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Protein

Isocitrate dehydrogenase [NADP] cytoplasmic

Gene

IDP2

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

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

Enzyme regulationi

By catabolite repression.

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

  • glyoxylate cycle Source: UniProtKB-KW
  • isocitrate metabolic process 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

BioCyciMetaCyc:YLR174W-MONOMER.
YEAST:YLR174W-MONOMER.
BRENDAi1.1.1.42. 984.
ReactomeiREACT_278278. Citric acid cycle (TCA cycle).
REACT_350026. NADPH regeneration.
SABIO-RKP41939.

Names & Taxonomyi

Protein namesi
Recommended name:
Isocitrate dehydrogenase [NADP] cytoplasmic (EC:1.1.1.42)
Short name:
IDH
Alternative name(s):
IDP
NADP(+)-specific ICDH
Oxalosuccinate decarboxylase
Gene namesi
Name:IDP2
Ordered Locus Names:YLR174W
ORF Names:L9470.12
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311 Componenti: Chromosome XII

Organism-specific databases

CYGDiYLR174w.
EuPathDBiFungiDB:YLR174W.
SGDiS000004164. IDP2.

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 – 412412Isocitrate dehydrogenase [NADP] cytoplasmicPRO_0000083587Add
BLAST

Post-translational modificationi

The N-terminus is blocked.

Proteomic databases

MaxQBiP41939.
PaxDbiP41939.
PeptideAtlasiP41939.
PRIDEiP41939.

Interactioni

Subunit structurei

Homodimer.

Protein-protein interaction databases

BioGridi31445. 18 interactions.
DIPiDIP-4252N.
IntActiP41939. 1 interaction.
MINTiMINT-545477.

Structurei

3D structure databases

ProteinModelPortaliP41939.
SMRiP41939. Positions 2-408.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

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

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0538.
GeneTreeiENSGT00390000012547.
HOGENOMiHOG000019858.
InParanoidiP41939.
KOiK00031.
OMAiFGQILES.
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.

P41939-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTKIKVANPI VEMDGDEQTR IIWHLIRDKL VLPYLDVDLK YYDLSVEYRD
60 70 80 90 100
QTNDQVTVDS ATATLKYGVA VKCATITPDE ARVEEFHLKK MWKSPNGTIR
110 120 130 140 150
NILGGTVFRE PIIIPRIPRL VPQWEKPIII GRHAFGDQYK ATDVIVPEEG
160 170 180 190 200
ELRLVYKSKS GTHDVDLKVF DYPEHGGVAM MMYNTTDSIE GFAKASFELA
210 220 230 240 250
IERKLPLYST TKNTILKKYD GKFKDVFEAM YARSYKEKFE SLGIWYEHRL
260 270 280 290 300
IDDMVAQMLK SKGGYIIAMK NYDGDVESDI VAQGFGSLGL MTSVLITPDG
310 320 330 340 350
KTFESEAAHG TVTRHFRQHQ QGKETSTNSI ASIFAWTRGI IQRGKLDNTP
360 370 380 390 400
DVVKFGQILE SATVNTVQED GIMTKDLALI LGKSERSAYV TTEEFIDAVE
410
SRLKKEFEAA AL
Length:412
Mass (Da):46,562
Last modified:October 1, 1996 - v2
Checksum:i83EB54CC56A29857
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti24 – 274HLIR → SFNQ in AAA64516 (PubMed:8068643).Curated
Sequence conflicti68 – 681G → R in AAA64516 (PubMed:8068643).Curated
Sequence conflicti185 – 1851T → N in AAA64516 (PubMed:8068643).Curated
Sequence conflicti232 – 2398ARSYKEKF → LEVIKRSL in AAA64516 (PubMed:8068643).Curated
Sequence conflicti267 – 2671I → M in AAA64516 (PubMed:8068643).Curated
Sequence conflicti306 – 3072EA → DR in AAA64516 (PubMed:8068643).Curated
Sequence conflicti316 – 3238FRQHQQGK → LTDYDKGR in AAA64516 (PubMed:8068643).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L26312 Genomic DNA. Translation: AAA64516.1.
U17246 Genomic DNA. Translation: AAB67464.1.
BK006945 Genomic DNA. Translation: DAA09494.1.
PIRiS51419.
RefSeqiNP_013275.1. NM_001182061.1.

Genome annotation databases

EnsemblFungiiYLR174W; YLR174W; YLR174W.
GeneIDi850871.
KEGGisce:YLR174W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L26312 Genomic DNA. Translation: AAA64516.1.
U17246 Genomic DNA. Translation: AAB67464.1.
BK006945 Genomic DNA. Translation: DAA09494.1.
PIRiS51419.
RefSeqiNP_013275.1. NM_001182061.1.

3D structure databases

ProteinModelPortaliP41939.
SMRiP41939. Positions 2-408.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi31445. 18 interactions.
DIPiDIP-4252N.
IntActiP41939. 1 interaction.
MINTiMINT-545477.

Proteomic databases

MaxQBiP41939.
PaxDbiP41939.
PeptideAtlasiP41939.
PRIDEiP41939.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYLR174W; YLR174W; YLR174W.
GeneIDi850871.
KEGGisce:YLR174W.

Organism-specific databases

CYGDiYLR174w.
EuPathDBiFungiDB:YLR174W.
SGDiS000004164. IDP2.

Phylogenomic databases

eggNOGiCOG0538.
GeneTreeiENSGT00390000012547.
HOGENOMiHOG000019858.
InParanoidiP41939.
KOiK00031.
OMAiFGQILES.
OrthoDBiEOG7G4QQD.

Enzyme and pathway databases

BioCyciMetaCyc:YLR174W-MONOMER.
YEAST:YLR174W-MONOMER.
BRENDAi1.1.1.42. 984.
ReactomeiREACT_278278. Citric acid cycle (TCA cycle).
REACT_350026. NADPH regeneration.
SABIO-RKP41939.

Miscellaneous databases

NextBioi967206.
PROiP41939.

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. "Isolation, characterization, and disruption of the yeast gene encoding cytosolic NADP-specific isocitrate dehydrogenase."
    Loftus T.M., Hall L.V., Anderson S.L., McAlister-Henn L.
    Biochemistry 33:9661-9667(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PARTIAL PROTEIN SEQUENCE, CHARACTERIZATION.
  2. "The nucleotide sequence of Saccharomyces cerevisiae chromosome XII."
    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.
    Nature 387:87-90(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  3. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  4. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  5. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiIDHC_YEAST
AccessioniPrimary (citable) accession number: P41939
Secondary accession number(s): D6VYH8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1995
Last sequence update: October 1, 1996
Last modified: July 22, 2015
This is version 130 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 2620 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

Complete proteome, Direct protein sequencing, 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 XII
    Yeast (Saccharomyces cerevisiae) chromosome XII: 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.