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Aconitate hydratase, mitochondrial (Aconitase) (EC 4.2.1.3) (Citrate hydro-lyase)

 ACON_YEAST              Reviewed;         778 AA.
P19414; D6VYU7;
01-NOV-1990, integrated into UniProtKB/Swiss-Prot.
01-NOV-1995, sequence version 2.
31-JAN-2018, entry version 178.
RecName: Full=Aconitate hydratase, mitochondrial;
Short=Aconitase;
EC=4.2.1.3 {ECO:0000269|PubMed:1972545};
AltName: Full=Citrate hydro-lyase;
Flags: Precursor;
Name=ACO1; Synonyms=GLU1; OrderedLocusNames=YLR304C;
ORFNames=L8003.22;
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina;
Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces.
NCBI_TaxID=559292;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, DISRUPTION PHENOTYPE, AND
CATALYTIC ACTIVITY.
STRAIN=ATCC 44774 / DBY747;
PubMed=1972545; DOI=10.1128/MCB.10.7.3551;
Gangloff S.P., Marguet D., Lauquin G.J.-M.;
"Molecular cloning of the yeast mitochondrial aconitase gene (ACO1)
and evidence of a synergistic regulation of expression by glucose plus
glutamate.";
Mol. Cell. Biol. 10:3551-3561(1990).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=9169871;
Johnston M., Hillier L.W., Riles L., Albermann K., Andre B.,
Ansorge W., Benes V., Brueckner M., Delius H., Dubois E.,
Duesterhoeft A., Entian K.-D., Floeth M., Goffeau A., Hebling U.,
Heumann K., Heuss-Neitzel D., Hilbert H., Hilger F., Kleine K.,
Koetter P., Louis E.J., Messenguy F., Mewes H.-W., Miosga T.,
Moestl D., Mueller-Auer S., Nentwich U., Obermaier B., Piravandi E.,
Pohl T.M., Portetelle D., Purnelle B., Rechmann S., Rieger M.,
Rinke M., Rose M., Scharfe M., Scherens B., Scholler P., Schwager C.,
Schwarz S., Underwood A.P., Urrestarazu L.A., Vandenbol M.,
Verhasselt P., Vierendeels F., Voet M., Volckaert G., Voss H.,
Wambutt R., Wedler E., Wedler H., Zimmermann F.K., Zollner A.,
Hani J., Hoheisel J.D.;
"The nucleotide sequence of Saccharomyces cerevisiae chromosome XII.";
Nature 387:87-90(1997).
[3]
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).
[4]
PROTEIN SEQUENCE OF 17-23, AND SUBCELLULAR LOCATION.
PubMed=15975908; DOI=10.1091/mbc.E04-11-1028;
Regev-Rudzki N., Karniely S., Ben-Haim N.N., Pines O.;
"Yeast aconitase in two locations and two metabolic pathways: seeing
small amounts is believing.";
Mol. Biol. Cell 16:4163-4171(2005).
[5]
DISRUPTION PHENOTYPE.
PubMed=10224250;
Przybyla-Zawislak B., Gadde D.M., Ducharme K., McCammon M.T.;
"Genetic and biochemical interactions involving tricarboxylic acid
cycle (TCA) function using a collection of mutants defective in all
TCA cycle genes.";
Genetics 152:153-166(1999).
[6]
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).
[7]
FUNCTION, AND SUBUNIT.
PubMed=15692048; DOI=10.1126/science.1106391;
Chen X.J., Wang X., Kaufman B.A., Butow R.A.;
"Aconitase couples metabolic regulation to mitochondrial DNA
maintenance.";
Science 307:714-717(2005).
[8]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-556, AND IDENTIFICATION
BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
STRAIN=ADR376;
PubMed=17330950; DOI=10.1021/pr060559j;
Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J.,
Elias J.E., Gygi S.P.;
"Large-scale phosphorylation analysis of alpha-factor-arrested
Saccharomyces cerevisiae.";
J. Proteome Res. 6:1190-1197(2007).
[9]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-409, AND IDENTIFICATION
BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
STRAIN=ATCC 76625 / YPH499;
PubMed=17761666; DOI=10.1074/mcp.M700098-MCP200;
Reinders J., Wagner K., Zahedi R.P., Stojanovski D., Eyrich B.,
van der Laan M., Rehling P., Sickmann A., Pfanner N., Meisinger C.;
"Profiling phosphoproteins of yeast mitochondria reveals a role of
phosphorylation in assembly of the ATP synthase.";
Mol. Cell. Proteomics 6:1896-1906(2007).
[10]
FUNCTION, AND SUBUNIT.
PubMed=17698960; DOI=10.1073/pnas.0703078104;
Chen X.J., Wang X., Butow R.A.;
"Yeast aconitase binds and provides metabolically coupled protection
to mitochondrial DNA.";
Proc. Natl. Acad. Sci. U.S.A. 104:13738-13743(2007).
[11]
DISRUPTION PHENOTYPE.
PubMed=18359281; DOI=10.1016/j.abb.2008.03.005;
Lin A.P., Hakala K.W., Weintraub S.T., McAlister-Henn L.;
"Suppression of metabolic defects of yeast isocitrate dehydrogenase
and aconitase mutants by loss of citrate synthase.";
Arch. Biochem. Biophys. 474:205-212(2008).
[12]
SUBCELLULAR LOCATION.
PubMed=18577574; DOI=10.1242/jcs.029207;
Regev-Rudzki N., Yogev O., Pines O.;
"The mitochondrial targeting sequence tilts the balance between
mitochondrial and cytosolic dual localization.";
J. Cell Sci. 121:2423-2431(2008).
[13]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-391, AND IDENTIFICATION
BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=19779198; DOI=10.1126/science.1172867;
Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.;
"Global analysis of Cdk1 substrate phosphorylation sites provides
insights into evolution.";
Science 325:1682-1686(2009).
[14]
SUBCELLULAR LOCATION.
PubMed=21440554; DOI=10.1016/j.jmb.2011.03.045;
Ben-Menachem R., Regev-Rudzki N., Pines O.;
"The aconitase C-terminal domain is an independent dual targeting
element.";
J. Mol. Biol. 409:113-123(2011).
[15]
FUNCTION, INDUCTION, AND MUTAGENESIS OF ARG-604.
PubMed=23106124; DOI=10.1111/mmi.12076;
Fazius F., Shelest E., Gebhardt P., Brock M.;
"The fungal alpha-aminoadipate pathway for lysine biosynthesis
requires two enzymes of the aconitase family for the isomerization of
homocitrate to homoisocitrate.";
Mol. Microbiol. 86:1508-1530(2012).
[16]
FUNCTION.
PubMed=24066190; DOI=10.1155/2013/493536;
Farooq M.A., Pracheil T.M., Dong Z., Xiao F., Liu Z.;
"Mitochondrial DNA instability in cells lacking aconitase correlates
with iron citrate toxicity.";
Oxid. Med. Cell. Longev. 2013:493536-493536(2013).
-!- FUNCTION: Catalyzes the isomerization of citrate to isocitrate via
cis-aconitate, a step in the citric acid cycle. Can also provide
minor contributions to the reversible dehydration of (R)-
homocitrate to cis-homoaconitate, a step in the alpha-aminoadipate
pathway for lysine biosynthesis. Plays also an essential role in
mtDNA maintenance. May directly protect mtDNA from accumulation of
point mutations and ssDNA breaks as a component of mitochondrial
nucleoids, or by preventing accumulation of iron citrate thereby
alleviating its detrimental effects in mitochondria.
{ECO:0000269|PubMed:15692048, ECO:0000269|PubMed:17698960,
ECO:0000269|PubMed:1972545, ECO:0000269|PubMed:23106124,
ECO:0000269|PubMed:24066190}.
-!- CATALYTIC ACTIVITY: Citrate = isocitrate.
{ECO:0000269|PubMed:1972545}.
-!- COFACTOR:
Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
Evidence={ECO:0000250};
Note=Binds 1 [4Fe-4S] cluster per subunit. {ECO:0000250};
-!- ENZYME REGULATION: Subject to catabolite regulation.
-!- PATHWAY: Carbohydrate metabolism; tricarboxylic acid cycle;
isocitrate from oxaloacetate: step 2/2.
{ECO:0000269|PubMed:1972545}.
-!- SUBUNIT: Monomer. Binds to mitochondrial DNA (mtDNA) and
identified as component of mitochondrial nucleoids.
{ECO:0000269|PubMed:15692048, ECO:0000269|PubMed:17698960}.
-!- SUBCELLULAR LOCATION: Mitochondrion. Cytoplasm. Note=Mainly
mitochondrial, small amounts are also detected in the cytosol with
a ratio of 94:6.
-!- INDUCTION: Highly induced in the absence of glutamate. Induction
is further increased when both glutamate and lysine are missing.
{ECO:0000269|PubMed:23106124}.
-!- DISRUPTION PHENOTYPE: Essential for growth on nonfermentable
carbon sources and for biosynthesis of glutamate. Causes a
dramatic increase in cellular citrate levels.
{ECO:0000269|PubMed:10224250, ECO:0000269|PubMed:18359281,
ECO:0000269|PubMed:1972545}.
-!- MISCELLANEOUS: The fermenting yeast S.cerevisiae has 2 aconitases,
ACO1 essential for the citric acid cycle, and ACO2 specifically
and exclusively contributing to lysine biosynthesis. In contrast,
in respiring filamentous fungi the ACO2 homologs (acoB) seem
enzymatically inactive and the ACO1 homolog (acoA) is solely
responsible for these functions.
-!- MISCELLANEOUS: Present with 96700 molecules/cell in log phase SD
medium. {ECO:0000269|PubMed:14562106}.
-!- SIMILARITY: Belongs to the aconitase/IPM isomerase family.
{ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; M33131; AAA34389.1; -; Genomic_DNA.
EMBL; U17243; AAB67348.1; -; Genomic_DNA.
EMBL; BK006945; DAA09613.1; -; Genomic_DNA.
PIR; S50387; S50387.
RefSeq; NP_013407.1; NM_001182192.1.
ProteinModelPortal; P19414; -.
SMR; P19414; -.
BioGrid; 31569; 196.
DIP; DIP-4679N; -.
IntAct; P19414; 33.
MINT; MINT-557728; -.
STRING; 4932.YLR304C; -.
iPTMnet; P19414; -.
MaxQB; P19414; -.
PaxDb; P19414; -.
PRIDE; P19414; -.
TopDownProteomics; P19414; -.
EnsemblFungi; YLR304C; YLR304C; YLR304C.
GeneID; 851013; -.
KEGG; sce:YLR304C; -.
EuPathDB; FungiDB:YLR304C; -.
SGD; S000004295; ACO1.
GeneTree; ENSGT00890000139397; -.
HOGENOM; HOG000224293; -.
InParanoid; P19414; -.
KO; K01681; -.
OMA; INLERMS; -.
OrthoDB; EOG092C0DQS; -.
BioCyc; MetaCyc:YLR304C-MONOMER; -.
BioCyc; YEAST:YLR304C-MONOMER; -.
UniPathway; UPA00223; UER00718.
PRO; PR:P19414; -.
Proteomes; UP000002311; Chromosome XII.
GO; GO:0005829; C:cytosol; IDA:SGD.
GO; GO:0005758; C:mitochondrial intermembrane space; TAS:Reactome.
GO; GO:0005759; C:mitochondrial matrix; IDA:SGD.
GO; GO:0042645; C:mitochondrial nucleoid; IDA:SGD.
GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-KW.
GO; GO:0003994; F:aconitate hydratase activity; IDA:SGD.
GO; GO:0003690; F:double-stranded DNA binding; IDA:SGD.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0003697; F:single-stranded DNA binding; IDA:SGD.
GO; GO:0000002; P:mitochondrial genome maintenance; IMP:SGD.
GO; GO:0006099; P:tricarboxylic acid cycle; IDA:SGD.
Gene3D; 3.20.19.10; -; 1.
Gene3D; 3.30.499.10; -; 2.
Gene3D; 3.40.1060.10; -; 1.
InterPro; IPR015931; Acnase/IPM_dHydase_lsu_aba_1/3.
InterPro; IPR001030; Acoase/IPM_deHydtase_lsu_aba.
InterPro; IPR015928; Aconitase/3IPM_dehydase_swvl.
InterPro; IPR015932; Aconitase/IPMdHydase_lsu_aba_2.
InterPro; IPR018136; Aconitase_4Fe-4S_BS.
InterPro; IPR036008; Aconitase_4Fe-4S_dom.
InterPro; IPR006248; Aconitase_mito-like.
InterPro; IPR000573; AconitaseA/IPMdHydase_ssu_swvl.
Pfam; PF00330; Aconitase; 1.
Pfam; PF00694; Aconitase_C; 1.
PRINTS; PR00415; ACONITASE.
SUPFAM; SSF53732; SSF53732; 1.
TIGRFAMs; TIGR01340; aconitase_mito; 1.
PROSITE; PS00450; ACONITASE_1; 1.
PROSITE; PS01244; ACONITASE_2; 1.
1: Evidence at protein level;
4Fe-4S; Complete proteome; Cytoplasm; Direct protein sequencing; Iron;
Iron-sulfur; Lyase; Metal-binding; Mitochondrion; Phosphoprotein;
Reference proteome; Transit peptide; Tricarboxylic acid cycle.
TRANSIT 1 16 Mitochondrion.
{ECO:0000269|PubMed:15975908}.
CHAIN 17 778 Aconitate hydratase, mitochondrial.
/FTId=PRO_0000000547.
REGION 188 190 Substrate binding. {ECO:0000250}.
REGION 667 668 Substrate binding. {ECO:0000250}.
METAL 382 382 Iron-sulfur (4Fe-4S). {ECO:0000250}.
METAL 445 445 Iron-sulfur (4Fe-4S). {ECO:0000250}.
METAL 448 448 Iron-sulfur (4Fe-4S). {ECO:0000250}.
BINDING 95 95 Substrate. {ECO:0000250}.
BINDING 471 471 Substrate. {ECO:0000250}.
BINDING 476 476 Substrate. {ECO:0000250}.
BINDING 604 604 Substrate. {ECO:0000250}.
MOD_RES 391 391 Phosphoserine.
{ECO:0000244|PubMed:19779198}.
MOD_RES 409 409 Phosphothreonine.
{ECO:0000244|PubMed:17761666}.
MOD_RES 556 556 Phosphoserine.
{ECO:0000244|PubMed:17330950}.
MUTAGEN 604 604 R->K: Strongly diminishes the catalytic
activity towards both known substrates,
aconitate and homoaconitate.
{ECO:0000269|PubMed:23106124}.
CONFLICT 527 549 DGLPQRGYDAGENTYQAPPADRS -> RWFASKEVMMLVRT
LTKLHLQTVA (in Ref. 1; AAA34389).
{ECO:0000305}.
SEQUENCE 778 AA; 85368 MW; AA9EB9A24388090E CRC64;
MLSARSAIKR PIVRGLATVS NLTRDSKVNQ NLLEDHSFIN YKQNVETLDI VRKRLNRPFT
YAEKILYGHL DDPHGQDIQR GVSYLKLRPD RVACQDATAQ MAILQFMSAG LPQVAKPVTV
HCDHLIQAQV GGEKDLKRAI DLNKEVYDFL ASATAKYNMG FWKPGSGIIH QIVLENYAFP
GALIIGTDSH TPNAGGLGQL AIGVGGADAV DVMAGRPWEL KAPKILGVKL TGKMNGWTSP
KDIILKLAGI TTVKGGTGKI VEYFGDGVDT FSATGMGTIC NMGAEIGATT SVFPFNKSMI
EYLEATGRGK IADFAKLYHK DLLSADKDAE YDEVVEIDLN TLEPYINGPF TPDLATPVSK
MKEVAVANNW PLDVRVGLIG SCTNSSYEDM SRSASIVKDA AAHGLKSKTI FTVTPGSEQI
RATIERDGQL ETFKEFGGIV LANACGPCIG QWDRRDIKKG DKNTIVSSYN RNFTSRNDGN
PQTHAFVASP ELVTAFAIAG DLRFNPLTDK LKDKDGNEFM LKPPHGDGLP QRGYDAGENT
YQAPPADRST VEVKVSPTSD RLQLLKPFKP WDGKDAKDMP ILIKAVGKTT TDHISMAGPW
LKYRGHLENI SNNYMIGAIN AENKKANCVK NVYTGEYKGV PDTARDYRDQ GIKWVVIGDE
NFGEGSSREH AALEPRFLGG FAIITKSFAR IHETNLKKQG LLPLNFKNPA DYDKINPDDR
IDILGLAELA PGKPVTMRVH PKNGKPWDAV LTHTFNDEQI EWFKYGSALN KIKADEKK


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