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Q07540

- FRDA_YEAST

UniProt

Q07540 - FRDA_YEAST

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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

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

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
Complete GO annotation...

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
Complete GO annotation...

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. 1 Publication
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. 1 Publication
Mutagenesisi93 – 931E → A: Impairs oligomerization and iron mineralization. 1 Publication
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. 1 Publication
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. 1 Publication
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. 1 Publication
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. 1 Publication
Mutagenesisi130 – 1301I → A: Impairs cell growth and lowers aconitase activity. 1 Publication
Mutagenesisi131 – 1311W → A: Impairs cell growth, lowers aconitase activity and strongly decreases interaction with ISU1. 1 Publication
Mutagenesisi131 – 1311W → F: Lowers aconitase activity and no effexct on interaction with ISU1. 1 Publication
Mutagenesisi141 – 1411R → A: Impairs cell growth and lowers aconitase activity. 1 Publication

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. 96 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.
InParanoidiQ07540.
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 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MIKRSLASLV RVSSVMGRRY MIAAAGGERA RFCPAVTNKK NHTVNTFQKR
60 70 80 90 100
FVESSTDGQV VPQEVLNLPL EKYHEEADDY LDHLLDSLEE LSEAHPDCIP
110 120 130 140 150
DVELSHGVMT LEIPAFGTYV INKQPPNKQI WLASPLSGPN RFDLLNGEWV
160 170
SLRNGTKLTD ILTEEVEKAI SKSQ
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. 96 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.
InParanoidi Q07540.
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

« Hide 'large scale' publications
  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 29, 2014
This is version 136 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