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86  structures 1967  species 3  interactions 2943  sequences 40  architectures

Family: Rubredoxin (PF00301)

Summary: Rubredoxin

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Rubredoxin Edit Wikipedia article

Rubredoxin
PDB 1s24 EBI.jpg
rubredoxin domain ii from pseudomonas oleovorans
Identifiers
Symbol Rubredoxin
Pfam PF00301
Pfam clan CL0045
InterPro IPR004039
PROSITE PDOC00179
SCOP 7rxn
SUPERFAMILY 7rxn

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.

Structure[edit]

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).

Structural representation of a rubredoxin active site.

Rubredoxin in some biochemical reactions[edit]

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[edit]

References[edit]

  • 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[edit]

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.

Rubredoxin Provide feedback

No Pfam abstract.

Internal database links

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.

Gene Ontology

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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 4 members:

COX5B Desulfoferrod_N Rubredoxin zf-CHCC

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
(43)
Full
(2943)
Representative proteomes NCBI
(2104)
Meta
(307)
RP15
(288)
RP35
(568)
RP55
(732)
RP75
(844)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(43)
Full
(2943)
Representative proteomes NCBI
(2104)
Meta
(307)
RP15
(288)
RP35
(568)
RP55
(732)
RP75
(844)
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
(43)
Full
(2943)
Representative proteomes NCBI
(2104)
Meta
(307)
RP15
(288)
RP35
(568)
RP55
(732)
RP75
(844)
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

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 View help on the curation process

Seed source: Prosite
Previous IDs: rubredoxin;
Type: Domain
Author: Finn RD
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 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 21.1 21.1
Trusted cut-off 21.1 21.2
Noise cut-off 21.0 21.0
Model length: 47
Family (HMM) version: 15
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 3 interactions for this family. More...

Rubrerythrin Pyr_redox_2 Rubredoxin

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 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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