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Protein

3-isopropylmalate dehydrogenase

Gene

LEU2

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the oxidation of 3-carboxy-2-hydroxy-4-methylpentanoate (3-isopropylmalate) to 3-carboxy-4-methyl-2-oxopentanoate. The product decarboxylates to 4-methyl-2 oxopentanoate.

Catalytic activityi

(2R,3S)-3-isopropylmalate + NAD+ = 4-methyl-2-oxopentanoate + CO2 + NADH.

Cofactori

Mg2+By similarity, Mn2+By similarityNote: Binds 1 Mg2+ or Mn2+ ion per subunit.By similarity

Pathwayi: L-leucine biosynthesis

This protein is involved in step 3 of the subpathway that synthesizes L-leucine from 3-methyl-2-oxobutanoate.
Proteins known to be involved in the 4 steps of the subpathway in this organism are:
  1. 2-isopropylmalate synthase (LEU4), 2-isopropylmalate synthase 2, mitochondrial (LEU9)
  2. 3-isopropylmalate dehydratase (LEU1)
  3. 3-isopropylmalate dehydrogenase (LEU2)
  4. Branched-chain-amino-acid aminotransferase, mitochondrial (BAT1), Branched-chain-amino-acid aminotransferase, cytosolic (BAT2)
This subpathway is part of the pathway L-leucine biosynthesis, which is itself part of Amino-acid biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes L-leucine from 3-methyl-2-oxobutanoate, the pathway L-leucine biosynthesis and in Amino-acid biosynthesis.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei97 – 971SubstrateBy similarity
Binding sitei107 – 1071SubstrateBy similarity
Binding sitei136 – 1361SubstrateBy similarity
Sitei143 – 1431Important for catalysisBy similarity
Sitei192 – 1921Important for catalysisBy similarity
Metal bindingi225 – 2251Magnesium or manganeseBy similarity
Binding sitei225 – 2251SubstrateBy similarity
Metal bindingi250 – 2501Magnesium or manganeseBy similarity
Metal bindingi254 – 2541Magnesium or manganeseBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi79 – 9012NADBy similarityAdd
BLAST
Nucleotide bindingi289 – 30012NADBy similarityAdd
BLAST

GO - Molecular functioni

  • 3-isopropylmalate dehydrogenase activity Source: SGD
  • magnesium ion binding Source: InterPro
  • NAD binding Source: InterPro

GO - Biological processi

  • glyoxylate cycle Source: SGD
  • leucine biosynthetic process Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Amino-acid biosynthesis, Branched-chain amino acid biosynthesis, Leucine biosynthesis

Keywords - Ligandi

Magnesium, Manganese, Metal-binding, NAD

Enzyme and pathway databases

BioCyciMetaCyc:YCL018W-MONOMER.
YEAST:YCL018W-MONOMER.
UniPathwayiUPA00048; UER00072.

Names & Taxonomyi

Protein namesi
Recommended name:
3-isopropylmalate dehydrogenase (EC:1.1.1.85)
Short name:
3-IPM-DH
Short name:
IMDH
Alternative name(s):
Beta-IPM dehydrogenase
Gene namesi
Name:LEU2
Ordered Locus Names:YCL018W
ORF Names:YCL18W
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome III

Organism-specific databases

EuPathDBiFungiDB:YCL018W.
SGDiS000000523. LEU2.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 3643643-isopropylmalate dehydrogenasePRO_0000083623Add
BLAST

Proteomic databases

PRIDEiP04173.

2D gel databases

SWISS-2DPAGEP04173.

Interactioni

Subunit structurei

Homodimer.By similarity

Protein-protein interaction databases

BioGridi30966. 15 interactions.
DIPiDIP-7880N.
IntActiP04173. 1 interaction.
MINTiMINT-4809760.

Structurei

3D structure databases

ProteinModelPortaliP04173.
SMRiP04173. Positions 5-364.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

GeneTreeiENSGT00550000076087.
HOGENOMiHOG000021112.
InParanoidiP04173.
KOiK00052.
OMAiHCGPEVV.
OrthoDBiEOG7BGHWF.

Family and domain databases

Gene3Di3.40.718.10. 1 hit.
InterProiIPR019818. IsoCit/isopropylmalate_DH_CS.
IPR024084. IsoPropMal-DH-like_dom.
IPR004429. Isopropylmalate_DH.
[Graphical view]
PfamiPF00180. Iso_dh. 1 hit.
[Graphical view]
SMARTiSM01329. Iso_dh. 1 hit.
[Graphical view]
TIGRFAMsiTIGR00169. leuB. 1 hit.
PROSITEiPS00470. IDH_IMDH. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P04173-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSAPKKIVVL PGDHVGQEIT AEAIKVLKAI SDVRSNVKFD FENHLIGGAA
60 70 80 90 100
IDATGVPLPD EALEASKKAD AVLLGAVGGP KWGTGSVRPE QGLLKIRKEL
110 120 130 140 150
QLYANLRPCN FASDSLLDLS PIKPQFAKGT DFVVVRELVG GIYFGKRKED
160 170 180 190 200
DGDGVAWDSE QYTVPEVQRI TRMAAFMALQ HEPPLPIWSL DKANVLASSR
210 220 230 240 250
LWRKTVEETI KNEFPTLKVQ HQLIDSAAMI LVKNPTHLNG IIITSNMFGD
260 270 280 290 300
IISDEASVIP GSLGLLPSAS LASLPDKNTA FGLYEPCHGS APDLPKNKVN
310 320 330 340 350
PIATILSAAM MLKLSLNLPE EGKAIEDAVK KVLDAGIRTG DLGGSNSTTE
360
VGDAVAEEVK KILA
Length:364
Mass (Da):38,953
Last modified:March 15, 2004 - v4
Checksum:i4F312E81D829E2A3
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti69 – 691A → V (PubMed:3010239).Curated
Sequence conflicti69 – 691A → V (PubMed:6330094).Curated
Sequence conflicti69 – 691A → V (Ref. 3) Curated
Sequence conflicti300 – 3001N → D (PubMed:6330094).Curated
Sequence conflicti300 – 3001N → D (Ref. 3) Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X03840 Genomic DNA. Translation: CAA27459.1.
X59720 Genomic DNA. Translation: CAA42366.2.
M12909 Genomic DNA. Translation: AAA66917.1.
BK006937 Genomic DNA. Translation: DAA07465.1.
PIRiS19344. DEBYI.
RefSeqiNP_009911.2. NM_001178665.1.

Genome annotation databases

EnsemblFungiiCAA42366; CAA42366; CAA42366.
YCL018W; YCL018W; YCL018W.
GeneIDi850342.
KEGGisce:YCL018W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X03840 Genomic DNA. Translation: CAA27459.1.
X59720 Genomic DNA. Translation: CAA42366.2.
M12909 Genomic DNA. Translation: AAA66917.1.
BK006937 Genomic DNA. Translation: DAA07465.1.
PIRiS19344. DEBYI.
RefSeqiNP_009911.2. NM_001178665.1.

3D structure databases

ProteinModelPortaliP04173.
SMRiP04173. Positions 5-364.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi30966. 15 interactions.
DIPiDIP-7880N.
IntActiP04173. 1 interaction.
MINTiMINT-4809760.

2D gel databases

SWISS-2DPAGEP04173.

Proteomic databases

PRIDEiP04173.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiCAA42366; CAA42366; CAA42366.
YCL018W; YCL018W; YCL018W.
GeneIDi850342.
KEGGisce:YCL018W.

Organism-specific databases

EuPathDBiFungiDB:YCL018W.
SGDiS000000523. LEU2.

Phylogenomic databases

GeneTreeiENSGT00550000076087.
HOGENOMiHOG000021112.
InParanoidiP04173.
KOiK00052.
OMAiHCGPEVV.
OrthoDBiEOG7BGHWF.

Enzyme and pathway databases

UniPathwayiUPA00048; UER00072.
BioCyciMetaCyc:YCL018W-MONOMER.
YEAST:YCL018W-MONOMER.

Miscellaneous databases

PROiP04173.

Family and domain databases

Gene3Di3.40.718.10. 1 hit.
InterProiIPR019818. IsoCit/isopropylmalate_DH_CS.
IPR024084. IsoPropMal-DH-like_dom.
IPR004429. Isopropylmalate_DH.
[Graphical view]
PfamiPF00180. Iso_dh. 1 hit.
[Graphical view]
SMARTiSM01329. Iso_dh. 1 hit.
[Graphical view]
TIGRFAMsiTIGR00169. leuB. 1 hit.
PROSITEiPS00470. IDH_IMDH. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "A 'hot-spot' for Ty transposition on the left arm of yeast chromosome III."
    Warmington J.R., Anwar R., Newlon C.S., Waring R.B., Davies R.W., Indge K.J., Oliver S.G.
    Nucleic Acids Res. 14:3475-3485(1986) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "Yeast LEU2. Repression of mRNA levels by leucine and primary structure of the gene product."
    Andreadis A., Hsu Y.-P., Hermodson M., Kohlhaw G., Schimmel P.
    J. Biol. Chem. 259:8059-8062(1984) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 38626 / AH22 / NRRL Y-12843.
  3. Lu Q.
    Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  4. "The complete DNA sequence of yeast chromosome III."
    Oliver S.G., van der Aart Q.J.M., Agostoni-Carbone M.L., Aigle M., Alberghina L., Alexandraki D., Antoine G., Anwar R., Ballesta J.P.G., Benit P., Berben G., Bergantino E., Biteau N., Bolle P.-A., Bolotin-Fukuhara M., Brown A., Brown A.J.P., Buhler J.-M.
    , Carcano C., Carignani G., Cederberg H., Chanet R., Contreras R., Crouzet M., Daignan-Fornier B., Defoor E., Delgado M.D., Demolder J., Doira C., Dubois E., Dujon B., Duesterhoeft A., Erdmann D., Esteban M., Fabre F., Fairhead C., Faye G., Feldmann H., Fiers W., Francingues-Gaillard M.-C., Franco L., Frontali L., Fukuhara H., Fuller L.J., Galland P., Gent M.E., Gigot D., Gilliquet V., Glansdorff N., Goffeau A., Grenson M., Grisanti P., Grivell L.A., de Haan M., Haasemann M., Hatat D., Hoenicka J., Hegemann J.H., Herbert C.J., Hilger F., Hohmann S., Hollenberg C.P., Huse K., Iborra F., Indge K.J., Isono K., Jacq C., Jacquet M., James C.M., Jauniaux J.-C., Jia Y., Jimenez A., Kelly A., Kleinhans U., Kreisl P., Lanfranchi G., Lewis C., van der Linden C.G., Lucchini G., Lutzenkirchen K., Maat M.J., Mallet L., Mannhaupt G., Martegani E., Mathieu A., Maurer C.T.C., McConnell D., McKee R.A., Messenguy F., Mewes H.-W., Molemans F., Montague M.A., Muzi Falconi M., Navas L., Newlon C.S., Noone D., Pallier C., Panzeri L., Pearson B.M., Perea J., Philippsen P., Pierard A., Planta R.J., Plevani P., Poetsch B., Pohl F.M., Purnelle B., Ramezani Rad M., Rasmussen S.W., Raynal A., Remacha M.A., Richterich P., Roberts A.B., Rodriguez F., Sanz E., Schaaff-Gerstenschlaeger I., Scherens B., Schweitzer B., Shu Y., Skala J., Slonimski P.P., Sor F., Soustelle C., Spiegelberg R., Stateva L.I., Steensma H.Y., Steiner S., Thierry A., Thireos G., Tzermia M., Urrestarazu L.A., Valle G., Vetter I., van Vliet-Reedijk J.C., Voet M., Volckaert G., Vreken P., Wang H., Warmington J.R., von Wettstein D., Wicksteed B.L., Wilson C., Wurst H., Xu G., Yoshikawa A., Zimmermann F.K., Sgouros J.G.
    Nature 357:38-46(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  5. Valles G., Volckaerts G.
    Submitted (JUN-2001) to the EMBL/GenBank/DDBJ databases
    Cited for: SEQUENCE REVISION TO 69.
  6. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  7. "Nucleotide sequence of the 3' terminal region of the LEU2 gene from Saccharomyces cerevisiae."
    Froman B.E., Tait R.C., Rodriguez R.L.
    Gene 31:257-261(1984) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 213-364.
  8. "A multidimensional chromatography technology for in-depth phosphoproteome analysis."
    Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.
    Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiLEU3_YEAST
AccessioniPrimary (citable) accession number: P04173
Secondary accession number(s): D6VQZ6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 20, 1987
Last sequence update: March 15, 2004
Last modified: July 6, 2016
This is version 152 of the entry and version 4 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  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 III
    Yeast (Saccharomyces cerevisiae) chromosome III: entries and gene names

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.