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 | |||||||||
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![]() mature human frataxin | |||||||||
Identifiers | |||||||||
Symbol | Frataxin_Cyay | ||||||||
Pfam | PF01491 | ||||||||
InterPro | IPR002908 | ||||||||
SCOPe | 1dlx / SUPFAM | ||||||||
TCDB | 9.B.21 | ||||||||
CDD | cd00503 | ||||||||
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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 experimental data in some species.[1][2][3]
References
- ^ 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.
- ^ 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.
- ^ 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.
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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
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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
HOMSTRAD: | Frataxin_Cyay |
SCOP: | 1dlx |
Transporter classification: | 9.B.21 |
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 homologous 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].
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Molecular function | ferric iron binding (GO:0008199) |
Biological process | iron-sulfur cluster assembly (GO:0016226) |
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.
Seed (245) |
Full (2170) |
Representative proteomes | UniProt (7832) |
NCBI (8062) |
Meta (102) |
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RP15 (313) |
RP35 (897) |
RP55 (1717) |
RP75 (3126) |
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Jalview | |||||||||
HTML | |||||||||
PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
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Seed (245) |
Full (2170) |
Representative proteomes | UniProt (7832) |
NCBI (8062) |
Meta (102) |
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RP15 (313) |
RP35 (897) |
RP55 (1717) |
RP75 (3126) |
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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: | Gibson TJ |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Gibson TJ |
Number in seed: | 245 |
Number in full: | 2170 |
Average length of the domain: | 106.20 aa |
Average identity of full alignment: | 32 % |
Average coverage of the sequence by the domain: | 65.87 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 109 | ||||||||||||
Family (HMM) version: | 17 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Interactions
There is 1 interaction for this family. More...
Frataxin_CyayStructures
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 100 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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