - InterPro entry for Rieske [2Fe-2S] region

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Cytochrome B6-F complex Fe-S subunit Provide feedback

The cytochrome B6-F complex mediates electron transfer between photosystem II (PSII) and photosystem I (PSI), cyclic electron flow around PSI, and state transitions. This domain corresponds to the alpha helical transmembrane domain of the cytochrome B6-F complex iron-sulphur subunit.

Literature references

Stroebel D, Choquet Y, Popot JL, Picot D; , Nature. 2003;426:413-418.: An atypical haem in the cytochrome b(6)f complex. PUBMED:14647374 EPMC:14647374

Internal database links

Similarity to PfamA using HHSearch:

UCR_Fe-S_N

External database links

PANDIT:	PF08802
Pseudofam:	PF08802
SYSTERS:	CytB6-F_Fe-S

This tab holds annotation information from the InterPro database.

InterPro entry IPR014909

The cytochrome b6-f complex mediates electron transfer between photosystem II (PSII) and photosystem I (PSI), cyclic electron flow around PSI, and state transitions. The cytochrome b6-f complex has 4 large subunits, these are: cytochrome b6, subunit IV (17 kDa polypeptide, PetD), cytochrome f and the Rieske protein, while the 4 small subunits are: PetG, PetL, PetM and PetN. The complex functions as a dimer.

This protein corresponds to the alpha helical transmembrane domain of the cytochrome b6-f complex Rieske iron-sulphur subunit.

Gene Ontology

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

Cellular component	thylakoid membrane (GO:0042651)
Molecular function	plastoquinol--plastocyanin reductase activity (GO:0009496)
Molecular function	2 iron, 2 sulfur cluster binding (GO:0051537)
Biological process	oxidation-reduction process (GO:0055114)

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

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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 (19)	Full (215)	Representative proteomes				NCBI (203)	Meta (111)
	Seed (19)	Full (215)	RP15 (20)	RP35 (54)	RP55 (73)	RP75 (83)	NCBI (203)	Meta (111)
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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 (19)	Full (215)	Representative proteomes				NCBI (203)	Meta (111)
	Seed (19)	Full (215)	RP15 (20)	RP35 (54)	RP55 (73)	RP75 (83)	NCBI (203)	Meta (111)
Alignment:
Format:
Order:	Tree Alphabetical
Sequence:	Inserts lower case All upper case
Gaps:
Download/view:	Download View

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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 (19)	Full (215)	Representative proteomes				NCBI (203)	Meta (111)
	Seed (19)	Full (215)	RP15 (20)	RP35 (54)	RP55 (73)	RP75 (83)	NCBI (203)	Meta (111)
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.

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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

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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

Seed source:

pdb_1q90

Previous IDs:

none

Type:

Domain

Author:

Mistry J

Number in seed:

19

Number in full:

215

Average length of the domain:

37.50 aa

Average identity of full alignment:

46 %

Average coverage of the sequence by the domain:

19.78 %

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	23.3	23.3
Trusted cut-off	23.5	23.8
Noise cut-off	23.2	23.1

Model length:

39

Family (HMM) version:

5

Download:

download the raw HMM for this family

Species distribution

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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.

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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 4 interactions for this family. More...

PetL Cytochrom_B_N Apocytochr_F_C Rieske

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 CytB6-F_Fe-S domain has been found. There are 9 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: CytB6-F_Fe-S (PF08802)

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