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24  structures 1409  species 1  interaction 1466  sequences 5  architectures

Family: Frataxin_Cyay (PF01491)

Summary: Frataxin-like domain

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This is the Wikipedia entry entitled "Frataxin-like domain". More...

Frataxin-like domain Edit Wikipedia article

Frataxin-like domain
PDB 1ekg EBI.jpg
mature human frataxin
Identifiers
Symbol Frataxin_Cyay
Pfam PF01491
InterPro IPR002908
SCOP 1dlx
SUPERFAMILY 1dlx
TCDB 9.B.21

In molecular biology, the frataxin-like domain is a protein domain found in proteins including eukaryotic frataxin and bacterial CyaY.

The bacterial CyaY proteins are iron-sulphur cluster (FeS) metabolism proteins which are homologous to eukaryotic frataxin. Partial phylogenetic profiling suggests that CyaY most likely functions as part of the ISC system for FeS cluster biosynthesis, and is supported by expermimental data in some species.[1][2][3]


References[edit]

  1. ^ Haft DH, Paulsen IT, Ward N, Selengut JD (2006). "Exopolysaccharide-associated protein sorting in environmental organisms: the PEP-CTERM/EpsH system. Application of a novel phylogenetic profiling heuristic". BMC Biol. 4: 29. doi:10.1186/1741-7007-4-29. PMC 1569441. PMID 16930487. 
  2. ^ Layer G, Ollagnier-de Choudens S, Sanakis Y, Fontecave M (June 2006). "Iron-sulfur cluster biosynthesis: characterization of Escherichia coli CYaY as an iron donor for the assembly of [2Fe-2S] clusters in the scaffold IscU". J. Biol. Chem. 281 (24): 16256–63. doi:10.1074/jbc.M513569200. PMID 16603772. 
  3. ^ Vivas E, Skovran E, Downs DM (February 2006). "Salmonella enterica strains lacking the frataxin homolog CyaY show defects in Fe-S cluster metabolism in vivo". J. Bacteriol. 188 (3): 1175–9. doi:10.1128/JB.188.3.1175-1179.2006. PMC 1347345. PMID 16428423. 

This article incorporates text from the public domain Pfam and InterPro IPR002908

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.

Frataxin-like domain Provide feedback

This family contains proteins that have a domain related to the globular C-terminus of Frataxin the protein that is mutated in Friedreich's ataxia. This domain is found in a family of bacterial proteins. The function of this domain is currently unknown. It has been suggested that this family is involved in iron transport.

Literature references

  1. Gibson TJ, Koonin EV, Musco G, Pastore A, Bork P; , Trends Neurosci 1996;19:465-468.: Friedreich's ataxia protein: phylogenetic evidence for mitochondrial dysfunction. PUBMED:8931268 EPMC:8931268


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002908

The eukaryotic proteins in this entry include frataxin, the protein that is mutated in Friedreich's ataxia [PUBMED:8931268], and related sequences. Friedreich's ataxia is a progressive neurodegenerative disorder caused by loss of function mutations in the gene encoding frataxin (FRDA). Frataxin mRNA is predominantly expressed in tissues with a high metabolic rate (including liver, kidney, brown fat and heart). Mouse and yeast frataxin homologues contain a potential N-terminal mitochondrial targeting sequence, and human frataxin has been observed to co-localise with a mitochondrial protein. Furthermore, disruption of the yeast gene has been shown to result in mitochondrial dysfunction. Friedreich's ataxia is thus believed to be a mitochondrial disease caused by a mutation in the nuclear genome (specifically, expansion of an intronic GAA triplet repeat) [PUBMED:8596916, PUBMED:8815938, PUBMED:9241270].

The bacterial proteins in this entry are iron-sulphur cluster (FeS) metabolism CyaY proteins hmologous to eukaryotic frataxin. Partial Phylogenetic Profiling [PUBMED:16930487] suggests that CyaY most likely functions as part of the ISC system for FeS cluster biosynthesis, and is supported by expermimental data in some species [PUBMED:16603772, PUBMED:16428423].

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Alignments

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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.

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(96)
Full
(1466)
Representative proteomes NCBI
(878)
Meta
(102)
RP15
(105)
RP35
(209)
RP55
(318)
RP75
(414)
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Format an alignment

  Seed
(96)
Full
(1466)
Representative proteomes NCBI
(878)
Meta
(102)
RP15
(105)
RP35
(209)
RP55
(318)
RP75
(414)
Alignment:
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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
(96)
Full
(1466)
Representative proteomes NCBI
(878)
Meta
(102)
RP15
(105)
RP35
(209)
RP55
(318)
RP75
(414)
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: Gibson TJ
Previous IDs: none
Type: Domain
Author: Gibson Tj, Bateman A
Number in seed: 96
Number in full: 1466
Average length of the domain: 106.10 aa
Average identity of full alignment: 41 %
Average coverage of the sequence by the domain: 86.45 %

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 21.3 21.3
Trusted cut-off 21.8 21.8
Noise cut-off 21.1 21.0
Model length: 109
Family (HMM) version: 11
Download: download the raw HMM for this family

Species distribution

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Interactions

There is 1 interaction for this family. More...

Frataxin_Cyay

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 Frataxin_Cyay domain has been found. There are 24 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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