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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 Mg2+ or Mn2+ ion per subunit.By similarity

Enzyme regulationi

By catabolite repression.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei77SubstrateBy similarity1
Binding sitei82NADPBy similarity1
Binding sitei109SubstrateBy similarity1
Binding sitei132SubstrateBy similarity1
Sitei139Critical for catalysisBy similarity1
Sitei212Critical for catalysisBy similarity1
Metal bindingi252Magnesium or manganeseBy similarity1
Binding sitei260NADPBy similarity1
Metal bindingi275Magnesium or manganeseBy similarity1
Binding sitei328NADP; via amide nitrogen and carbonyl oxygenBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi75 – 77NADPBy similarity3
Nucleotide bindingi310 – 315NADPBy similarity6

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.
ReactomeiR-SCE-389542. NADPH regeneration.
R-SCE-6798695. Neutrophil degranulation.
R-SCE-71403. Citric acid cycle (TCA cycle).
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
Proteomesi
  • UP000002311 Componenti: Chromosome XII

Organism-specific databases

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)DescriptionActionsGraphical viewLength
ChainiPRO_00000835871 – 412Isocitrate dehydrogenase [NADP] cytoplasmicAdd BLAST412

Post-translational modificationi

The N-terminus is blocked.

Proteomic databases

MaxQBiP41939.
PRIDEiP41939.

Interactioni

Subunit structurei

Homodimer.

Protein-protein interaction databases

BioGridi31445. 18 interactors.
DIPiDIP-4252N.
IntActiP41939. 1 interactor.
MINTiMINT-545477.

Structurei

3D structure databases

ProteinModelPortaliP41939.
SMRiP41939.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni94 – 100Substrate bindingBy similarity7

Sequence similaritiesi

Phylogenomic databases

GeneTreeiENSGT00860000135234.
HOGENOMiHOG000019858.
InParanoidiP41939.
KOiK00031.
OMAiEYPVYNF.
OrthoDBiEOG092C2D51.

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.
SMARTiSM01329. Iso_dh. 1 hit.
[Graphical view]
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)DescriptionActionsGraphical viewLength
Sequence conflicti24 – 27HLIR → SFNQ in AAA64516 (PubMed:8068643).Curated4
Sequence conflicti68G → R in AAA64516 (PubMed:8068643).Curated1
Sequence conflicti185T → N in AAA64516 (PubMed:8068643).Curated1
Sequence conflicti232 – 239ARSYKEKF → LEVIKRSL in AAA64516 (PubMed:8068643).Curated8
Sequence conflicti267I → M in AAA64516 (PubMed:8068643).Curated1
Sequence conflicti306 – 307EA → DR in AAA64516 (PubMed:8068643).Curated2
Sequence conflicti316 – 323FRQHQQGK → LTDYDKGR in AAA64516 (PubMed:8068643).Curated8

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.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi31445. 18 interactors.
DIPiDIP-4252N.
IntActiP41939. 1 interactor.
MINTiMINT-545477.

Proteomic databases

MaxQBiP41939.
PRIDEiP41939.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

EuPathDBiFungiDB:YLR174W.
SGDiS000004164. IDP2.

Phylogenomic databases

GeneTreeiENSGT00860000135234.
HOGENOMiHOG000019858.
InParanoidiP41939.
KOiK00031.
OMAiEYPVYNF.
OrthoDBiEOG092C2D51.

Enzyme and pathway databases

BioCyciMetaCyc:YLR174W-MONOMER.
YEAST:YLR174W-MONOMER.
BRENDAi1.1.1.42. 984.
ReactomeiR-SCE-389542. NADPH regeneration.
R-SCE-6798695. Neutrophil degranulation.
R-SCE-71403. Citric acid cycle (TCA cycle).
SABIO-RKP41939.

Miscellaneous databases

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.
SMARTiSM01329. Iso_dh. 1 hit.
[Graphical view]
TIGRFAMsiTIGR00127. nadp_idh_euk. 1 hit.
PROSITEiPS00470. IDH_IMDH. 1 hit.
[Graphical view]
ProtoNetiSearch...

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: November 30, 2016
This is version 141 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

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.