Summary: 2Fe-2S iron-sulfur cluster binding domain
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Ferredoxin Edit Wikipedia article
Ferredoxins (from Latin ferrum: iron + redox, often abbreviated "fd") are ironâ€“sulfur proteins that mediate electron transfer in a range of metabolic reactions. The term "ferredoxin" was coined by D.C. Wharton of the DuPont Co. and applied to the "iron protein" first purified in 1962 by Mortenson, Valentine, and Carnahan from the anaerobic bacterium Clostridium pasteurianum.
Another redox protein, isolated from spinach chloroplasts, was termed "chloroplast ferredoxin". The chloroplast ferredoxin is involved in both cyclic and non-cyclic photophosphorylation reactions of photosynthesis. In non-cyclic photophosphorylation, ferredoxin is the last electron acceptor thus reducing the enzyme NADP+ reductase. It accepts electrons produced from sunlight-excited chlorophyll and transfers them to the enzyme ferredoxin: NADP+ oxidoreductase EC 18.104.22.168.
Ferredoxins are small proteins containing iron and sulfur atoms organized as ironâ€“sulfur clusters. These biological "capacitors" can accept or discharge electrons, with the effect of a change in the oxidation state of the iron atoms between +2 and +3. In this way, ferredoxin acts as an electron transfer agent in biological redox reactions.
Ferredoxins can be classified according to the nature of their ironâ€“sulfur clusters and by sequence similarity.
- 1 Fe2S2 ferredoxins
- 2 Fe4S4 and Fe3S4 ferredoxins
- 3 Human proteins from ferredoxin family
- 4 References
- 5 Further reading
- 6 External links
|2Fe-2S iron-sulfur cluster binding domain|
Structural representation of an Fe2S2 ferredoxin.
|SCOPe||3fxc / SUPFAM|
Members of the 2Feâ€“2S ferredoxin superfamily (InterPro: IPR036010) have a general core structure consisting of beta(2)-alpha-beta(2), which includes putidaredoxin, terpredoxin, and adrenodoxin. They are proteins of around one hundred amino acids with four conserved cysteine residues to which the 2Feâ€“2S cluster is ligated. This conserved region is also found as a domain in various metabolic enzymes and in multidomain proteins, such as aldehyde oxidoreductase (N-terminal), xanthine oxidase (N-terminal), phthalate dioxygenase reductase (C-terminal), succinate dehydrogenase ironâ€“sulphur protein (N-terminal), and methane monooxygenase reductase (N-terminal).
One group of ferredoxins, originally found in chloroplast membranes, has been termed "chloroplast-type" or "plant-type" (InterPro: IPR010241). Its active center is a [Fe2S2] cluster, where the iron atoms are tetrahedrally coordinated both by inorganic sulfur atoms and by sulfurs of four conserved cysteine (Cys) residues.
In chloroplasts, Fe2S2 ferredoxins function as electron carriers in the photosynthetic electron transport chain and as electron donors to various cellular proteins, such as glutamate synthase, nitrite reductase and sulfite reductase. In hydroxylating bacterial dioxygenase systems, they serve as intermediate electron-transfer carriers between reductase flavoproteins and oxygenase.
The Fe2S2 ferredoxin from Clostridium pasteurianum (Cp2FeFd; nitrogenase has been revealed. Homologous ferredoxins from Azotobacter vinelandii (Av2FeFdI; ) and Aquifex aeolicus (AaFd; ) have been characterized. The crystal structure of AaFd has been solved. AaFd exists as a dimer. The structure of AaFd monomer is different from other Fe2S2 ferredoxins. The fold belongs to the Î±+Î² class, with first four Î²-strands and two Î±-helices adopting a variant of the thioredoxin fold. UniProt categorizes these as the "2Fe2S Shethna-type ferredoxin" family.) has been recognized as distinct protein family on the basis of its amino acid sequence, spectroscopic properties of its ironâ€“sulfur cluster and the unique ligand swapping ability of two cysteine ligands to the [Fe2S2] cluster. Although the physiological role of this ferredoxin remains unclear, a strong and specific interaction of Cp2FeFd with the molybdenum-iron protein of
Crystal structure of human ferredoxin-1 (FDX1).
|Locus||Chr. 11 q22.3|
Adrenodoxin (adrenal ferredoxin; InterPro: IPR001055), putidaredoxin, and terpredoxin make up a family of soluble Fe2S2 proteins that act as single electron carriers, mainly found in eukaryotic mitochondria and Proteobacteria. The human variant of adrenodoxin is referred to as ferredoxin-1 and ferredoxin-2. In mitochondrial monooxygenase systems, adrenodoxin transfers an electron from NADPH:adrenodoxin reductase to membrane-bound cytochrome P450. In bacteria, putidaredoxin and terpredoxin transfer electrons between corresponding NADH-dependent ferredoxin reductases and soluble P450s. The exact functions of other members of this family are not known, although Escherichia coli Fdx is shown to be involved in biogenesis of Feâ€“S clusters. Despite low sequence similarity between adrenodoxin-type and plant-type ferredoxins, the two classes have a similar folding topology.
Ferredoxin-1 in humans participates in the synthesis of thyroid hormones. It also transfers electrons from adrenodoxin reductase to CYP11A1, a CYP450 enzyme responsible for cholesterol side chain cleavage. FDX-1 has the capability to bind to metals and proteins. Ferredoxin-2 participates in heme A and ironâ€“sulphur protein synthesis.
Fe4S4 and Fe3S4 ferredoxins
The [Fe4S4] ferredoxins may be further subdivided into low-potential (bacterial-type) and high-potential (HiPIP) ferredoxins.
Low- and high-potential ferredoxins are related by the following redox scheme:
The formal oxidation numbers of the iron ions can be [2Fe3+, 2Fe2+] or [1Fe3+, 3Fe2+] in low-potential ferredoxins. The oxidation numbers of the iron ions in high-potential ferredoxins can be [3Fe3+, 1Fe2+] or [2Fe3+, 2Fe2+].
|3Fe-4S binding domain|
Structural representation of an Fe3S4 ferredoxin.
|SCOPe||5fd1 / SUPFAM|
A group of Fe4S4 ferredoxins, originally found in bacteria, has been termed "bacterial-type". Bacterial-type ferredoxins may in turn be subdivided into further groups, based on their sequence properties. Most contain at least one conserved domain, including four cysteine residues that bind to a [Fe4S4] cluster. In Pyrococcus furiosus Fe4S4 ferredoxin, one of the conserved Cys residues is substituted with aspartic acid.
During the evolution of bacterial-type ferredoxins, intrasequence gene duplication, transposition and fusion events occurred, resulting in the appearance of proteins with multiple ironâ€“sulfur centers. In some bacterial ferredoxins, one of the duplicated domains has lost one or more of the four conserved Cys residues. These domains have either lost their ironâ€“sulfur binding property or bind to a [Fe3S4] cluster instead of a [Fe4S4] cluster and dicluster-type.
3-D structures are known for a number of monocluster and dicluster bacterial-type ferredoxins. The fold belongs to the Î±+Î² class, with 2-7 Î±-helices and four Î²-strands forming a barrel-like structure, and an extruded loop containing three "proximal" Cys ligands of the ironâ€“sulfur cluster.
High-potential ironâ€“sulfur proteins
High potential ironâ€“sulfur proteins (HiPIPs) form a unique family of Fe4S4 ferredoxins that function in anaerobic electron transport chains. Some HiPIPs have a redox potential higher than any other known ironâ€“sulfur protein (e.g., HiPIP from Rhodopila globiformis has a redox potential of ca. 450 mV). Several HiPIPs have so far been characterized structurally, their folds belonging to the Î±+Î² class. As in other bacterial ferredoxins, the [Fe4S4] unit forms a cubane-type cluster and is ligated to the protein via four Cys residues.
Human proteins from ferredoxin family
- Mortenson LE, Valentine RC, Carnahan JE (June 1962). "An electron transport factor from Clostridium pasteurianum". Biochemical and Biophysical Research Communications. 7 (6): 448â€“52. doi:10.1016/0006-291X(62)90333-9. PMID 14476372.
- Valentine RC (December 1964). "BACTERIAL FERREDOXIN". Bacteriological Reviews. 28: 497â€“517. PMC 441251. PMID 14244728.
- Tagawa K, Arnon DI (August 1962). "Ferredoxins as electron carriers in photosynthesis and in the biological production and consumption of hydrogen gas". Nature. 195 (4841): 537â€“43. Bibcode:1962Natur.195..537T. doi:10.1038/195537a0. PMID 14039612.
- Armengaud J, Sainz G, Jouanneau Y, Sieker LC (February 2001). "Crystallization and preliminary X-ray diffraction analysis of a [2Fe-2S] ferredoxin (FdVI) from Rhodobacter capsulatus". Acta Crystallographica Section D. 57 (Pt 2): 301â€“3. doi:10.1107/S0907444900017832. PMID 11173487.
- Sevrioukova IF (April 2005). "Redox-dependent structural reorganization in putidaredoxin, a vertebrate-type [2Fe-2S] ferredoxin from Pseudomonas putida". Journal of Molecular Biology. 347 (3): 607â€“21. doi:10.1016/j.jmb.2005.01.047. PMID 15755454.
- Mo H, Pochapsky SS, Pochapsky TC (April 1999). "A model for the solution structure of oxidized terpredoxin, a Fe2S2 ferredoxin from Pseudomonas". Biochemistry. 38 (17): 5666â€“75. CiteSeerX 10.1.1.34.4745. doi:10.1021/bi983063r. PMID 10220356.
- Beilke D, Weiss R, LÃ¶hr F, Pristovsek P, Hannemann F, Bernhardt R, RÃ¼terjans H (June 2002). "A new electron transport mechanism in mitochondrial steroid hydroxylase systems based on structural changes upon the reduction of adrenodoxin". Biochemistry. 41 (25): 7969â€“78. doi:10.1021/bi0160361. PMID 12069587.
- Yeh AP, Ambroggio XI, Andrade SL, Einsle O, Chatelet C, Meyer J, Rees DC (September 2002). "High resolution crystal structures of the wild type and Cys-55-->Ser and Cys-59-->Ser variants of the thioredoxin-like [2Fe-2S] ferredoxin from Aquifex aeolicus". The Journal of Biological Chemistry. 277 (37): 34499â€“507. doi:10.1074/jbc.M205096200. PMID 12089152.
- family:"2fe2s shethna type ferredoxin family"
- doi:10.2210/pdb3p1m/pdb. ; Chaikuad A, Johansson, C, Krojer, T, Yue, WW, Phillips, C, Bray, JE, Pike, ACW, Muniz, JRC, Vollmar, M, Weigelt, J, Arrowsmith, CH, Edwards, AM, Bountra, C, Kavanagh, K, Oppermann, U (2010). "Crystal structure of human ferredoxin-1 (FDX1) in complex with iron-sulfur cluster". To be Published.
- Peterson JA, Lorence MC, Amarneh B (April 1990). "Putidaredoxin reductase and putidaredoxin. Cloning, sequence determination, and heterologous expression of the proteins". The Journal of Biological Chemistry. 265 (11): 6066â€“73. PMID 2180940.
- Peterson JA, Lu JY, Geisselsoder J, Graham-Lorence S, Carmona C, Witney F, Lorence MC (July 1992). "Cytochrome P-450terp. Isolation and purification of the protein and cloning and sequencing of its operon". The Journal of Biological Chemistry. 267 (20): 14193â€“203. PMID 1629218.
- Tokumoto U, Takahashi Y (July 2001). "Genetic analysis of the isc operon in Escherichia coli involved in the biogenesis of cellular iron-sulfur proteins". Journal of Biochemistry. 130 (1): 63â€“71. doi:10.1093/oxfordjournals.jbchem.a002963. PMID 11432781.
- "Entrez Gene: FDX1 ferredoxin 1".
- "FDX2 ferredoxin 2 [Homo sapiens (human)] - Gene - NCBI". www.ncbi.nlm.nih.gov. Retrieved 8 April 2019.
- Fukuyama K, Matsubara H, Tsukihara T, Katsube Y (November 1989). "Structure of [4Fe-4S] ferredoxin from Bacillus thermoproteolyticus refined at 2.3 A resolution. Structural comparisons of bacterial ferredoxins". Journal of Molecular Biology. 210 (2): 383â€“98. doi:10.1016/0022-2836(89)90338-0. PMID 2600971.
- DuÃ©e ED, Fanchon E, Vicat J, Sieker LC, Meyer J, Moulis JM (November 1994). "Refined crystal structure of the 2[4Fe-4S] ferredoxin from Clostridium acidurici at 1.84 A resolution". Journal of Molecular Biology. 243 (4): 683â€“95. doi:10.1016/0022-2836(94)90041-8. PMID 7966291.
- Bruschi M, Guerlesquin F (1988). "Structure, function and evolution of bacterial ferredoxins". FEMS Microbiology Reviews. 4 (2): 155â€“75. doi:10.1111/j.1574-6968.1988.tb02741.x. PMID 3078742.
- Ciurli S, Musiani F (2005). "High potential iron-sulfur proteins and their role as soluble electron carriers in bacterial photosynthesis: tale of a discovery". Photosynthesis Research. 85 (1): 115â€“31. doi:10.1007/s11120-004-6556-4. PMID 15977063.
- Fukuyama K (2004). "Structure and function of plant-type ferredoxins". Photosynthesis Research. 81 (3): 289â€“301. doi:10.1023/B:PRES.0000036882.19322.0a. PMID 16034533.
- Grinberg AV, Hannemann F, Schiffler B, MÃ¼ller J, Heinemann U, Bernhardt R (September 2000). "Adrenodoxin: structure, stability, and electron transfer properties". Proteins. 40 (4): 590â€“612. doi:10.1002/1097-0134(20000901)40:4<590::AID-PROT50>3.0.CO;2-P. PMID 10899784.
- Holden HM, Jacobson BL, Hurley JK, Tollin G, Oh BH, Skjeldal L, Chae YK, Cheng H, Xia B, Markley JL (February 1994). "Structure-function studies of [2Fe-2S] ferredoxins". Journal of Bioenergetics and Biomembranes. 26 (1): 67â€“88. doi:10.1007/BF00763220. PMID 8027024.
- Meyer J (November 2001). "Ferredoxins of the third kind". FEBS Letters. 509 (1): 1â€“5. doi:10.1016/S0014-5793(01)03049-6. PMID 11734195.
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.
2Fe-2S iron-sulfur cluster binding domain Provide feedback
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Internal database links
|SCOOP:||DHODB_Fe-S_bind Fer2_2 Fer2_3 Fer2_4 NAD_binding_6 NADH-G_4Fe-4S_3|
|Similarity to PfamA using HHSearch:||Fer2_3 Fer2_4|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR001041
Ferredoxins are small, acidic, electron transfer proteins that are ubiquitous in biological redox systems. They have either 4Fe-4S, 3Fe-4S, or 2Fe-2S cluster. Among them, ferredoxin with one 2Fe-2S cluster per molecule are present in plants, animals, and bacteria, and form a distinct Ferredoxin family [PUBMED:2065785]. They are proteins of around one hundred amino acids with four conserved cysteine residues to which the 2Fe-2S cluster is ligated. This conserved region is also found as a domain in various metabolic enzymes.
Several structures of the 2Fe-2S ferredoxin-type domain have been determined [PUBMED:8586613]. The domain is classified as a beta-grasp, which is characterised as having a beta-sheet comprised of four beta-strands and one alpha-helix flanking the sheet. The two Fe atoms are coordinated tetrahedrally by the two inorganic S atoms and four cysteinyl S atoms.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||electron transfer activity (GO:0009055)|
|iron-sulfur cluster binding (GO:0051536)|
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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The 2Fe-2S ferredoxin family have a general core structure consisting of beta(2)-alpha-beta(2) which abeta-grasp type fold. The domani is around one hundred amino acids with four conserved cysteine residues to which the 2Fe-2S cluster is ligated.
The clan contains the following 5 members:DHODB_Fe-S_bind Fer2 Fer2_2 Fer2_3 Fer2_4
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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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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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.
|Number in seed:||206|
|Number in full:||39911|
|Average length of the domain:||75.20 aa|
|Average identity of full alignment:||20 %|
|Average coverage of the sequence by the domain:||23.35 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||27|
|Download:||download the raw HMM for this family|
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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the More....
This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.
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.
In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:
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Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.
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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".
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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The tree shows the occurrence of this domain across different species. More...
We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.
Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.
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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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There are 24 interactions for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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 Fer2 domain has been found. There are 361 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 sequence.
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