Frataxin
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| Frataxin
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| Available structures: For the file format that describes the 3D structures of molecules found in the Protein Data Bank, see Protein Data Bank (file format).
The Protein Data Bank (PDB) is a repository for 3-D structural data of proteins and nucleic acids. These data, typically obtained by X-ray crystallography or NMR spectroscopy, are submitted by biologists and biochemists from around the world, are released into the public domain, and can be accessed for free. HistoryFounded in 1971 by Drs. Edgar Meyer and Walter Hamilton Brookhaven National Laboratory, management of the Protein Data Bank was transferred in 1998 to members of the Research Collaboratory for Structural Bioinformatics (RCSB). The Worldwide Protein Data Bank (wwPDB) consists of organizations that act as deposition, data processing and distribution centers for PDB data. The founding members are RCSB PDB (USA), MSD-EBI (Europe) and PDBj (Japan). The BMRB (USA) group joined the wwPDB in 2006. The mission of the wwPDB is to maintain a single Protein Data Bank Archive of macromolecular structural data that is freely and publicly available to the global community. The PDB is a key resource in structural biology and is critical to more recent work in structural genomics. Countless derived databases and projects have been developed to integrate and classify the PDB in terms of protein structure, protein function and protein evolution. GrowthWhen the PDB was originally founded it contained just 7 protein structures. Since then it has undergone an approximate exponential growth in the number of structures, which does not show any sign of falling off. The growth rate of the PDB has been the subject of fairly extensive analysis. ContentsAs of 26 September, 2006, the database contained 39,051 released atomic coordinate entries (or "structures"), 35,767 of that proteins, the rest being nucleic acids, nucleic acid-protein complexes, and a few other molecules. About 5,000 new structures are released each year. Data are stored in the mmCIF format specifically developed for the purpose. Note that the database stores information about the exact location of all atoms in a large biomolecule (although, usually without the hydrogen atoms, as their positions are more of a statistical estimate); if one is only interested in sequence data, i.e. the list of amino acids making up a particular protein or the list of nucleotides making up a particular nucleic acid, the much larger databases from Swiss-Prot and the International Nucleotide Sequence Database Collaboration should be used. StatisticsAs of 11 September, 2007, the "PDB Holdings List" at RCSB reported the following statistics:
Note that theoretical models are no longer accepted in the PDB. 22461 structures in the PDB have a structure factor file. 3138 structures in the PDB have an NMR restraint file. The current breakdown of holdings is updated weekly. File formatThrough the years the PDB file format has undergone many, many changes and revisions. Its original format was dictated by the width of computer punch cards.
This legacy format has caused many problems with the format, and consequently there are 'clean-up' projects; The MMDB uses ASN.1 (and an XML conversion of this format). The wwPDB members RCSB PDB, MSD-EBI, and PDBj are working together to make the data uniform across the archive. Some believe this to be desirable; others argue that, without a universal repository of information (i.e., a common dictionary), it is not possible to draw comparisons. Each structure published in PDB receives a four-character alphanumeric identifier, its PDB ID. This should not be used as an identifier for biomolecules, since often several structures for the same molecule (in different environments or conformations) are contained in PDB with different PDB IDs. If a biologist submits structure data for a protein or nucleic acid, wwPDB staff reviews and annotates the entry. The data are then automatically checked for plausibility. The source code for this validation software has been released for free. The main data base accepts only experimentally derived structures, and not theoretically predicted ones (see protein structure prediction). Various funding agencies and scientific journals now require scientists to submit their structure data to PDB. Viewing the dataThe structural data can be used to visualize the biomolecules with appropriate software, such as VMD, RasMol, PyMOL, Jmol, MDL Chime, QuteMol, web browser VRML plugin or any web-based software designed to visualize and analyse the protein structures such as STING. A recent desktop software addition is Sirius. The RCSB PDB website also contains resources for education, structural genomics, and related software. ReferencesPrinted
Online
Other external links
Links to enzyme database data
Molecular graphic visualisation tools
The Protein Data Bank (PDB) is a repository for 3-D structural data of proteins and nucleic acids. These data, typically obtained by X-ray crystallography or NMR spectroscopy, are submitted by biologists and biochemists from around the world, are released into the public domain, and can be accessed for free. HistoryFounded in 1971 by Drs. Edgar Meyer and Walter Hamilton Brookhaven National Laboratory, management of the Protein Data Bank was transferred in 1998 to members of the Research Collaboratory for Structural Bioinformatics (RCSB). The Worldwide Protein Data Bank (wwPDB) consists of organizations that act as deposition, data processing and distribution centers for PDB data. The founding members are RCSB PDB (USA), MSD-EBI (Europe) and PDBj (Japan). The BMRB (USA) group joined the wwPDB in 2006. The mission of the wwPDB is to maintain a single Protein Data Bank Archive of macromolecular structural data that is freely and publicly available to the global community. The PDB is a key resource in structural biology and is critical to more recent work in structural genomics. Countless derived databases and projects have been developed to integrate and classify the PDB in terms of protein structure, protein function and protein evolution. GrowthWhen the PDB was originally founded it contained just 7 protein structures. Since then it has undergone an approximate exponential growth in the number of structures, which does not show any sign of falling off. The growth rate of the PDB has been the subject of fairly extensive analysis. ContentsAs of 26 September, 2006, the database contained 39,051 released atomic coordinate entries (or "structures"), 35,767 of that proteins, the rest being nucleic acids, nucleic acid-protein complexes, and a few other molecules. About 5,000 new structures are released each year. Data are stored in the mmCIF format specifically developed for the purpose. Note that the database stores information about the exact location of all atoms in a large biomolecule (although, usually without the hydrogen atoms, as their positions are more of a statistical estimate); if one is only interested in sequence data, i.e. the list of amino acids making up a particular protein or the list of nucleotides making up a particular nucleic acid, the much larger databases from Swiss-Prot and the International Nucleotide Sequence Database Collaboration should be used. StatisticsAs of 11 September, 2007, the "PDB Holdings List" at RCSB reported the following statistics:
Note that theoretical models are no longer accepted in the PDB. 22461 structures in the PDB have a structure factor file. 3138 structures in the PDB have an NMR restraint file. The current breakdown of holdings is updated weekly. File formatThrough the years the PDB file format has undergone many, many changes and revisions. Its original format was dictated by the width of computer punch cards.
This legacy format has caused many problems with the format, and consequently there are 'clean-up' projects; The MMDB uses ASN.1 (and an XML conversion of this format). The wwPDB members RCSB PDB, MSD-EBI, and PDBj are working together to make the data uniform across the archive. Some believe this to be desirable; others argue that, without a universal repository of information (i.e., a common dictionary), it is not possible to draw comparisons. Each structure published in PDB receives a four-character alphanumeric identifier, its PDB ID. This should not be used as an identifier for biomolecules, since often several structures for the same molecule (in different environments or conformations) are contained in PDB with different PDB IDs. If a biologist submits structure data for a protein or nucleic acid, wwPDB staff reviews and annotates the entry. The data are then automatically checked for plausibility. The source code for this validation software has been released for free. The main data base accepts only experimentally derived structures, and not theoretically predicted ones (see protein structure prediction). Various funding agencies and scientific journals now require scientists to submit their structure data to PDB. Viewing the dataThe structural data can be used to visualize the biomolecules with appropriate software, such as VMD, RasMol, PyMOL, Jmol, MDL Chime, QuteMol, web browser VRML plugin or any web-based software designed to visualize and analyse the protein structures such as STING. A recent desktop software addition is Sirius. The RCSB PDB website also contains resources for education, structural genomics, and related software. ReferencesPrinted
Online
Other external links
Links to enzyme database data
Molecular graphic visualisation tools
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| Identifiers | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Symbol(s) | FXN; FA; CyaY; FARR; FRDA; MGC57199; X25 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| External IDs | OMIM: 606829 MGI: 1096879 Homologene: 47908 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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| RNA expression pattern | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Orthologs | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Human | Mouse | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Entrez | 2395 | 14297 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Ensembl | ENSG00000165060 | ENSMUSG00000059363 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Uniprot | Q16595 | Q3TV21 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Refseq | NM_000144 (mRNA) NP_000135 (protein) | XM_989030 (mRNA) XP_994124 (protein) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Location | Chr 9: 70.84 - 70.88 Mb | Chr 19: 24.33 - 24.35 Mb | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Pubmed search | [9] | [10] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Frataxin' is a small protein, localized to the mitochondrion. The function of frataxin is not entirely clear, but it seems to be involved in assembly of iron-sulfur clusters.
Deficiency of frataxin is the cause of Friedrich's ataxia, a hereditary trinucleotide repeat disorder.
This nuclear gene encodes a mitochondrial protein which belongs to FRATAXIN family. The protein functions in regulating mitochondrial iron transport and respiration. The expansion of intronic trinucleotide repeat GAA results in Friedreich ataxia. Alternative splicing occurs at this locus and two transcript variants encoding distinct isoforms have been identified.[1]
References
Further reading
- Montermini L, Rodius F, Pianese L, et al. (1995). "The Friedreich ataxia critical region spans a 150-kb interval on chromosome 9q13.". Am. J. Hum. Genet. 57 (5): 1061-7. PMID 7485155.
- Campuzano V, Montermini L, Moltò MD, et al. (1996). "Friedreich's ataxia: autosomal recessive disease caused by an intronic GAA triplet repeat expansion.". Science 271 (5254): 1423-7. PMID 8596916.
- Carvajal JJ, Pook MA, dos Santos M, et al. (1996). "The Friedreich's ataxia gene encodes a novel phosphatidylinositol-4- phosphate 5-kinase.". Nat. Genet. 14 (2): 157-62. doi:10.1038/ng1096-157. PMID 8841185.
- Bidichandani SI, Ashizawa T, Patel PI (1997). "Atypical Friedreich ataxia caused by compound heterozygosity for a novel missense mutation and the GAA triplet-repeat expansion.". Am. J. Hum. Genet. 60 (5): 1251-6. PMID 9150176.
- Babcock M, de Silva D, Oaks R, et al. (1997). "Regulation of mitochondrial iron accumulation by Yfh1p, a putative homolog of frataxin.". Science 276 (5319): 1709-12. PMID 9180083.
- Koutnikova H, Campuzano V, Foury F, et al. (1997). "Studies of human, mouse and yeast homologues indicate a mitochondrial function for frataxin.". Nat. Genet. 16 (4): 345-51. doi:10.1038/ng0897-345. PMID 9241270.
- Wilson RB, Roof DM (1997). "Respiratory deficiency due to loss of mitochondrial DNA in yeast lacking the frataxin homologue.". Nat. Genet. 16 (4): 352-7. doi:10.1038/ng0897-352. PMID 9241271.
- Campuzano V, Montermini L, Lutz Y, et al. (1998). "Frataxin is reduced in Friedreich ataxia patients and is associated with mitochondrial membranes.". Hum. Mol. Genet. 6 (11): 1771-80. PMID 9302253.
- Rötig A, de Lonlay P, Chretien D, et al. (1997). "Aconitase and mitochondrial iron-sulphur protein deficiency in Friedreich ataxia.". Nat. Genet. 17 (2): 215-7. doi:10.1038/ng1097-215. PMID 9326946.
- Jiralerspong S, Liu Y, Montermini L, et al. (1997). "Frataxin shows developmentally regulated tissue-specific expression in the mouse embryo.". Neurobiol. Dis. 4 (2): 103-13. doi:10.1006/nbdi.1997.0139. PMID 9331900.
- Koutnikova H, Campuzano V, Koenig M (1998). "Maturation of wild-type and mutated frataxin by the mitochondrial processing peptidase.". Hum. Mol. Genet. 7 (9): 1485-9. PMID 9700204.
- Zühlke C, Laccone F, Cossée M, et al. (1998). "Mutation of the start codon in the FRDA1 gene: linkage analysis of three pedigrees with the ATG to ATT transversion points to a unique common ancestor.". Hum. Genet. 103 (1): 102-5. PMID 9737785.
- Bartolo C, Mendell JR, Prior TW (1999). "Identification of a missense mutation in a Friedreich's ataxia patient: implications for diagnosis and carrier studies.". Am. J. Med. Genet. 79 (5): 396-9. PMID 9779809.
- Cossée M, Dürr A, Schmitt M, et al. (1999). "Friedreich's ataxia: point mutations and clinical presentation of compound heterozygotes.". Ann. Neurol. 45 (2): 200-6. PMID 9989622.
- Coppola G, De Michele G, Cavalcanti F, et al. (1999). "Why do some Friedreich's ataxia patients retain tendon reflexes? A clinical, neurophysiological and molecular study.". J. Neurol. 246 (5): 353-7. PMID 10399865.
- Branda SS, Cavadini P, Adamec J, et al. (1999). "Yeast and human frataxin are processed to mature form in two sequential steps by the mitochondrial processing peptidase.". J. Biol. Chem. 274 (32): 22763-9. PMID 10428860.
- Gordon DM, Shi Q, Dancis A, Pain D (1999). "Maturation of frataxin within mammalian and yeast mitochondria: one-step processing by matrix processing peptidase.". Hum. Mol. Genet. 8 (12): 2255-62. PMID 10545606.
- Forrest SM, Knight M, Delatycki MB, et al. (2000). "The correlation of clinical phenotype in Friedreich ataxia with the site of point mutations in the FRDA gene.". Neurogenetics 1 (4): 253-7. PMID 10732799.
- Al-Mahdawi S, Pook M, Chamberlain S (2000). "A novel missense mutation (L198R) in the Friedreich's ataxia gene.". Hum. Mutat. 16 (1): 95. doi:<95::AID-HUMU29>3.0.CO;2-E 10.1002/1098-1004(200007)16:1<95::AID-HUMU29>3.0.CO;2-E. PMID 10874325.
- Dhe-Paganon S, Shigeta R, Chi YI, et al. (2000). "Crystal structure of human frataxin.". J. Biol. Chem. 275 (40): 30753-6. doi:10.1074/jbc.C000407200. PMID 10900192.
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Some of the initial content on this page may be incorporated in part from copyleft sources in the public domain including wikis such as Wikipedia and AskDrWiki. Drug information for patients came from the The National Library of Medicine. Infectious disease information may have come from the Centers for Disease Control (CDC). Differential Diagnoses are drawn from clinicians as well as an amalgamation of 3 sources: 1.The Disease Database; 2. Kahan, Scott, Smith, Ellen G. In A Page: Signs and Symptoms. Malden, Massachusetts: Blackwell Publishing, 2004:3; 3. Sailer, Christian, Wasner, Susanne. Differential Diagnosis Pocket. Hermosa Beach, CA: Borm Bruckmeir Publishing LLC, 2002:7 .
