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Protein

Isocitrate dehydrogenase [NADP] cytoplasmic

Gene

Idh1

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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

  1. isocitrate dehydrogenase (NADP+) activity Source: UniProtKB
  2. magnesium ion binding Source: UniProtKB
  3. NAD binding Source: InterPro
  4. NADP binding Source: RGD

GO - Biological processi

  1. 2-oxoglutarate metabolic process Source: UniProtKB
  2. female gonad development Source: RGD
  3. glutathione metabolic process Source: Ensembl
  4. glyoxylate cycle Source: UniProtKB-KW
  5. isocitrate metabolic process Source: UniProtKB
  6. response to organic cyclic compound Source: RGD
  7. response to oxidative stress Source: Ensembl
  8. response to steroid hormone Source: RGD
  9. 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

BRENDAi1.1.1.42. 5301.
ReactomeiREACT_282401. Abnormal conversion of 2-oxoglutarate to 2-hydroxyglutarate.
REACT_335079. NADPH regeneration.

Names & Taxonomyi

Protein namesi
Recommended name:
Isocitrate dehydrogenase [NADP] cytoplasmic (EC:1.1.1.42)
Short name:
IDH
Alternative name(s):
Cytosolic NADP-isocitrate dehydrogenase
IDP
NADP(+)-specific ICDH
Oxalosuccinate decarboxylase
Gene namesi
Name:Idh1
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
ProteomesiUP000002494 Componenti: Chromosome 9

Organism-specific databases

RGDi2862. Idh1.

Subcellular locationi

GO - Cellular componenti

  1. cytosol Source: Ensembl
  2. extracellular vesicular exosome Source: Ensembl
  3. mitochondrion Source: Ensembl
  4. peroxisome Source: HGNC
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11RemovedBy similarity
Chaini2 – 414413Isocitrate dehydrogenase [NADP] cytoplasmicPRO_0000083580Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylserineBy similarity
Modified residuei42 – 421PhosphotyrosineBy similarity
Modified residuei81 – 811N6-acetyllysineBy similarity
Modified residuei126 – 1261N6-succinyllysineBy similarity
Modified residuei224 – 2241N6-acetyllysineBy similarity
Modified residuei233 – 2331N6-acetyllysineBy similarity
Modified residuei243 – 2431N6-acetyllysineBy similarity
Modified residuei321 – 3211N6-acetyllysineBy similarity
Modified residuei400 – 4001N6-succinyllysineBy similarity

Post-translational modificationi

The N-terminus is blocked.
Acetylation at Lys-374 dramatically reduces catalytic activity.By similarity

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

PaxDbiP41562.
PRIDEiP41562.

PTM databases

PhosphoSiteiP41562.

Expressioni

Tissue specificityi

Ovary, mammary gland and liver.

Gene expression databases

ExpressionAtlasiP41562. baseline and differential.
GenevestigatoriP41562.

Interactioni

Subunit structurei

Homodimer.

Protein-protein interaction databases

BioGridi246640. 1 interaction.
MINTiMINT-4565540.

Structurei

3D structure databases

ProteinModelPortaliP41562.
SMRiP41562. Positions 4-413.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

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

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0538.
GeneTreeiENSGT00390000012547.
HOGENOMiHOG000019858.
HOVERGENiHBG006119.
InParanoidiP41562.
KOiK00031.
OMAiIHNFEDC.
OrthoDBiEOG7QNVKS.
PhylomeDBiP41562.

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.

Sequence processingi: The displayed sequence is further processed into a mature form.

P41562-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSRKIHGGSV VEMQGDEMTR IIWELIKEKL ILPYVELDLH SYDLGIENRD
60 70 80 90 100
ATNDQVTKDA AEAIKKYNVG VKCATITPDE KRVEEFKLKQ MWKSPNGTIR
110 120 130 140 150
NILGGTVFRE AIICKNIPRL VTGWVKPIII GRHAYGDQYR ATDFVVPGPG
160 170 180 190 200
KVEITYTPKD GSQKVTYLVH DFEEGGGVAM GMYNQDKSIE DFAHSSFQMA
210 220 230 240 250
LSKGWPLYLS TKNTILKKYD GRFKDIFQEI YDKQYKSKFE AQKIWYEHRL
260 270 280 290 300
IDDMVAQAMK SEGGFIWACK NYDGDVQSDS VAQGYGSLGM MTSVLICPDG
310 320 330 340 350
KTVEAEAAHG TVTRHYRMYQ KGQETSTNPI ASIFAWSRGL AHRAKLDNNT
360 370 380 390 400
ELSFFANALE EVCIETIEAG FMTKDLAACI KGLPNVQRSD YLNTFEFMDK
410
LGENLKAKLA QAKL
Length:414
Mass (Da):46,734
Last modified:November 1, 1995 - v1
Checksum:iCF69EE8746DC1AF6
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L35317 mRNA. Translation: AAA59356.1.
PIRiA54756.
RefSeqiNP_113698.1. NM_031510.1.
XP_006245111.1. XM_006245049.2.
XP_008765298.1. XM_008767076.1.
UniGeneiRn.3561.

Genome annotation databases

EnsembliENSRNOT00000020322; ENSRNOP00000020322; ENSRNOG00000015020.
GeneIDi24479.
KEGGirno:24479.
UCSCiRGD:2862. rat.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L35317 mRNA. Translation: AAA59356.1.
PIRiA54756.
RefSeqiNP_113698.1. NM_031510.1.
XP_006245111.1. XM_006245049.2.
XP_008765298.1. XM_008767076.1.
UniGeneiRn.3561.

3D structure databases

ProteinModelPortaliP41562.
SMRiP41562. Positions 4-413.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi246640. 1 interaction.
MINTiMINT-4565540.

PTM databases

PhosphoSiteiP41562.

Proteomic databases

PaxDbiP41562.
PRIDEiP41562.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSRNOT00000020322; ENSRNOP00000020322; ENSRNOG00000015020.
GeneIDi24479.
KEGGirno:24479.
UCSCiRGD:2862. rat.

Organism-specific databases

CTDi3417.
RGDi2862. Idh1.

Phylogenomic databases

eggNOGiCOG0538.
GeneTreeiENSGT00390000012547.
HOGENOMiHOG000019858.
HOVERGENiHBG006119.
InParanoidiP41562.
KOiK00031.
OMAiIHNFEDC.
OrthoDBiEOG7QNVKS.
PhylomeDBiP41562.

Enzyme and pathway databases

BRENDAi1.1.1.42. 5301.
ReactomeiREACT_282401. Abnormal conversion of 2-oxoglutarate to 2-hydroxyglutarate.
REACT_335079. NADPH regeneration.

Miscellaneous databases

NextBioi603439.
PROiP41562.

Gene expression databases

ExpressionAtlasiP41562. baseline and differential.
GenevestigatoriP41562.

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

  1. "Cytosolic NADP(+)-dependent isocitrate dehydrogenase. Isolation of rat cDNA and study of tissue-specific and developmental expression of mRNA."
    Jennings G.T., Sechi S., Stevenson P.M., Tuckey R.C., Parmelee D., McAlister-Henn L.
    J. Biol. Chem. 269:23128-23134(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Strain: Sprague-Dawley.
    Tissue: Liver.
  2. Lubec G., Afjehi-Sadat L.
    Submitted (NOV-2006) to UniProtKB
    Cited for: PROTEIN SEQUENCE OF 389-400, IDENTIFICATION BY MASS SPECTROMETRY.
    Strain: Sprague-Dawley.
    Tissue: Spinal cord.
  3. "Structural characterization of cytosolic NADP(+)-dependent isocitrate dehydrogenase from rat ovary."
    Sechi S., Parmelee D., Roller P.R., Jennings G.T.
    Enzyme Protein 48:27-36(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: PARTIAL PROTEIN SEQUENCE, CHARACTERIZATION.
    Tissue: Ovary.

Entry informationi

Entry nameiIDHC_RAT
AccessioniPrimary (citable) accession number: P41562
Secondary accession number(s): P80300
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1995
Last sequence update: November 1, 1995
Last modified: April 1, 2015
This is version 114 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

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.