Summary: Rubredoxin
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Rubredoxin Edit Wikipedia article
| Rubredoxin | |||||||||
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rubredoxin domain ii from pseudomonas oleovorans
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| Identifiers | |||||||||
| Symbol | Rubredoxin | ||||||||
| Pfam | PF00301 | ||||||||
| Pfam clan | CL0045 | ||||||||
| InterPro | IPR004039 | ||||||||
| PROSITE | PDOC00179 | ||||||||
| SCOP | 7rxn | ||||||||
| SUPERFAMILY | 7rxn | ||||||||
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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.
Contents
Structure
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. While the vast majority of rubredoxins are soluble, there exists a membrane-bound rubredoxin, referred to as rubredoxin A, in oxygenic photoautotrophs.[1]
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 to the human eye).
Rubredoxin in some biochemical reactions
EC 1.14.15.2 camphor 1,2-monooxygenase [(+)-camphor,reduced-rubredoxin:oxygen oxidoreductase (1,2-lactonizing)]
- (+)-bornane-2,5-dione + reduced rubredoxin + O2 = 5-oxo-1,2-campholide + oxidized rubredoxin + H2O
EC 1.14.15.3 alkane 1-monooxygenase (alkane,reduced-rubredoxin:oxygen 1-oxidoreductase)
- octane + reduced rubredoxin + O2 = 1-octanol + oxidized rubredoxin + H2O
EC 1.15.1.2 superoxide reductase (rubredoxin:superoxide oxidoreductase)
- reduced rubredoxin + superoxide + 2 H+ = rubredoxin + H2O2
EC 1.18.1.1 rubredoxin—NAD+ reductase (rubredoxin:NAD+ oxidoreductase)
- reduced rubredoxin + NAD+ = oxidized rubredoxin + NADH + H+
EC 1.18.1.4 rubredoxin—NAD(P)+ reductase (rubredoxin:NAD(P)+ oxidoreductase)
- reduced rubredoxin + NAD(P)+ = oxidized rubredoxin + NAD(P)H + H+
See also
References
- ^ Calderon, R. H., García-Cerdán, J. G., Malnoë, A., Cook, R., Russell, J. J., Gaw, C., Dent, R. M., de Vitry, C. and Niyogi, K. K. (July 2013). "A Conserved Rubredoxin Is Necessary for Photosystem II Accumulation in Diverse Oxygenic Photoautotrophs". The Journal of Biological Chemistry. 288: 26688–26696. doi:10.1074/jbc.M113.487629. PMC 3772215
. PMID 23900844.
Further reading
- 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
External links
- PDB: 1IRO - X-ray structure of rubredoxin from Clostridium pasteurianum
- PDB: 1VCX - neutron diffraction structure of rubredoxin from Pyrococcus furiosus
- InterPro: IPR001052 - InterPro entry for rubredoxin
- A Little Iron-Sulfur Protein
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No Pfam abstract.
Internal database links
| SCOOP: | PHD_4 Zn-ribbon_8 |
| Similarity to PfamA using HHSearch: | PHD_4 |
External database links
| HOMSTRAD: | rub |
| PROSITE: | PDOC00179 |
| SCOP: | 7rxn |
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.Gene Ontology
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) |
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 Rubredoxin (CL0045), which has the following description:
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 5 members:
COX5B Desulfoferrod_N Methyltransf_13 Rubredoxin zf-CHCCAlignments
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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...
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| Seed (26) |
Full (4692) |
Representative proteomes | UniProt (13230) |
NCBI (14269) |
Meta (302) |
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| RP15 (1168) |
RP35 (3113) |
RP55 (4743) |
RP75 (6945) |
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| PP/heatmap | 1 | ||||||||
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
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| Seed (26) |
Full (4692) |
Representative proteomes | UniProt (13230) |
NCBI (14269) |
Meta (302) |
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|---|---|---|---|---|---|---|---|---|---|
| RP15 (1168) |
RP35 (3113) |
RP55 (4743) |
RP75 (6945) |
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| Raw Stockholm | |||||||||
| Gzipped | |||||||||
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
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: | rubredoxin; |
| Type: | Domain |
| Sequence Ontology: | SO:0000417 |
| Author: |
Finn RD 
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| Number in seed: | 26 |
| Number in full: | 4692 |
| Average length of the domain: | 46.40 aa |
| Average identity of full alignment: | 50 % |
| Average coverage of the sequence by the domain: | 32.32 % |
HMM information
| HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
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| Model details: |
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| Model length: | 47 | ||||||||||||
| Family (HMM) version: | 20 | ||||||||||||
| Download: | download the raw HMM for this family |
Species distribution
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Colour assignments
Archea
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Eukaryota
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Bacteria
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Viruses
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Interactions
There is 1 interaction for this family. More...
RubredoxinStructures
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 104 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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