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Q07540

- FRDA_YEAST

UniProt

Q07540 - FRDA_YEAST

Protein

Frataxin homolog, mitochondrial

Gene

YFH1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 135 (01 Oct 2014)
      Sequence version 1 (01 Nov 1996)
      Previous versions | rss
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    Functioni

    Promotes the biosynthesis of heme as well as the assembly and repair of iron-sulfur clusters by delivering Fe2+ to proteins involved in these pathways. Plays a role in the protection against iron-catalyzed oxidative stress through its ability to catalyze the oxidation of Fe2+ to Fe3+. Can store large amounts of the metal in the form of a ferrihydrite mineral by oligomerization. May be involved in regulation of the mitochondrial electron transport chain.6 Publications

    Catalytic activityi

    4 Fe2+ + 4 H+ + O2 = 4 Fe3+ + 2 H2O.1 Publication

    GO - Molecular functioni

    1. ferric iron binding Source: InterPro
    2. ferrous iron binding Source: SGD
    3. ferroxidase activity Source: SGD
    4. iron chaperone activity Source: SGD
    5. protein binding Source: IntAct

    GO - Biological processi

    1. cellular iron ion homeostasis Source: SGD
    2. glutathione metabolic process Source: SGD
    3. heme biosynthetic process Source: UniProtKB-KW
    4. ion transport Source: UniProtKB-KW
    5. iron-sulfur cluster assembly Source: SGD
    6. mitochondrial electron transport, succinate to ubiquinone Source: UniProtKB
    7. response to iron(II) ion Source: UniProtKB
    8. response to oxidative stress Source: UniProtKB

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    Heme biosynthesis, Ion transport, Iron storage, Iron transport, Transport

    Keywords - Ligandi

    Iron

    Enzyme and pathway databases

    BioCyciMetaCyc:G3O-29519-MONOMER.
    YEAST:G3O-29519-MONOMER.
    ReactomeiREACT_189012. Mitochondrial protein import.
    REACT_189017. Mitochondrial iron-sulfur cluster biogenesis.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Frataxin homolog, mitochondrial (EC:1.16.3.1)
    Cleaved into the following chain:
    Gene namesi
    Name:YFH1
    Ordered Locus Names:YDL120W
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome IV

    Organism-specific databases

    CYGDiYDL120w.
    SGDiS000002278. YFH1.

    Subcellular locationi

    Mitochondrion matrix 2 Publications

    GO - Cellular componenti

    1. mitochondrial inner membrane Source: Reactome
    2. mitochondrial intermembrane space Source: Reactome
    3. mitochondrial matrix Source: SGD
    4. mitochondrion Source: SGD

    Keywords - Cellular componenti

    Mitochondrion

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi79 – 791D → A: Nearly abolishes ferroxidase avtivity, slows down oligomerization, impairs resistance to iron-catalyzed oxidative stress, no effect on Fe(2+) delivery and cell growth; when associated with A-82. 2 Publications
    Mutagenesisi82 – 821D → A: Nearly abolishes ferroxidase avtivity, slows down oligomerization, impairs resistance to iron-catalyzed oxidative stress, no effect on Fe(2+) delivery and cell growth; when associated with A-79. 2 Publications
    Mutagenesisi93 – 931E → A: Impairs oligomerization and iron mineralization. 2 Publications
    Mutagenesisi93 – 931E → A: Impairs resistance to iron-catalyzed oxidative stress, no effect on Fe(2+) delivery and cell growth; when associated with A-97 and A-103. 2 Publications
    Mutagenesisi97 – 971D → A: Impairs resistance to iron-catalyzed oxidative stress, no effect on Fe(2+) delivery and cell growth; when associated with A-93 and A-103. 2 Publications
    Mutagenesisi103 – 1031E → A: Impairs resistance to iron-catalyzed oxidative stress, no effect on Fe(2+) delivery and cell growth; when associated with A-93 and A-97. 2 Publications
    Mutagenesisi122 – 1243NKQ → ATA: Impairs cell growth, lowers activity of motochondrial iron-sulfur cluster-containing enzymes, no effect on iron binding and oligomerization. 1 Publication
    Mutagenesisi129 – 1291Q → A: Impairs cell growth and lowers aconitase activity. 2 Publications
    Mutagenesisi130 – 1301I → A: Impairs cell growth and lowers aconitase activity. 2 Publications
    Mutagenesisi131 – 1311W → A: Impairs cell growth, lowers aconitase activity and strongly decreases interaction with ISU1. 2 Publications
    Mutagenesisi131 – 1311W → F: Lowers aconitase activity and no effexct on interaction with ISU1. 2 Publications
    Mutagenesisi141 – 1411R → A: Impairs cell growth and lowers aconitase activity. 2 Publications

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Transit peptidei1 – 2121MitochondrionCuratedAdd
    BLAST
    Chaini22 – 174153Frataxin homolog intermediate formPRO_0000010135Add
    BLAST
    Chaini52 – 174123Frataxin homolog, mitochondrialPRO_0000010136Add
    BLAST

    Post-translational modificationi

    Processed in two steps by mitochondrial processing peptidase (MPP). MPP first cleaves the precursor to intermediate form and subsequently converts the intermediate to mature size protein.

    Proteomic databases

    MaxQBiQ07540.
    PaxDbiQ07540.

    Expressioni

    Gene expression databases

    GenevestigatoriQ07540.

    Interactioni

    Subunit structurei

    Monomer; increments in mitochondrial iron uptake induce stepwise assembly of species ranging from trimers to 24-mers. Interacts with ISU1. Interacts with YHB1, SDH1, SDH2, AIM45 and CIR1.7 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    ISU1Q030204EBI-2206814,EBI-29901
    YHB1P396762EBI-2206814,EBI-6905

    Protein-protein interaction databases

    BioGridi31943. 95 interactions.
    DIPiDIP-7485N.
    IntActiQ07540. 11 interactions.
    MINTiMINT-4300743.
    STRINGi4932.YDL120W.

    Structurei

    Secondary structure

    1
    174
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Turni64 – 674
    Helixi76 – 8813
    Turni89 – 913
    Beta strandi92 – 943
    Beta strandi96 – 994
    Beta strandi101 – 1044
    Beta strandi106 – 1127
    Turni114 – 1163
    Beta strandi119 – 1224
    Beta strandi126 – 1283
    Beta strandi131 – 1344
    Turni135 – 1373
    Beta strandi138 – 15114
    Turni152 – 1543
    Helixi158 – 17114

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2FQLX-ray3.01A52-174[»]
    2GA5NMR-A53-174[»]
    3OEQX-ray2.96A52-174[»]
    3OERX-ray3.20A52-174[»]
    4EC2X-ray3.00A52-174[»]
    ProteinModelPortaliQ07540.
    SMRiQ07540. Positions 52-172.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ07540.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the frataxin family.Curated

    Keywords - Domaini

    Transit peptide

    Phylogenomic databases

    eggNOGiCOG1965.
    GeneTreeiENSGT00390000005811.
    HOGENOMiHOG000190729.
    OMAiHEEADDY.
    OrthoDBiEOG7WDNF7.

    Family and domain databases

    Gene3Di3.30.920.10. 1 hit.
    InterProiIPR017789. Frataxin.
    IPR002908. Frataxin/CyaY.
    IPR020895. Frataxin_CS.
    [Graphical view]
    PANTHERiPTHR16821. PTHR16821. 1 hit.
    PfamiPF01491. Frataxin_Cyay. 1 hit.
    [Graphical view]
    SUPFAMiSSF55387. SSF55387. 1 hit.
    TIGRFAMsiTIGR03421. FeS_CyaY. 1 hit.
    TIGR03422. mito_frataxin. 1 hit.
    PROSITEiPS01344. FRATAXIN_1. 1 hit.
    PS50810. FRATAXIN_2. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    Q07540-1 [UniParc]FASTAAdd to Basket

    « Hide

    MIKRSLASLV RVSSVMGRRY MIAAAGGERA RFCPAVTNKK NHTVNTFQKR    50
    FVESSTDGQV VPQEVLNLPL EKYHEEADDY LDHLLDSLEE LSEAHPDCIP 100
    DVELSHGVMT LEIPAFGTYV INKQPPNKQI WLASPLSGPN RFDLLNGEWV 150
    SLRNGTKLTD ILTEEVEKAI SKSQ 174
    Length:174
    Mass (Da):19,490
    Last modified:November 1, 1996 - v1
    Checksum:iAB1FF7478EF0E5D6
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Z74168 Genomic DNA. Translation: CAA98688.1.
    AY558160 Genomic DNA. Translation: AAS56486.1.
    BK006938 Genomic DNA. Translation: DAA11740.1.
    PIRiS67663.
    RefSeqiNP_010163.1. NM_001180179.1.

    Genome annotation databases

    EnsemblFungiiYDL120W; YDL120W; YDL120W.
    GeneIDi851437.
    KEGGisce:YDL120W.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Z74168 Genomic DNA. Translation: CAA98688.1 .
    AY558160 Genomic DNA. Translation: AAS56486.1 .
    BK006938 Genomic DNA. Translation: DAA11740.1 .
    PIRi S67663.
    RefSeqi NP_010163.1. NM_001180179.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2FQL X-ray 3.01 A 52-174 [» ]
    2GA5 NMR - A 53-174 [» ]
    3OEQ X-ray 2.96 A 52-174 [» ]
    3OER X-ray 3.20 A 52-174 [» ]
    4EC2 X-ray 3.00 A 52-174 [» ]
    ProteinModelPortali Q07540.
    SMRi Q07540. Positions 52-172.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 31943. 95 interactions.
    DIPi DIP-7485N.
    IntActi Q07540. 11 interactions.
    MINTi MINT-4300743.
    STRINGi 4932.YDL120W.

    Proteomic databases

    MaxQBi Q07540.
    PaxDbi Q07540.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YDL120W ; YDL120W ; YDL120W .
    GeneIDi 851437.
    KEGGi sce:YDL120W.

    Organism-specific databases

    CYGDi YDL120w.
    SGDi S000002278. YFH1.

    Phylogenomic databases

    eggNOGi COG1965.
    GeneTreei ENSGT00390000005811.
    HOGENOMi HOG000190729.
    OMAi HEEADDY.
    OrthoDBi EOG7WDNF7.

    Enzyme and pathway databases

    BioCyci MetaCyc:G3O-29519-MONOMER.
    YEAST:G3O-29519-MONOMER.
    Reactomei REACT_189012. Mitochondrial protein import.
    REACT_189017. Mitochondrial iron-sulfur cluster biogenesis.

    Miscellaneous databases

    EvolutionaryTracei Q07540.
    NextBioi 968672.
    PROi Q07540.

    Gene expression databases

    Genevestigatori Q07540.

    Family and domain databases

    Gene3Di 3.30.920.10. 1 hit.
    InterProi IPR017789. Frataxin.
    IPR002908. Frataxin/CyaY.
    IPR020895. Frataxin_CS.
    [Graphical view ]
    PANTHERi PTHR16821. PTHR16821. 1 hit.
    Pfami PF01491. Frataxin_Cyay. 1 hit.
    [Graphical view ]
    SUPFAMi SSF55387. SSF55387. 1 hit.
    TIGRFAMsi TIGR03421. FeS_CyaY. 1 hit.
    TIGR03422. mito_frataxin. 1 hit.
    PROSITEi PS01344. FRATAXIN_1. 1 hit.
    PS50810. FRATAXIN_2. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "The nucleotide sequence of Saccharomyces cerevisiae chromosome IV."
      Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G., Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C., Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F., Delaveau T.
      , del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M., Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T., Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C., Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S., Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L., Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H., Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M., Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M., Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A., Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G., Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E., Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S., Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D., Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V., Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E., Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M., Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X., Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A., Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T., Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L., Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E., Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L., Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M., Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K., Mewes H.-W., Zollner A., Zaccaria P.
      Nature 387:75-78(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    2. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    3. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    4. "Regulation of mitochondrial iron accumulation by Yfh1p, a putative homolog of frataxin."
      Babcock M., de Silva D., Oaks R., Davis-Kaplan S., Jiralerspong S., Montermini L., Pandolfo M., Kaplan J.
      Science 276:1709-1712(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, SUBCELLULAR LOCATION.
    5. "The yeast frataxin homologue mediates mitochondrial iron efflux. Evidence for a mitochondrial iron cycle."
      Radisky D.C., Babcock M.C., Kaplan J.
      J. Biol. Chem. 274:4497-4499(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, SUBCELLULAR LOCATION.
    6. "Maturation of frataxin within mammalian and yeast mitochondria: one-step processing by matrix processing peptidase."
      Gordon D.M., Shi Q., Dancis A., Pain D.
      Hum. Mol. Genet. 8:2255-2262(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROCESSING.
    7. "Yeast and human frataxin are processed to mature form in two sequential steps by the mitochondrial processing peptidase."
      Branda S.S., Cavadini P., Adamec J., Kalousek F., Taroni F., Isaya G.
      J. Biol. Chem. 274:22763-22769(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROCESSING.
    8. "Saccharomyces cerevisiae ISU1 and ISU2: members of a well-conserved gene family for iron-sulfur cluster assembly."
      Garland S.A., Hoff K., Vickery L.E., Culotta V.C.
      J. Mol. Biol. 294:897-907(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH ISU1.
    9. "An interaction between frataxin and Isu1/Nfs1 that is crucial for Fe/S cluster synthesis on Isu1."
      Gerber J., Muhlenhoff U., Lill R.
      EMBO Rep. 4:906-911(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH ISU1.
    10. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
    11. "Frataxin interacts functionally with mitochondrial electron transport chain proteins."
      Gonzalez-Cabo P., Vazquez-Manrique R.P., Garcia-Gimeno M.A., Sanz P., Palau F.
      Hum. Mol. Genet. 14:2091-2098(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, INTERACTION WITH YHB1; SDH1; SDH2; AIM45 AND CIR1.
    12. "Mitochondrial iron detoxification is a primary function of frataxin that limits oxidative damage and preserves cell longevity."
      Gakh O., Park S., Liu G., Macomber L., Imlay J.A., Ferreira G.C., Isaya G.
      Hum. Mol. Genet. 15:467-479(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, MUTAGENESIS OF ASP-79; ASP-82; GLU-93; ASP-97 AND GLU-103.
    13. "Binding of yeast frataxin to the scaffold for Fe-S cluster biogenesis, Isu."
      Wang T., Craig E.A.
      J. Biol. Chem. 283:12674-12679(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH ISU1, MUTAGENESIS OF 122-ASN--GLU-124.
    14. "Frataxin interacts with Isu1 through a conserved tryptophan in its beta-sheet."
      Leidgens S., De Smet S., Foury F.
      Hum. Mol. Genet. 19:276-286(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION IN IRON-SULFUR CLUSTER BIOSYNTHESIS, INTERACTION WITH ISU1, MUTAGENESIS OF GLN-129; ILE-130; TRP-131 AND ARG-141.
    15. "The structures of frataxin oligomers reveal the mechanism for the delivery and detoxification of iron."
      Karlberg T., Schagerlof U., Gakh O., Park S., Ryde U., Lindahl M., Leath K., Garman E., Isaya G., Al-Karadaghi S.
      Structure 14:1535-1546(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (3.01 ANGSTROMS) OF 52-174 ALONE AND IN COMPLEX WITH IRON, ELECTRON MICROSCOPY OF MUTANT ALA-73, FUNCTION, SUBUNIT.
    16. "Structural basis of the iron storage function of frataxin from single-particle reconstruction of the iron-loaded oligomer."
      Schagerlof U., Elmlund H., Gakh O., Nordlund G., Hebert H., Lindahl M., Isaya G., Al-Karadaghi S.
      Biochemistry 47:4948-4954(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: ELECTRON MICROSCOPY OF MUTANT ALA-73 (13 ANGSTROMS), SUBUNIT.

    Entry informationi

    Entry nameiFRDA_YEAST
    AccessioniPrimary (citable) accession number: Q07540
    Secondary accession number(s): D6VRN0
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 15, 1999
    Last sequence update: November 1, 1996
    Last modified: October 1, 2014
    This is version 135 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Present with 1560 molecules/cell in log phase SD medium.1 Publication

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families
    3. Yeast
      Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
    4. Yeast chromosome IV
      Yeast (Saccharomyces cerevisiae) chromosome IV: entries and gene names

    External Data

    Dasty 3