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Frataxin homolog, mitochondrial (EC 1.16.3.1) [Cleaved into: Frataxin homolog intermediate form]

 FRDA_YEAST              Reviewed;         174 AA.
Q07540; D6VRN0;
15-JUL-1999, integrated into UniProtKB/Swiss-Prot.
01-NOV-1996, sequence version 1.
22-NOV-2017, entry version 161.
RecName: Full=Frataxin homolog, mitochondrial;
EC=1.16.3.1;
Contains:
RecName: Full=Frataxin homolog intermediate form;
Flags: Precursor;
Name=YFH1; OrderedLocusNames=YDL120W;
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina;
Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces.
NCBI_TaxID=559292;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=9169867;
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.;
"The nucleotide sequence of Saccharomyces cerevisiae chromosome IV.";
Nature 387:75-78(1997).
[2]
GENOME REANNOTATION.
STRAIN=ATCC 204508 / S288c;
PubMed=24374639; DOI=10.1534/g3.113.008995;
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.;
"The reference genome sequence of Saccharomyces cerevisiae: Then and
now.";
G3 (Bethesda) 4:389-398(2014).
[3]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=17322287; DOI=10.1101/gr.6037607;
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., Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G.,
Kolodner R.D., LaBaer J.;
"Approaching a complete repository of sequence-verified protein-
encoding clones for Saccharomyces cerevisiae.";
Genome Res. 17:536-543(2007).
[4]
FUNCTION, AND SUBCELLULAR LOCATION.
PubMed=9180083; DOI=10.1126/science.276.5319.1709;
Babcock M., de Silva D., Oaks R., Davis-Kaplan S., Jiralerspong S.,
Montermini L., Pandolfo M., Kaplan J.;
"Regulation of mitochondrial iron accumulation by Yfh1p, a putative
homolog of frataxin.";
Science 276:1709-1712(1997).
[5]
FUNCTION, AND SUBCELLULAR LOCATION.
PubMed=9988680; DOI=10.1074/jbc.274.8.4497;
Radisky D.C., Babcock M.C., Kaplan J.;
"The yeast frataxin homologue mediates mitochondrial iron efflux.
Evidence for a mitochondrial iron cycle.";
J. Biol. Chem. 274:4497-4499(1999).
[6]
PROCESSING.
PubMed=10545606; DOI=10.1093/hmg/8.12.2255;
Gordon D.M., Shi Q., Dancis A., Pain D.;
"Maturation of frataxin within mammalian and yeast mitochondria: one-
step processing by matrix processing peptidase.";
Hum. Mol. Genet. 8:2255-2262(1999).
[7]
PROCESSING.
PubMed=10428860; DOI=10.1074/jbc.274.32.22763;
Branda S.S., Cavadini P., Adamec J., Kalousek F., Taroni F., Isaya G.;
"Yeast and human frataxin are processed to mature form in two
sequential steps by the mitochondrial processing peptidase.";
J. Biol. Chem. 274:22763-22769(1999).
[8]
INTERACTION WITH ISU1.
PubMed=10588895; DOI=10.1006/jmbi.1999.3294;
Garland S.A., Hoff K., Vickery L.E., Culotta V.C.;
"Saccharomyces cerevisiae ISU1 and ISU2: members of a well-conserved
gene family for iron-sulfur cluster assembly.";
J. Mol. Biol. 294:897-907(1999).
[9]
INTERACTION WITH ISU1.
PubMed=12947415; DOI=10.1038/sj.embor.embor918;
Gerber J., Muhlenhoff U., Lill R.;
"An interaction between frataxin and Isu1/Nfs1 that is crucial for
Fe/S cluster synthesis on Isu1.";
EMBO Rep. 4:906-911(2003).
[10]
LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
PubMed=14562106; DOI=10.1038/nature02046;
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A.,
Dephoure N., O'Shea E.K., Weissman J.S.;
"Global analysis of protein expression in yeast.";
Nature 425:737-741(2003).
[11]
FUNCTION, AND INTERACTION WITH YHB1; SDH1; SDH2; AIM45 AND CIR1.
PubMed=15961414; DOI=10.1093/hmg/ddi214;
Gonzalez-Cabo P., Vazquez-Manrique R.P., Garcia-Gimeno M.A., Sanz P.,
Palau F.;
"Frataxin interacts functionally with mitochondrial electron transport
chain proteins.";
Hum. Mol. Genet. 14:2091-2098(2005).
[12]
FUNCTION, CATALYTIC ACTIVITY, AND MUTAGENESIS OF ASP-79; ASP-82;
GLU-93; ASP-97 AND GLU-103.
PubMed=16371422; DOI=10.1093/hmg/ddi461;
Gakh O., Park S., Liu G., Macomber L., Imlay J.A., Ferreira G.C.,
Isaya G.;
"Mitochondrial iron detoxification is a primary function of frataxin
that limits oxidative damage and preserves cell longevity.";
Hum. Mol. Genet. 15:467-479(2006).
[13]
INTERACTION WITH ISU1, AND MUTAGENESIS OF 122-ASN--GLU-124.
PubMed=18319250; DOI=10.1074/jbc.M800399200;
Wang T., Craig E.A.;
"Binding of yeast frataxin to the scaffold for Fe-S cluster
biogenesis, Isu.";
J. Biol. Chem. 283:12674-12679(2008).
[14]
FUNCTION IN IRON-SULFUR CLUSTER BIOSYNTHESIS, INTERACTION WITH ISU1,
AND MUTAGENESIS OF GLN-129; ILE-130; TRP-131 AND ARG-141.
PubMed=19884169; DOI=10.1093/hmg/ddp495;
Leidgens S., De Smet S., Foury F.;
"Frataxin interacts with Isu1 through a conserved tryptophan in its
beta-sheet.";
Hum. Mol. Genet. 19:276-286(2010).
[15]
X-RAY CRYSTALLOGRAPHY (3.01 ANGSTROMS) OF 52-174 ALONE AND IN COMPLEX
WITH IRON, ELECTRON MICROSCOPY OF MUTANT ALA-73, FUNCTION, AND
SUBUNIT.
PubMed=17027502; DOI=10.1016/j.str.2006.08.010;
Karlberg T., Schagerlof U., Gakh O., Park S., Ryde U., Lindahl M.,
Leath K., Garman E., Isaya G., Al-Karadaghi S.;
"The structures of frataxin oligomers reveal the mechanism for the
delivery and detoxification of iron.";
Structure 14:1535-1546(2006).
[16]
ELECTRON MICROSCOPY OF MUTANT ALA-73 (13 ANGSTROMS), AND SUBUNIT.
PubMed=18393441; DOI=10.1021/bi800052m;
Schagerlof U., Elmlund H., Gakh O., Nordlund G., Hebert H.,
Lindahl M., Isaya G., Al-Karadaghi S.;
"Structural basis of the iron storage function of frataxin from
single-particle reconstruction of the iron-loaded oligomer.";
Biochemistry 47:4948-4954(2008).
-!- FUNCTION: Promotes the biosynthesis of heme as well as the
assembly and repair of iron-sulfur clusters by delivering Fe(2+)
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 Fe(2+) to Fe(3+). 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.
{ECO:0000269|PubMed:15961414, ECO:0000269|PubMed:16371422,
ECO:0000269|PubMed:17027502, ECO:0000269|PubMed:19884169,
ECO:0000269|PubMed:9180083, ECO:0000269|PubMed:9988680}.
-!- CATALYTIC ACTIVITY: 4 Fe(2+) + 4 H(+) + O(2) = 4 Fe(3+) + 2 H(2)O.
{ECO:0000269|PubMed:16371422}.
-!- SUBUNIT: 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. {ECO:0000269|PubMed:10588895, ECO:0000269|PubMed:12947415,
ECO:0000269|PubMed:15961414, ECO:0000269|PubMed:17027502,
ECO:0000269|PubMed:18319250, ECO:0000269|PubMed:18393441,
ECO:0000269|PubMed:19884169}.
-!- INTERACTION:
Self; NbExp=2; IntAct=EBI-2206814, EBI-2206814;
Q03020:ISU1; NbExp=4; IntAct=EBI-2206814, EBI-29901;
P39676:YHB1; NbExp=2; IntAct=EBI-2206814, EBI-6905;
-!- SUBCELLULAR LOCATION: Mitochondrion matrix
{ECO:0000269|PubMed:9180083, ECO:0000269|PubMed:9988680}.
-!- PTM: 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. {ECO:0000269|PubMed:14562106}.
-!- SIMILARITY: Belongs to the frataxin family. {ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; Z74168; CAA98688.1; -; Genomic_DNA.
EMBL; AY558160; AAS56486.1; -; Genomic_DNA.
EMBL; BK006938; DAA11740.1; -; Genomic_DNA.
PIR; S67663; S67663.
RefSeq; NP_010163.1; NM_001180179.1.
PDB; 2FQL; X-ray; 3.01 A; A=52-174.
PDB; 2GA5; NMR; -; A=53-174.
PDB; 3OEQ; X-ray; 2.96 A; A=52-174.
PDB; 3OER; X-ray; 3.20 A; A=52-174.
PDB; 4EC2; X-ray; 3.00 A; A=52-174.
PDB; 5T0V; EM; 17.50 A; A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R/S/T/U/V/W/X=52-172.
PDB; 5TRE; EM; 15.60 A; A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R/S/T/U/V/W/X=52-172.
PDBsum; 2FQL; -.
PDBsum; 2GA5; -.
PDBsum; 3OEQ; -.
PDBsum; 3OER; -.
PDBsum; 4EC2; -.
PDBsum; 5T0V; -.
PDBsum; 5TRE; -.
ProteinModelPortal; Q07540; -.
SMR; Q07540; -.
BioGrid; 31943; 101.
DIP; DIP-7485N; -.
IntAct; Q07540; 11.
MINT; MINT-4300743; -.
STRING; 4932.YDL120W; -.
TCDB; 9.B.21.1.2; the frataxin (frataxin) family.
MaxQB; Q07540; -.
PRIDE; Q07540; -.
EnsemblFungi; YDL120W; YDL120W; YDL120W.
GeneID; 851437; -.
KEGG; sce:YDL120W; -.
EuPathDB; FungiDB:YDL120W; -.
SGD; S000002278; YFH1.
GeneTree; ENSGT00390000005811; -.
HOGENOM; HOG000190729; -.
InParanoid; Q07540; -.
KO; K19054; -.
OMA; SGPNRFD; -.
OrthoDB; EOG092C5EQR; -.
BioCyc; MetaCyc:G3O-29519-MONOMER; -.
BioCyc; YEAST:G3O-29519-MONOMER; -.
Reactome; R-SCE-1362409; Mitochondrial iron-sulfur cluster biogenesis.
EvolutionaryTrace; Q07540; -.
PRO; PR:Q07540; -.
Proteomes; UP000002311; Chromosome IV.
GO; GO:0005743; C:mitochondrial inner membrane; TAS:Reactome.
GO; GO:0005758; C:mitochondrial intermembrane space; TAS:Reactome.
GO; GO:0005759; C:mitochondrial matrix; IDA:SGD.
GO; GO:0005739; C:mitochondrion; IDA:SGD.
GO; GO:0051537; F:2 iron, 2 sulfur cluster binding; IBA:GO_Central.
GO; GO:0008199; F:ferric iron binding; IBA:GO_Central.
GO; GO:0008198; F:ferrous iron binding; IDA:SGD.
GO; GO:0004322; F:ferroxidase activity; IDA:SGD.
GO; GO:0042802; F:identical protein binding; IPI:IntAct.
GO; GO:0034986; F:iron chaperone activity; IDA:SGD.
GO; GO:0006879; P:cellular iron ion homeostasis; IDA:SGD.
GO; GO:0034599; P:cellular response to oxidative stress; IBA:GO_Central.
GO; GO:0006749; P:glutathione metabolic process; IMP:SGD.
GO; GO:0006783; P:heme biosynthetic process; IEA:UniProtKB-KW.
GO; GO:0006811; P:ion transport; IEA:UniProtKB-KW.
GO; GO:0018283; P:iron incorporation into metallo-sulfur cluster; IBA:GO_Central.
GO; GO:0016226; P:iron-sulfur cluster assembly; IDA:SGD.
GO; GO:0006121; P:mitochondrial electron transport, succinate to ubiquinone; IMP:UniProtKB.
GO; GO:0007005; P:mitochondrion organization; IBA:GO_Central.
GO; GO:0006626; P:protein targeting to mitochondrion; TAS:Reactome.
GO; GO:0010040; P:response to iron(II) ion; IMP:UniProtKB.
GO; GO:0006979; P:response to oxidative stress; IMP:UniProtKB.
Gene3D; 3.30.920.10; -; 1.
InterPro; IPR017789; Frataxin.
InterPro; IPR002908; Frataxin/CyaY.
InterPro; IPR036524; Frataxin/CyaY_sf.
InterPro; IPR020895; Frataxin_CS.
PANTHER; PTHR16821; PTHR16821; 1.
Pfam; PF01491; Frataxin_Cyay; 1.
SMART; SM01219; Frataxin_Cyay; 1.
SUPFAM; SSF55387; SSF55387; 1.
TIGRFAMs; TIGR03421; FeS_CyaY; 1.
TIGRFAMs; TIGR03422; mito_frataxin; 1.
PROSITE; PS01344; FRATAXIN_1; 1.
PROSITE; PS50810; FRATAXIN_2; 1.
1: Evidence at protein level;
3D-structure; Complete proteome; Heme biosynthesis; Ion transport;
Iron; Iron storage; Iron transport; Mitochondrion; Oxidoreductase;
Reference proteome; Transit peptide; Transport.
TRANSIT 1 21 Mitochondrion. {ECO:0000305}.
CHAIN 22 174 Frataxin homolog intermediate form.
/FTId=PRO_0000010135.
CHAIN 52 174 Frataxin homolog, mitochondrial.
/FTId=PRO_0000010136.
MUTAGEN 79 79 D->A: Nearly abolishes ferroxidase
activity, slows down oligomerization,
impairs resistance to iron-catalyzed
oxidative stress, no effect on Fe(2+)
delivery and cell growth; when associated
with A-82. {ECO:0000269|PubMed:16371422}.
MUTAGEN 82 82 D->A: Nearly abolishes ferroxidase
activity, slows down oligomerization,
impairs resistance to iron-catalyzed
oxidative stress, no effect on Fe(2+)
delivery and cell growth; when associated
with A-79. {ECO:0000269|PubMed:16371422}.
MUTAGEN 93 93 E->A: Impairs oligomerization and iron
mineralization.
{ECO:0000269|PubMed:16371422}.
MUTAGEN 93 93 E->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.
{ECO:0000269|PubMed:16371422}.
MUTAGEN 97 97 D->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.
{ECO:0000269|PubMed:16371422}.
MUTAGEN 103 103 E->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.
{ECO:0000269|PubMed:16371422}.
MUTAGEN 122 124 NKQ->ATA: Impairs cell growth, lowers
activity of motochondrial iron-sulfur
cluster-containing enzymes, no effect on
iron binding and oligomerization.
{ECO:0000269|PubMed:18319250}.
MUTAGEN 129 129 Q->A: Impairs cell growth and lowers
aconitase activity.
{ECO:0000269|PubMed:19884169}.
MUTAGEN 130 130 I->A: Impairs cell growth and lowers
aconitase activity.
{ECO:0000269|PubMed:19884169}.
MUTAGEN 131 131 W->A: Impairs cell growth, lowers
aconitase activity and strongly decreases
interaction with ISU1.
{ECO:0000269|PubMed:19884169}.
MUTAGEN 131 131 W->F: Lowers aconitase activity and no
effexct on interaction with ISU1.
{ECO:0000269|PubMed:19884169}.
MUTAGEN 141 141 R->A: Impairs cell growth and lowers
aconitase activity.
{ECO:0000269|PubMed:19884169}.
TURN 64 67 {ECO:0000244|PDB:3OEQ}.
HELIX 76 88 {ECO:0000244|PDB:3OEQ}.
TURN 89 91 {ECO:0000244|PDB:3OEQ}.
STRAND 92 94 {ECO:0000244|PDB:3OEQ}.
STRAND 96 99 {ECO:0000244|PDB:2FQL}.
STRAND 101 104 {ECO:0000244|PDB:3OEQ}.
STRAND 106 112 {ECO:0000244|PDB:3OEQ}.
TURN 114 116 {ECO:0000244|PDB:3OEQ}.
STRAND 119 122 {ECO:0000244|PDB:3OEQ}.
STRAND 126 128 {ECO:0000244|PDB:3OEQ}.
STRAND 131 134 {ECO:0000244|PDB:3OEQ}.
TURN 135 137 {ECO:0000244|PDB:3OEQ}.
STRAND 138 151 {ECO:0000244|PDB:3OEQ}.
TURN 152 154 {ECO:0000244|PDB:3OEQ}.
HELIX 158 171 {ECO:0000244|PDB:3OEQ}.
SEQUENCE 174 AA; 19490 MW; AB1FF7478EF0E5D6 CRC64;
MIKRSLASLV RVSSVMGRRY MIAAAGGERA RFCPAVTNKK NHTVNTFQKR FVESSTDGQV
VPQEVLNLPL EKYHEEADDY LDHLLDSLEE LSEAHPDCIP DVELSHGVMT LEIPAFGTYV
INKQPPNKQI WLASPLSGPN RFDLLNGEWV SLRNGTKLTD ILTEEVEKAI SKSQ


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