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3-isopropylmalate dehydratase (EC 4.2.1.33) (Alpha-IPM isomerase) (IPMI) (Isopropylmalate isomerase)

 LEUC_YEAST              Reviewed;         779 AA.
P07264; D6VUC8;
01-APR-1988, integrated into UniProtKB/Swiss-Prot.
01-OCT-1996, sequence version 3.
23-MAY-2018, entry version 181.
RecName: Full=3-isopropylmalate dehydratase;
EC=4.2.1.33;
AltName: Full=Alpha-IPM isomerase;
Short=IPMI;
AltName: Full=Isopropylmalate isomerase;
Name=LEU1; OrderedLocusNames=YGL009C;
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].
STRAIN=ATCC 46191 / IL125-2B;
PubMed=1840714; DOI=10.1002/yea.320070310;
Skala J., Capieaux E., Balzi E., Chen W., Goffeau A.;
"Complete sequence of the Saccharomyces cerevisiae LEU1 gene encoding
isopropylmalate isomerase.";
Yeast 7:281-285(1991).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=9169869;
Tettelin H., Agostoni-Carbone M.L., Albermann K., Albers M.,
Arroyo J., Backes U., Barreiros T., Bertani I., Bjourson A.J.,
Brueckner M., Bruschi C.V., Carignani G., Castagnoli L., Cerdan E.,
Clemente M.L., Coblenz A., Coglievina M., Coissac E., Defoor E.,
Del Bino S., Delius H., Delneri D., de Wergifosse P., Dujon B.,
Durand P., Entian K.-D., Eraso P., Escribano V., Fabiani L.,
Fartmann B., Feroli F., Feuermann M., Frontali L., Garcia-Gonzalez M.,
Garcia-Saez M.I., Goffeau A., Guerreiro P., Hani J., Hansen M.,
Hebling U., Hernandez K., Heumann K., Hilger F., Hofmann B.,
Indge K.J., James C.M., Klima R., Koetter P., Kramer B., Kramer W.,
Lauquin G., Leuther H., Louis E.J., Maillier E., Marconi A.,
Martegani E., Mazon M.J., Mazzoni C., McReynolds A.D.K.,
Melchioretto P., Mewes H.-W., Minenkova O., Mueller-Auer S.,
Nawrocki A., Netter P., Neu R., Nombela C., Oliver S.G., Panzeri L.,
Paoluzi S., Plevani P., Portetelle D., Portillo F., Potier S.,
Purnelle B., Rieger M., Riles L., Rinaldi T., Robben J.,
Rodrigues-Pousada C., Rodriguez-Belmonte E., Rodriguez-Torres A.M.,
Rose M., Ruzzi M., Saliola M., Sanchez-Perez M., Schaefer B.,
Schaefer M., Scharfe M., Schmidheini T., Schreer A., Skala J.,
Souciet J.-L., Steensma H.Y., Talla E., Thierry A., Vandenbol M.,
van der Aart Q.J.M., Van Dyck L., Vanoni M., Verhasselt P., Voet M.,
Volckaert G., Wambutt R., Watson M.D., Weber N., Wedler E., Wedler H.,
Wipfli P., Wolf K., Wright L.F., Zaccaria P., Zimmermann M.,
Zollner A., Kleine K.;
"The nucleotide sequence of Saccharomyces cerevisiae chromosome VII.";
Nature 387:81-84(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]
NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-48.
PubMed=6323436;
Hsu Y.-P., Schimmel P.R.;
"Yeast LEU1. Repression of mRNA levels by leucine and relationship of
5'-noncoding region to that of LEU2.";
J. Biol. Chem. 259:3714-3719(1984).
[5]
NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 740-779.
STRAIN=ATCC 46191 / IL125-2B;
PubMed=1882553; DOI=10.1002/yea.320070311;
Chen W., Balzi E., Capieaux E., Choder M., Goffeau A.;
"The DNA sequencing of the 17 kb HindIII fragment spanning the LEU1
and ATE1 loci on chromosome VII from Saccharomyces cerevisiae reveals
the PDR6 gene, a new member of the genetic network controlling
pleiotropic drug resistance.";
Yeast 7:287-299(1991).
[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]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-488, 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).
[8]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=17287358; DOI=10.1073/pnas.0607084104;
Chi A., Huttenhower C., Geer L.Y., Coon J.J., Syka J.E.P., Bai D.L.,
Shabanowitz J., Burke D.J., Troyanskaya O.G., Hunt D.F.;
"Analysis of phosphorylation sites on proteins from Saccharomyces
cerevisiae by electron transfer dissociation (ETD) mass
spectrometry.";
Proc. Natl. Acad. Sci. U.S.A. 104:2193-2198(2007).
[9]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=18407956; DOI=10.1074/mcp.M700468-MCP200;
Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
"A multidimensional chromatography technology for in-depth
phosphoproteome analysis.";
Mol. Cell. Proteomics 7:1389-1396(2008).
[10]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-488; THR-494 AND
SER-495, 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).
[11]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=22814378; DOI=10.1073/pnas.1210303109;
Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A.,
Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E.,
Timmerman E., Prieto J., Arnesen T., Sherman F., Gevaert K.,
Aldabe R.;
"N-terminal acetylome analyses and functional insights of the N-
terminal acetyltransferase NatB.";
Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012).
-!- FUNCTION: Catalyzes the isomerization between 2-isopropylmalate
and 3-isopropylmalate, via the formation of 2-isopropylmaleate.
-!- CATALYTIC ACTIVITY: (2R,3S)-3-isopropylmalate = (2S)-2-
isopropylmalate.
-!- COFACTOR:
Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
Evidence={ECO:0000250};
Note=Binds 1 [4Fe-4S] cluster per subunit. {ECO:0000250};
-!- PATHWAY: Amino-acid biosynthesis; L-leucine biosynthesis; L-
leucine from 3-methyl-2-oxobutanoate: step 2/4.
-!- SUBUNIT: Monomer.
-!- MISCELLANEOUS: Present with 96300 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; S57886; AAB19612.1; -; Genomic_DNA.
EMBL; Z72531; CAA96709.1; -; Genomic_DNA.
EMBL; K01969; AAA34742.1; -; Genomic_DNA.
EMBL; S58126; -; NOT_ANNOTATED_CDS; Genomic_DNA.
EMBL; BK006941; DAA08089.1; -; Genomic_DNA.
PIR; S64011; S64011.
RefSeq; NP_011506.1; NM_001180874.1.
ProteinModelPortal; P07264; -.
BioGrid; 33237; 84.
DIP; DIP-6715N; -.
IntAct; P07264; 10.
MINT; P07264; -.
STRING; 4932.YGL009C; -.
iPTMnet; P07264; -.
MaxQB; P07264; -.
PaxDb; P07264; -.
PRIDE; P07264; -.
EnsemblFungi; YGL009C; YGL009C; YGL009C.
GeneID; 852875; -.
KEGG; sce:YGL009C; -.
EuPathDB; FungiDB:YGL009C; -.
SGD; S000002977; LEU1.
GeneTree; ENSGT00730000114222; -.
HOGENOM; HOG000226972; -.
InParanoid; P07264; -.
KO; K01702; -.
OMA; THATVDH; -.
OrthoDB; EOG092C0T13; -.
BioCyc; YEAST:YGL009C-MONOMER; -.
UniPathway; UPA00048; UER00071.
PRO; PR:P07264; -.
Proteomes; UP000002311; Chromosome VII.
GO; GO:0009316; C:3-isopropylmalate dehydratase complex; IEA:InterPro.
GO; GO:0010494; C:cytoplasmic stress granule; IDA:SGD.
GO; GO:0005829; C:cytosol; IDA:SGD.
GO; GO:0003861; F:3-isopropylmalate dehydratase activity; IMP:SGD.
GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-KW.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0009098; P:leucine biosynthetic process; IMP:SGD.
CDD; cd01583; IPMI; 1.
CDD; cd01577; IPMI_Swivel; 1.
Gene3D; 3.20.19.10; -; 1.
Gene3D; 3.30.499.10; -; 1.
HAMAP; MF_01026; LeuC_type1; 1.
HAMAP; MF_01031; LeuD_type1; 1.
InterPro; IPR004430; 3-IsopropMal_deHydase_lsu.
InterPro; IPR004431; 3-IsopropMal_deHydase_ssu.
InterPro; IPR012235; 3-IsopropMal_deHydtase_ssu/lsu.
InterPro; IPR015931; Acnase/IPM_dHydase_lsu_aba_1/3.
InterPro; IPR001030; Acoase/IPM_deHydtase_lsu_aba.
InterPro; IPR015928; Aconitase/3IPM_dehydase_swvl.
InterPro; IPR018136; Aconitase_4Fe-4S_BS.
InterPro; IPR036008; Aconitase_4Fe-4S_dom.
InterPro; IPR000573; AconitaseA/IPMdHydase_ssu_swvl.
InterPro; IPR033941; IPMI_cat.
InterPro; IPR033940; IPMI_Swivel.
Pfam; PF00330; Aconitase; 1.
Pfam; PF00694; Aconitase_C; 1.
PIRSF; PIRSF001418; ACN; 1.
PRINTS; PR00415; ACONITASE.
SUPFAM; SSF53732; SSF53732; 1.
TIGRFAMs; TIGR00170; leuC; 1.
TIGRFAMs; TIGR00171; leuD; 1.
PROSITE; PS00450; ACONITASE_1; 1.
PROSITE; PS01244; ACONITASE_2; 1.
1: Evidence at protein level;
4Fe-4S; Amino-acid biosynthesis;
Branched-chain amino acid biosynthesis; Complete proteome; Iron;
Iron-sulfur; Leucine biosynthesis; Lyase; Metal-binding;
Phosphoprotein; Reference proteome.
CHAIN 1 779 3-isopropylmalate dehydratase.
/FTId=PRO_0000076894.
METAL 360 360 Iron-sulfur (4Fe-4S). {ECO:0000250}.
METAL 421 421 Iron-sulfur (4Fe-4S). {ECO:0000250}.
METAL 424 424 Iron-sulfur (4Fe-4S). {ECO:0000250}.
MOD_RES 488 488 Phosphoserine.
{ECO:0000244|PubMed:17330950,
ECO:0000244|PubMed:19779198}.
MOD_RES 494 494 Phosphothreonine.
{ECO:0000244|PubMed:19779198}.
MOD_RES 495 495 Phosphoserine.
{ECO:0000244|PubMed:19779198}.
CONFLICT 291 291 N -> TLKH (in Ref. 1; AAB19612).
{ECO:0000305}.
CONFLICT 423 423 I -> M (in Ref. 1; AAB19612).
{ECO:0000305}.
CONFLICT 459 459 M -> I (in Ref. 1; AAB19612).
{ECO:0000305}.
CONFLICT 744 744 R -> K (in Ref. 1; AAB19612 and 5;
S58126). {ECO:0000305}.
SEQUENCE 779 AA; 85794 MW; BD409A9702AE3E57 CRC64;
MVYTPSKGPR TLYDKVFDAH VVHQDENGSF LLYIDRHLVH EVTSPQAFEG LENAGRKVRR
VDCTLATVDH NIPTESRKNF KSLDTFIKQT DSRLQVKTLE NNVKQFGVPY FGMSDARQGI
VHTIGPEEGF TLPGTTVVCG DSHTSTHGAF GSLAFGIGTS EVEHVLATQT IIQAKSKNMR
ITVNGKLSPG ITSKDLILYI IGLIGTAGGT GCVIEFAGEA IEALSMEARM SMCNMAIEAG
ARAGMIKPDE TTFQYTKGRP LAPKGAEWEK AVAYWKTLKT DEGAKFDHEI NIEAVDVIPT
ITWGTSPQDA LPITGSVPDP KNVTDPIKKS GMERALAYMG LEPNTPLKSI KVDKVFIGSC
TNGRIEDLRS AAAVVRGQKL ASNIKLAMVV PGSGLVKKQA EAEGLDKIFQ EAGFEWREAG
CSICLGMNPD ILDAYERCAS TSNRNFEGRQ GALSRTHLMS PAMAAAAGIA GHFVDIREFE
YKDQDQSSPK VEVTSEDEKE LESAAYDHAE PVQPEDAPQD IANDELKDIP VKSDDTPAKP
SSSGMKPFLT LEGISAPLDK ANVDTDAIIP KQFLKTIKRT GLKKGLFYEW RFRKDDQGKD
QETDFVLNVE PWREAEILVV TGDNFGCGSS REHAPWALKD FGIKSIIAPS YGDIFYNNSF
KNGLLPIRLD QQIIIDKLIP IANKGGKLCV DLPNQKILDS DGNVLVDHFE IEPFRKHCLV
NGLDDIGITL QKEEYISRYE ALRREKYSFL EGGSKLLKFD NVPKRKAVTT TFDKVHQDW


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