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Protein

Isocitrate dehydrogenase [NADP]

Gene

IDP3

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Protein inferred from homologyi

Functioni

May function in the production of NADPH for fatty acid and sterol synthesis.

Catalytic activityi

Isocitrate + NADP+ = 2-oxoglutarate + CO2 + NADPH.

Cofactori

Mg2+By similarity, Mn2+By similarityNote: Binds 1 Mg(2+) or Mn2+ ion per subunit.By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei77 – 771SubstrateBy similarity
Binding sitei82 – 821NADPBy similarity
Binding sitei109 – 1091SubstrateBy similarity
Binding sitei132 – 1321SubstrateBy similarity
Sitei139 – 1391Critical for catalysisBy similarity
Sitei212 – 2121Critical for catalysisBy similarity
Metal bindingi252 – 2521Magnesium or manganeseBy similarity
Binding sitei260 – 2601NADPBy similarity
Metal bindingi275 – 2751Magnesium or manganeseBy similarity
Binding sitei328 – 3281NADP; via amide nitrogen and carbonyl oxygenBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi75 – 773NADPBy similarity
Nucleotide bindingi310 – 3156NADPBy similarity

GO - Molecular functioni

  • isocitrate dehydrogenase (NADP+) activity Source: SGD
  • magnesium ion binding Source: InterPro
  • NAD binding Source: InterPro

GO - Biological processi

  • fatty acid beta-oxidation Source: SGD
  • glyoxylate cycle Source: UniProtKB-KW
  • isocitrate metabolic process Source: InterPro
  • NADPH regeneration Source: SGD
  • tricarboxylic acid cycle Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Glyoxylate bypass, Tricarboxylic acid cycle

Keywords - Ligandi

Magnesium, Manganese, Metal-binding, NADP

Enzyme and pathway databases

BioCyciYEAST:YNL009W-MONOMER.
ReactomeiREACT_278278. Citric acid cycle (TCA cycle).
REACT_350026. NADPH regeneration.
SABIO-RKP53982.

Names & Taxonomyi

Protein namesi
Recommended name:
Isocitrate dehydrogenase [NADP] (EC:1.1.1.42)
Short name:
IDH
Alternative name(s):
IDP
NADP(+)-specific ICDH
Oxalosuccinate decarboxylase
Gene namesi
Name:IDP3
Ordered Locus Names:YNL009W
ORF Names:N2870
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311 Componenti: Chromosome XIV

Organism-specific databases

CYGDiYNL009w.
EuPathDBiFungiDB:YNL009W.
SGDiS000004954. IDP3.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: SGD
  • peroxisome Source: SGD
Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 420420Isocitrate dehydrogenase [NADP]PRO_0000083588Add
BLAST

Proteomic databases

MaxQBiP53982.
PaxDbiP53982.
PeptideAtlasiP53982.
PRIDEiP53982.

Interactioni

Protein-protein interaction databases

BioGridi35816. 29 interactions.
DIPiDIP-4693N.
IntActiP53982. 4 interactions.
MINTiMINT-473180.

Structurei

3D structure databases

ProteinModelPortaliP53982.
SMRiP53982. Positions 2-404.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni94 – 1007Substrate bindingBy similarity

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0538.
GeneTreeiENSGT00390000012547.
HOGENOMiHOG000019858.
InParanoidiP53982.
KOiK00031.
OMAiGGIAMAM.
OrthoDBiEOG7G4QQD.

Family and domain databases

Gene3Di3.40.718.10. 1 hit.
InterProiIPR019818. IsoCit/isopropylmalate_DH_CS.
IPR004790. Isocitrate_DH_NADP.
IPR024084. IsoPropMal-DH-like_dom.
[Graphical view]
PANTHERiPTHR11822. PTHR11822. 1 hit.
PfamiPF00180. Iso_dh. 1 hit.
[Graphical view]
PIRSFiPIRSF000108. IDH_NADP. 1 hit.
TIGRFAMsiTIGR00127. nadp_idh_euk. 1 hit.
PROSITEiPS00470. IDH_IMDH. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P53982-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSKIKVVHPI VEMDGDEQTR VIWKLIKEKL ILPYLDVDLK YYDLSIQERD
60 70 80 90 100
RTNDQVTKDS SYATLKYGVA VKCATITPDE ARMKEFNLKE MWKSPNGTIR
110 120 130 140 150
NILGGTVFRE PIIIPKIPRL VPHWEKPIII GRHAFGDQYR ATDIKIKKAG
160 170 180 190 200
KLRLQFSSDD GKENIDLKVY EFPKSGGIAM AMFNTNDSIK GFAKASFELA
210 220 230 240 250
LKRKLPLFFT TKNTILKNYD NQFKQIFDNL FDKEYKEKFQ ALKITYEHRL
260 270 280 290 300
IDDMVAQMLK SKGGFIIAMK NYDGDVQSDI VAQGFGSLGL MTSILITPDG
310 320 330 340 350
KTFESEAAHG TVTRHFRKHQ RGEETSTNSI ASIFAWTRAI IQRGKLDNTD
360 370 380 390 400
DVIKFGNLLE KATLDTVQVG GKMTKDLALM LGKTNRSSYV TTEEFIDEVA
410 420
KRLQNMMLSS NEDKKGMCKL
Length:420
Mass (Da):47,856
Last modified:October 1, 1996 - v1
Checksum:i4094007E13FCD506
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z71285 Genomic DNA. Translation: CAA95869.1.
AY693154 Genomic DNA. Translation: AAT93173.1.
BK006947 Genomic DNA. Translation: DAA10534.1.
PIRiS62921.
RefSeqiNP_014389.3. NM_001182848.3.

Genome annotation databases

EnsemblFungiiYNL009W; YNL009W; YNL009W.
GeneIDi855723.
KEGGisce:YNL009W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z71285 Genomic DNA. Translation: CAA95869.1.
AY693154 Genomic DNA. Translation: AAT93173.1.
BK006947 Genomic DNA. Translation: DAA10534.1.
PIRiS62921.
RefSeqiNP_014389.3. NM_001182848.3.

3D structure databases

ProteinModelPortaliP53982.
SMRiP53982. Positions 2-404.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi35816. 29 interactions.
DIPiDIP-4693N.
IntActiP53982. 4 interactions.
MINTiMINT-473180.

Proteomic databases

MaxQBiP53982.
PaxDbiP53982.
PeptideAtlasiP53982.
PRIDEiP53982.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYNL009W; YNL009W; YNL009W.
GeneIDi855723.
KEGGisce:YNL009W.

Organism-specific databases

CYGDiYNL009w.
EuPathDBiFungiDB:YNL009W.
SGDiS000004954. IDP3.

Phylogenomic databases

eggNOGiCOG0538.
GeneTreeiENSGT00390000012547.
HOGENOMiHOG000019858.
InParanoidiP53982.
KOiK00031.
OMAiGGIAMAM.
OrthoDBiEOG7G4QQD.

Enzyme and pathway databases

BioCyciYEAST:YNL009W-MONOMER.
ReactomeiREACT_278278. Citric acid cycle (TCA cycle).
REACT_350026. NADPH regeneration.
SABIO-RKP53982.

Miscellaneous databases

NextBioi980090.
PROiP53982.

Family and domain databases

Gene3Di3.40.718.10. 1 hit.
InterProiIPR019818. IsoCit/isopropylmalate_DH_CS.
IPR004790. Isocitrate_DH_NADP.
IPR024084. IsoPropMal-DH-like_dom.
[Graphical view]
PANTHERiPTHR11822. PTHR11822. 1 hit.
PfamiPF00180. Iso_dh. 1 hit.
[Graphical view]
PIRSFiPIRSF000108. IDH_NADP. 1 hit.
TIGRFAMsiTIGR00127. nadp_idh_euk. 1 hit.
PROSITEiPS00470. IDH_IMDH. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The nucleotide sequence of Saccharomyces cerevisiae chromosome XIV and its evolutionary implications."
    Philippsen P., Kleine K., Poehlmann R., Duesterhoeft A., Hamberg K., Hegemann J.H., Obermaier B., Urrestarazu L.A., Aert R., Albermann K., Altmann R., Andre B., Baladron V., Ballesta J.P.G., Becam A.-M., Beinhauer J.D., Boskovic J., Buitrago M.J.
    , Bussereau F., Coster F., Crouzet M., D'Angelo M., Dal Pero F., De Antoni A., del Rey F., Doignon F., Domdey H., Dubois E., Fiedler T.A., Fleig U., Floeth M., Fritz C., Gaillardin C., Garcia-Cantalejo J.M., Glansdorff N., Goffeau A., Gueldener U., Herbert C.J., Heumann K., Heuss-Neitzel D., Hilbert H., Hinni K., Iraqui Houssaini I., Jacquet M., Jimenez A., Jonniaux J.-L., Karpfinger-Hartl L., Lanfranchi G., Lepingle A., Levesque H., Lyck R., Maftahi M., Mallet L., Maurer C.T.C., Messenguy F., Mewes H.-W., Moestl D., Nasr F., Nicaud J.-M., Niedenthal R.K., Pandolfo D., Pierard A., Piravandi E., Planta R.J., Pohl T.M., Purnelle B., Rebischung C., Remacha M.A., Revuelta J.L., Rinke M., Saiz J.E., Sartorello F., Scherens B., Sen-Gupta M., Soler-Mira A., Urbanus J.H.M., Valle G., Van Dyck L., Verhasselt P., Vierendeels F., Vissers S., Voet M., Volckaert G., Wach A., Wambutt R., Wedler H., Zollner A., Hani J.
    Nature 387:93-98(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  2. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  3. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 204508 / S288c.

Entry informationi

Entry nameiIDHH_YEAST
AccessioniPrimary (citable) accession number: P53982
Secondary accession number(s): D6W1G8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: October 1, 1996
Last modified: July 22, 2015
This is version 124 of the entry and version 1 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. SIMILARITY comments
    Index of protein domains and families
  2. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  3. Yeast chromosome XIV
    Yeast (Saccharomyces cerevisiae) chromosome XIV: entries and gene names

External Data

Dasty 3

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 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.