This is the Wikipedia entry entitled "Rubredoxin". More...
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Rubredoxin Edit Wikipedia article
rubredoxin domain ii from pseudomonas oleovorans
Rubredoxins are a class of low-molecular-weight iron-containing proteins found in sulfur-metabolizing bacteria and archaea. Sometimes rubredoxins are classified as iron-sulfur proteins; however, in contrast to iron-sulfur proteins, rubredoxins do not contain inorganic sulfide. Like cytochromes, ferredoxins and Rieske proteins, rubredoxins participate in electron transfer in biological systems.
The 3-D structures of a number of rubredoxins have been solved. The fold belongs to the α+β class, with 2 α-helices and 2-3 β-strands. Rubredoxin active site contains an iron ion which is coordinated by the sulfurs of four conserved cysteine residues forming an almost regular tetrahedron. This is sometimes denoted as a [1Fe-0S] or an Fe1S0 system, in analogy to the nomenclature for iron-sulfur proteins.
Rubredoxins perform one-electron transfer processes. The central iron atom changes between the +2 and +3 oxidation states. In both oxidation states, the metal remains high spin, which helps to minimize structural changes. The reduction potential of a rubredoxin is typically in the range +50 mV to -50 mV.
This iron-sulphur protein is an electron carrier, and it is easy to distinguish its metallic centre changes: the oxidized state is reddish (due to a ligand metal charge transfer), while the reduced state is colourless (because the electron transition has an energy of the infrared level, which is imperceptible for the human eye).
Rubredoxin in some biochemical reactions
- (+)-bornane-2,5-dione + reduced rubredoxin + O2 = 5-oxo-1,2-campholide + oxidized rubredoxin + H2O
- octane + reduced rubredoxin + O2 = 1-octanol + oxidized rubredoxin + H2O
- reduced rubredoxin + superoxide + 2 H+ = rubredoxin + H2O2
- reduced rubredoxin + NAD+ = oxidized rubredoxin + NADH + H+
- reduced rubredoxin + NAD(P)+ = oxidized rubredoxin + NAD(P)H + H+
- Stephen J. Lippard, Jeremy M. Berg, Principles of Bioinorganic Chemistry, University Science Books, 1994, ISBN 0-935702-72-5
- J.J.R. Fraústo da Silva and R.J.P. Williams, The biological chemistry of the elements: The inorganic chemistry of life, 2nd Edition, Oxford University Press, 2001, ISBN 0-19-850848-4
- PDB 1IRO - X-ray structure of rubredoxin from Clostridium pasteurianum
- PDB 1VCX - neutron diffraction structure of rubredoxin from Pyrococcus furiosus
- IPR001052 - InterPro entry for rubredoxin
- A Little Iron-Sulfur Protein
|This protein-related article is a stub. You can help Wikipedia by expanding it.|
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Internal database links
|Similarity to PfamA using HHSearch:||TF_Zn_Ribbon|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR024935
Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [PUBMED:2244884, PUBMED:1992166], sometimes replacing ferredoxin as an electron carrier [PUBMED:7726577]. Rubredoxins possess a 45- to 55-residue domain containing one iron atom tetrahedrally coordinated to four cysteinyl residues. Structural analysis of the domains have shown them to be folded into a short three-stranded antiparallel beta-sheet and a number of loops [PUBMED:3441010, PUBMED:1303768, PUBMED:7830611, PUBMED:8646540].This entry represents the rubredoxin domain.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||iron ion binding (GO:0005506)|
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
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EGFdomains, and finally a single
- the UniProt description of the protein sequence
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The Rubredoxin clan is comprised of three families:Rubredoxin, COX5B and desulforedoxin.Rubredoxin domains are small domains (5-6 kDa) and bind one iron atom tetrahedrally bound by four cysteine residues.Similar, desulforedoxin domains are small (4 kDa), but usually form homodimers. Each monomer binds one iron atom, but in a distorted tetrahedral arrangement. COX5B domains are membrane-anchored rubredoxin-like domains. The domain in the Rubredoxin clan are usually comprised of 2 alpha helixes and 2-3 beta strands.
The clan contains the following 4 members:COX5B Desulfoferrod_N Rubredoxin zf-CHCC
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Curation and family details
|Number in seed:||43|
|Number in full:||2943|
|Average length of the domain:||46.10 aa|
|Average identity of full alignment:||48 %|
|Average coverage of the sequence by the domain:||23.38 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||15|
|Download:||download the raw HMM for this family|
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There are 3 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 Rubredoxin domain has been found. There are 86 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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