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Protein

Isocitrate dehydrogenase [NADP], mitochondrial

Gene

Idh2

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

Functioni

Plays a role in intermediary metabolism and energy production. It may tightly associate or interact with the pyruvate dehydrogenase complex (By similarity).By similarity

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

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei117SubstrateBy similarity1
Binding sitei122NADPBy similarity1
Binding sitei149SubstrateBy similarity1
Binding sitei172SubstrateBy similarity1
Sitei179Critical for catalysisBy similarity1
Sitei251Critical for catalysisBy similarity1
Metal bindingi291Magnesium or manganeseBy similarity1
Binding sitei299NADPBy similarity1
Metal bindingi314Magnesium or manganeseBy similarity1
Binding sitei367NADP; via amide nitrogen and carbonyl oxygenBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi115 – 117NADPBy similarity3
Nucleotide bindingi349 – 354NADPBy similarity6

GO - Molecular functioni

GO - Biological processi

  • 2-oxoglutarate metabolic process Source: UniProtKB
  • glyoxylate cycle Source: UniProtKB-KW
  • isocitrate metabolic process Source: UniProtKB
  • NADP biosynthetic process Source: RGD
  • negative regulation of glial cell migration Source: RGD
  • negative regulation of glial cell proliferation Source: RGD
  • negative regulation of matrix metallopeptidase secretion Source: RGD
  • 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.
ReactomeiR-RNO-71403. Citric acid cycle (TCA cycle).
SABIO-RKP56574.

Names & Taxonomyi

Protein namesi
Recommended name:
Isocitrate dehydrogenase [NADP], mitochondrial (EC:1.1.1.42)
Short name:
IDH
Alternative name(s):
ICD-M
IDP
NADP(+)-specific ICDH
Oxalosuccinate decarboxylase
Gene namesi
Name:Idh2
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Chromosome 1

Organism-specific databases

RGDi1597139. Idh2.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Mitochondrion

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Transit peptidei1 – 39MitochondrionBy similarityAdd BLAST39
ChainiPRO_000008358140 – 452Isocitrate dehydrogenase [NADP], mitochondrialAdd BLAST413

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei45N6-acetyllysineBy similarity1
Modified residuei48N6-acetyllysineBy similarity1
Modified residuei67N6-acetyllysineBy similarity1
Modified residuei69N6-acetyllysineBy similarity1
Modified residuei80N6-acetyllysine; alternateBy similarity1
Modified residuei80N6-succinyllysine; alternateBy similarity1
Modified residuei106N6-acetyllysine; alternateBy similarity1
Modified residuei106N6-succinyllysine; alternateBy similarity1
Modified residuei155N6-acetyllysineBy similarity1
Modified residuei166N6-acetyllysine; alternateBy similarity1
Modified residuei166N6-succinyllysine; alternateBy similarity1
Modified residuei180N6-acetyllysine; alternateBy similarity1
Modified residuei180N6-succinyllysine; alternateBy similarity1
Modified residuei193N6-acetyllysine; alternateBy similarity1
Modified residuei193N6-succinyllysine; alternateBy similarity1
Modified residuei199N6-acetyllysineBy similarity1
Modified residuei256N6-acetyllysine; alternateBy similarity1
Modified residuei256N6-succinyllysine; alternateBy similarity1
Modified residuei263N6-acetyllysineBy similarity1
Modified residuei272N6-acetyllysineBy similarity1
Modified residuei275N6-acetyllysineBy similarity1
Modified residuei280N6-acetyllysineBy similarity1
Modified residuei282N6-acetyllysine; alternateBy similarity1
Modified residuei282N6-succinyllysine; alternateBy similarity1
Modified residuei384N6-acetyllysine; alternateBy similarity1
Modified residuei384N6-succinyllysine; alternateBy similarity1
Modified residuei400N6-acetyllysineBy similarity1
Modified residuei413N6-acetyllysineBy similarity1
Modified residuei442N6-acetyllysineBy similarity1

Post-translational modificationi

Acetylation at Lys-413 dramatically reduces catalytic activity. Deacetylated by SIRT3 (By similarity).By similarity

Keywords - PTMi

Acetylation

Proteomic databases

PaxDbiP56574.
PRIDEiP56574.

PTM databases

iPTMnetiP56574.
PhosphoSitePlusiP56574.

Expressioni

Gene expression databases

BgeeiENSRNOG00000013949.
ExpressionAtlasiP56574. baseline and differential.
GenevisibleiP56574. RN.

Interactioni

Subunit structurei

Homodimer.By similarity

Protein-protein interaction databases

BioGridi262802. 2 interactors.
IntActiP56574. 1 interactor.
MINTiMINT-1794004.
STRINGi10116.ENSRNOP00000019059.

Structurei

3D structure databases

ProteinModelPortaliP56574.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni134 – 140Substrate bindingBy similarity7

Sequence similaritiesi

Keywords - Domaini

Transit peptide

Phylogenomic databases

eggNOGiKOG1526. Eukaryota.
COG0538. LUCA.
GeneTreeiENSGT00390000012547.
HOGENOMiHOG000019858.
HOVERGENiHBG006119.
InParanoidiP56574.
KOiK00031.
OMAiGSGPKEW.
OrthoDBiEOG091G06IY.
PhylomeDBiP56574.
TreeFamiTF300428.

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.

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

P56574-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAGYLRAVSS LCRASGSTRT WAPAALNVPS WPEQPRRHYA EKRIKVEKPV
60 70 80 90 100
VEMDGDEMTR IIWQFIKEKL ILPHVDVQLK YFDLGLPNRD QTNDQVTIDS
110 120 130 140 150
ALATQKYSVA VKCATITPDE ARVEEFKLKK MWKSPNGTIR NILGGTVFRE
160 170 180 190 200
PIICKNIPRL VPGWTKPITI GRHAHGDQYK ATDFVVDRAG MFKLVFTPKD
210 220 230 240 250
GSGAKEWEVY NFPAGGVGMG MYNTDESISG FAHSCFQYSI QKKWPLYLST
260 270 280 290 300
KNTIMKAYDG RFKDIFQEIF DKHYKTDFDK NKIWYEHRLI DDMVAQVLKS
310 320 330 340 350
SGGFVWACKN YDGDVQSDIL AQGFGSLGLM TSVLVCPDGK TIEAEAAHGT
360 370 380 390 400
VTRHYREHQK GRPTSTNPIA SIFAWTRGLE HRGKLDGNQD LIRFAQTLEK
410 420 430 440 450
VCVQTVESGA MTKDLAGCIH GLSNVKLNEH FLNTTDFLDT IKSNLDRALG

KQ
Length:452
Mass (Da):50,967
Last modified:December 12, 2006 - v2
Checksum:i2466E1CC2C2CE9D1
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti49P → K AA sequence (Ref. 2) Curated1
Sequence conflicti52E → V AA sequence (Ref. 2) Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BC076398 mRNA. Translation: AAH76398.1.
RefSeqiNP_001014183.1. NM_001014161.1.
UniGeneiRn.3490.

Genome annotation databases

EnsembliENSRNOT00000019059; ENSRNOP00000019059; ENSRNOG00000013949.
GeneIDi361596.
KEGGirno:361596.
UCSCiRGD:1597139. rat.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BC076398 mRNA. Translation: AAH76398.1.
RefSeqiNP_001014183.1. NM_001014161.1.
UniGeneiRn.3490.

3D structure databases

ProteinModelPortaliP56574.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi262802. 2 interactors.
IntActiP56574. 1 interactor.
MINTiMINT-1794004.
STRINGi10116.ENSRNOP00000019059.

PTM databases

iPTMnetiP56574.
PhosphoSitePlusiP56574.

Proteomic databases

PaxDbiP56574.
PRIDEiP56574.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSRNOT00000019059; ENSRNOP00000019059; ENSRNOG00000013949.
GeneIDi361596.
KEGGirno:361596.
UCSCiRGD:1597139. rat.

Organism-specific databases

CTDi3418.
RGDi1597139. Idh2.

Phylogenomic databases

eggNOGiKOG1526. Eukaryota.
COG0538. LUCA.
GeneTreeiENSGT00390000012547.
HOGENOMiHOG000019858.
HOVERGENiHBG006119.
InParanoidiP56574.
KOiK00031.
OMAiGSGPKEW.
OrthoDBiEOG091G06IY.
PhylomeDBiP56574.
TreeFamiTF300428.

Enzyme and pathway databases

BRENDAi1.1.1.42. 5301.
ReactomeiR-RNO-71403. Citric acid cycle (TCA cycle).
SABIO-RKP56574.

Miscellaneous databases

PROiP56574.

Gene expression databases

BgeeiENSRNOG00000013949.
ExpressionAtlasiP56574. baseline and differential.
GenevisibleiP56574. RN.

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 nameiIDHP_RAT
AccessioniPrimary (citable) accession number: P56574
Secondary accession number(s): Q6DGF1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 15, 1998
Last sequence update: December 12, 2006
Last modified: November 2, 2016
This is version 112 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Miscellaneous

On the 2D-gel the determined pI of this protein (spot P8) is: 9.0, its MW is: 42 kDa.

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

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.