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318  structures 3458  species 10  interactions 13057  sequences 95  architectures

Family: Rieske (PF00355)

Summary: Rieske [2Fe-2S] domain

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Rieske protein". More...

Rieske protein Edit Wikipedia article

1bcc opm.png
Identifiers
Symbol Rieske
Pfam PF00355
InterPro IPR005806
PROSITE PDOC00177
SCOP 1rie
SUPERFAMILY 1rie
TCDB 3.E.2
OPM protein 1q90
Cytochrome B6-F complex Fe-S subunit, alpha helical transmembrane domain
PDB 1vf5 EBI.jpg
crystal structure of cytochrome b6f complex from m.laminosus
Identifiers
Symbol CytB6-F_Fe-S
Pfam PF08802
InterPro IPR014909

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]

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 difference, 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.

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)15–17-Cys-Xaa-Xaa-His
Rieske iron-sulfur center

3D structure

The crystal structures of a number of Rieske proteins are known. The overall fold, comprising two subdomains, is dominated by antiparallel β-structure and contains variable numbers of α-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 β-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 Nδ atoms. The ligands coordinating the cluster originate from two loops; each loop contributes one Cys and one His.

Subfamilies

Human proteins containing this domain

AIFM3; RFESD; UQCRFS1;

References

  1. ^ 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): 338–344. doi:10.1016/0006-291X(64)90171-8. 
  2. ^ 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): 1301–1313. doi:10.1007/s00775-008-0413-4. PMID 18719951. 
  3. ^ 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): 95–9. doi:10.1111/j.1432-1033.1985.tb08898.x. PMID 2986972. 
  4. ^ 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): 569–79. doi:10.1111/j.1432-1033.1986.tb09437.x. PMID 3004982. 
  5. ^ 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): 13805–11. PMID 2820981. 
  6. ^ a b Madueño 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): 289–99. doi:10.1007/BF00014496. PMID 1391772. 
  7. ^ 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): 257–64. doi:10.1016/S0014-5793(97)00772-2. PMID 9256231. 

Further reading

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.

Rieske [2Fe-2S] domain Provide feedback

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. In hyperthermophilic archaea there is a SKTPCX(2-3)C motif at the C-terminus. The cysteines in this motif form a disulphide bridge, which stabilises the protein [4].

Literature references

  1. Iwata S, Saynovits M, Link TA, Michel H , Structure 1996;4:567-579.: 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. PUBMED:8736555 EPMC:8736555

  2. Huang JT, Struck F, Matzinger DF, Levings CS; , Proc Natl Acad Sci U S A 1991;88:10716-10720.: Functional analysis in yeast of cDNA coding for the mitochondrial Rieske iron-sulfur protein of higher plants. PUBMED:1961737 EPMC:1961737

  3. Brandt U, Yu L, Yu CA, Trumpower BL; , J Biol Chem 1993;268:8387-8390.: 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. PUBMED:8386158 EPMC:8386158

  4. Botelho HM, Leal SS, Veith A, Prosinecki V, Bauer C, Frohlich R, Kletzin A, Gomes CM;, J Biol Inorg Chem. 2010;15:271-281.: Role of a novel disulfide bridge within the all-beta fold of soluble Rieske proteins. PUBMED:19862563 EPMC:19862563


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR017941

There are multiple types of iron-sulphur clusters which are grouped into three main categories based on their atomic content: [2Fe-2S], [3Fe-4S], [4Fe-4S] (see PROSITEDOC), and other hybrid or mixed metal types. Two general types of [2Fe-2S] clusters are known and they differ in their coordinating residues. The ferredoxin-type [2Fe-2S] clusters are coordinated to the protein by four cysteine residues (see PROSITEDOC). The Rieske-type [2Fe-2S] cluster is coordinated to its protein by two cysteine residues and two histidine residues [PUBMED:16168954, PUBMED:16271700].

The structure of several Rieske domains has been solved [PUBMED:8736555]. It contains three layers of antiparallel beta sheets forming two beta sandwiches. Both beta sandwiches share the central sheet 2. The metal-binding site is at the top of the beta sandwich formed by the sheets 2 and 3. The Fe1 iron of the Rieske cluster is coordinated by two cysteines while the other iron Fe2 is coordinated by two histidines. Two inorganic sulphide ions bridge the two iron ions forming a flat, rhombic cluster.

Rieske-type iron-sulphur clusters are common to electron transfer chains of mitochondria and chloroplast and to non-haem iron oxygenase systems:

  • The Rieske protein of the Ubiquinol-cytochrome c reductase (EC) (also known as the bc1 complex or complex III), a complex of the electron transport chains of mitochondria and of some aerobic prokaryotes; it catalyses the oxidoreduction of ubiquinol and cytochrome c.
  • The Rieske protein of chloroplastic plastoquinone-plastocyanin reductase (EC) (also known as the b6f complex). It is functionally similar to the bc1 complex and catalyses the oxidoreduction of plastoquinol and cytochrome f.
  • Bacterial naphthalene 1,2-dioxygenase subunit alpha, a component of the naphthalene dioxygenase (NDO) multicomponent enzyme system which catalyses the incorporation of both atoms of molecular oxygen into naphthalene to form cis-naphthalene dihydrodiol.
  • Bacterial 3-phenylpropionate dioxygenase ferredoxin subunit.
  • Bacterial toluene monoxygenase.
  • Bacterial biphenyl dioxygenase.

Gene Ontology

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

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 ISP-domain (CL0516), which has the following description:

This superfamily is characterised by Rieske Iron-sulfur families of the [2Fe-2S] type including NADH-nitrite reductase small subunit NirD proteins. This domain has an all-beta rubredoxin-like fold.

The clan contains the following 2 members:

Rieske Rieske_2

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...

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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
(146)
Full
(13057)
Representative proteomes NCBI
(11916)
Meta
(6165)
RP15
(1183)
RP35
(2635)
RP55
(3671)
RP75
(4393)
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Format an alignment

  Seed
(146)
Full
(13057)
Representative proteomes NCBI
(11916)
Meta
(6165)
RP15
(1183)
RP35
(2635)
RP55
(3671)
RP75
(4393)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(146)
Full
(13057)
Representative proteomes NCBI
(11916)
Meta
(6165)
RP15
(1183)
RP35
(2635)
RP55
(3671)
RP75
(4393)
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

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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 View help on the curation process

Seed source: Prosite & Pfam-B_31 (release 4.1)
Previous IDs: none
Type: Domain
Author: Finn RD, Griffiths-Jones SR, Eberhardt R
Number in seed: 146
Number in full: 13057
Average length of the domain: 94.20 aa
Average identity of full alignment: 19 %
Average coverage of the sequence by the domain: 31.33 %

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 20.3 20.3
Trusted cut-off 20.3 20.3
Noise cut-off 20.2 20.2
Model length: 97
Family (HMM) version: 21
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 10 interactions for this family. More...

Molydop_binding CytB6-F_Fe-S Rieske Cytochrom_B_C Cytochrom_C1 Ring_hydroxyl_B Molybdopterin Pyr_redox_2 Cytochrom_B_N Ring_hydroxyl_A

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 Rieske domain has been found. There are 318 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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