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Q07540 (FRDA_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified June 11, 2014. Version 133. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Frataxin homolog, mitochondrial

EC=1.16.3.1

Cleaved into the following chain:

  1. Frataxin homolog intermediate form
Gene names
Name:YFH1
Ordered Locus Names:YDL120W
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length174 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.4 Ref.5 Ref.11 Ref.12 Ref.14 Ref.15

Catalytic activity

4 Fe2+ + 4 H+ + O2 = 4 Fe3+ + 2 H2O. Ref.12

Subunit structure

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. Ref.8 Ref.9 Ref.11 Ref.13 Ref.14 Ref.15 Ref.16

Subcellular location

Mitochondrion matrix Ref.4 Ref.5.

Post-translational modification

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.

Miscellaneous

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

Sequence similarities

Belongs to the frataxin family.

Ontologies

Keywords
   Biological processHeme biosynthesis
Ion transport
Iron storage
Iron transport
Transport
   Cellular componentMitochondrion
   DomainTransit peptide
   LigandIron
   Molecular functionOxidoreductase
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processcellular iron ion homeostasis

Inferred from direct assay Ref.4. Source: SGD

glutathione metabolic process

Inferred from mutant phenotype PubMed 18562474. Source: SGD

heme biosynthetic process

Inferred from electronic annotation. Source: UniProtKB-KW

ion transport

Inferred from electronic annotation. Source: UniProtKB-KW

iron-sulfur cluster assembly

Inferred from direct assay Ref.9. Source: SGD

mitochondrial electron transport, succinate to ubiquinone

Inferred from mutant phenotype Ref.11. Source: UniProtKB

response to iron(II) ion

Inferred from mutant phenotype Ref.12. Source: UniProtKB

response to oxidative stress

Inferred from mutant phenotype Ref.12. Source: UniProtKB

   Cellular_componentmitochondrial inner membrane

Traceable author statement. Source: Reactome

mitochondrial intermembrane space

Traceable author statement. Source: Reactome

mitochondrial matrix

Inferred from direct assay Ref.7. Source: SGD

mitochondrion

Inferred from direct assay Ref.4PubMed 9241271. Source: SGD

   Molecular_functionferric iron binding

Inferred from electronic annotation. Source: InterPro

ferrous iron binding

Inferred from direct assay PubMed 10930361PubMed 16784228. Source: SGD

ferroxidase activity

Inferred from direct assay PubMed 12149269PubMed 12732649. Source: SGD

iron chaperone activity

Inferred from direct assay PubMed 12732649. Source: SGD

protein binding

Inferred from physical interaction Ref.9Ref.11PubMed 17186026. Source: IntAct

Complete GO annotation...

Binary interactions

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Transit peptide1 – 2121Mitochondrion Probable
Chain22 – 174153Frataxin homolog intermediate form
PRO_0000010135
Chain52 – 174123Frataxin homolog, mitochondrial
PRO_0000010136

Experimental info

Mutagenesis791D → 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. Ref.12
Mutagenesis821D → 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. Ref.12
Mutagenesis931E → A: Impairs oligomerization and iron mineralization. Ref.12
Mutagenesis931E → 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. Ref.12
Mutagenesis971D → 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. Ref.12
Mutagenesis1031E → 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. Ref.12
Mutagenesis122 – 1243NKQ → ATA: Impairs cell growth, lowers activity of motochondrial iron-sulfur cluster-containing enzymes, no effect on iron binding and oligomerization. Ref.13
Mutagenesis1291Q → A: Impairs cell growth and lowers aconitase activity. Ref.14
Mutagenesis1301I → A: Impairs cell growth and lowers aconitase activity. Ref.14
Mutagenesis1311W → A: Impairs cell growth, lowers aconitase activity and strongly decreases interaction with ISU1. Ref.14
Mutagenesis1311W → F: Lowers aconitase activity and no effexct on interaction with ISU1. Ref.14
Mutagenesis1411R → A: Impairs cell growth and lowers aconitase activity. Ref.14

Secondary structure

.......................... 174
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q07540 [UniParc].

Last modified November 1, 1996. Version 1.
Checksum: AB1FF7478EF0E5D6

FASTA17419,490
        10         20         30         40         50         60 
MIKRSLASLV RVSSVMGRRY MIAAAGGERA RFCPAVTNKK NHTVNTFQKR FVESSTDGQV 

        70         80         90        100        110        120 
VPQEVLNLPL EKYHEEADDY LDHLLDSLEE LSEAHPDCIP DVELSHGVMT LEIPAFGTYV 

       130        140        150        160        170 
INKQPPNKQI WLASPLSGPN RFDLLNGEWV SLRNGTKLTD ILTEEVEKAI SKSQ 

« Hide

References

« Hide 'large scale' references
[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. expand/collapse author list , 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]"The reference genome sequence of Saccharomyces cerevisiae: Then and now."
Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R., Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S., Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.
G3 (Bethesda) 4:389-398(2014) [PubMed] [Europe PMC] [Abstract]
Cited for: GENOME REANNOTATION.
Strain: ATCC 204508 / S288c.
[3]"Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae."
Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F., Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J., Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J. expand/collapse author list , Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D., LaBaer J.
Genome Res. 17:536-543(2007) [PubMed] [Europe PMC] [Abstract]
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]"Global analysis of protein expression in yeast."
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S.
Nature 425:737-741(2003) [PubMed] [Europe PMC] [Abstract]
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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
Z74168 Genomic DNA. Translation: CAA98688.1.
AY558160 Genomic DNA. Translation: AAS56486.1.
BK006938 Genomic DNA. Translation: DAA11740.1.
PIRS67663.
RefSeqNP_010163.1. NM_001180179.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2FQLX-ray3.01A52-174[»]
2GA5NMR-A53-174[»]
3OEQX-ray2.96A52-174[»]
3OERX-ray3.20A52-174[»]
4EC2X-ray3.00A52-174[»]
ProteinModelPortalQ07540.
SMRQ07540. Positions 52-172.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid31943. 95 interactions.
DIPDIP-7485N.
IntActQ07540. 11 interactions.
MINTMINT-4300743.
STRING4932.YDL120W.

Proteomic databases

MaxQBQ07540.
PaxDbQ07540.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYDL120W; YDL120W; YDL120W.
GeneID851437.
KEGGsce:YDL120W.

Organism-specific databases

CYGDYDL120w.
SGDS000002278. YFH1.

Phylogenomic databases

eggNOGCOG1965.
GeneTreeENSGT00390000005811.
HOGENOMHOG000190729.
OMAHEEADDY.
OrthoDBEOG7WDNF7.

Enzyme and pathway databases

BioCycMetaCyc:G3O-29519-MONOMER.
YEAST:G3O-29519-MONOMER.
ReactomeREACT_118590. Mitochondrial Protein Import (yeast).

Gene expression databases

GenevestigatorQ07540.

Family and domain databases

Gene3D3.30.920.10. 1 hit.
InterProIPR017789. Frataxin.
IPR002908. Frataxin/CyaY.
IPR020895. Frataxin_CS.
[Graphical view]
PANTHERPTHR16821. PTHR16821. 1 hit.
PfamPF01491. Frataxin_Cyay. 1 hit.
[Graphical view]
SUPFAMSSF55387. SSF55387. 1 hit.
TIGRFAMsTIGR03421. FeS_CyaY. 1 hit.
TIGR03422. mito_frataxin. 1 hit.
PROSITEPS01344. FRATAXIN_1. 1 hit.
PS50810. FRATAXIN_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceQ07540.
NextBio968672.
PROQ07540.

Entry information

Entry nameFRDA_YEAST
AccessionPrimary (citable) accession number: Q07540
Secondary accession number(s): D6VRN0
Entry history
Integrated into UniProtKB/Swiss-Prot: July 15, 1999
Last sequence update: November 1, 1996
Last modified: June 11, 2014
This is version 133 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome IV

Yeast (Saccharomyces cerevisiae) chromosome IV: entries and gene names

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references