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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 Mg(2+) or Mn2+ ion per subunit.By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei117 – 1171SubstrateBy similarity
Binding sitei122 – 1221NADPBy similarity
Binding sitei149 – 1491SubstrateBy similarity
Binding sitei172 – 1721SubstrateBy similarity
Sitei179 – 1791Critical for catalysisBy similarity
Sitei251 – 2511Critical for catalysisBy similarity
Metal bindingi291 – 2911Magnesium or manganeseBy similarity
Binding sitei299 – 2991NADPBy similarity
Metal bindingi314 – 3141Magnesium or manganeseBy similarity
Binding sitei367 – 3671NADP; via amide nitrogen and carbonyl oxygenBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi115 – 1173NADPBy similarity
Nucleotide bindingi349 – 3546NADPBy similarity

GO - Molecular functioni

GO - Biological processi

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_338796. 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
ProteomesiUP000002494 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)LengthDescriptionGraphical viewFeature identifierActions
Transit peptidei1 – 3939MitochondrionBy similarityAdd
BLAST
Chaini40 – 452413Isocitrate dehydrogenase [NADP], mitochondrialPRO_0000083581Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei45 – 451N6-acetyllysineBy similarity
Modified residuei48 – 481N6-acetyllysineBy similarity
Modified residuei67 – 671N6-acetyllysineBy similarity
Modified residuei69 – 691N6-acetyllysineBy similarity
Modified residuei80 – 801N6-acetyllysine; alternateBy similarity
Modified residuei80 – 801N6-succinyllysine; alternateBy similarity
Modified residuei106 – 1061N6-acetyllysine; alternateBy similarity
Modified residuei106 – 1061N6-succinyllysine; alternateBy similarity
Modified residuei155 – 1551N6-acetyllysineBy similarity
Modified residuei166 – 1661N6-acetyllysine; alternateBy similarity
Modified residuei166 – 1661N6-succinyllysine; alternateBy similarity
Modified residuei180 – 1801N6-acetyllysine; alternateBy similarity
Modified residuei180 – 1801N6-succinyllysine; alternateBy similarity
Modified residuei193 – 1931N6-acetyllysine; alternateBy similarity
Modified residuei193 – 1931N6-succinyllysine; alternateBy similarity
Modified residuei199 – 1991N6-acetyllysineBy similarity
Modified residuei256 – 2561N6-acetyllysine; alternateBy similarity
Modified residuei256 – 2561N6-succinyllysine; alternateBy similarity
Modified residuei263 – 2631N6-acetyllysineBy similarity
Modified residuei272 – 2721N6-acetyllysineBy similarity
Modified residuei275 – 2751N6-acetyllysineBy similarity
Modified residuei280 – 2801N6-acetyllysineBy similarity
Modified residuei282 – 2821N6-acetyllysine; alternateBy similarity
Modified residuei282 – 2821N6-succinyllysine; alternateBy similarity
Modified residuei360 – 3601N6-acetyllysineBy similarity
Modified residuei384 – 3841N6-acetyllysine; alternateBy similarity
Modified residuei384 – 3841N6-succinyllysine; alternateBy similarity
Modified residuei400 – 4001N6-acetyllysineBy similarity
Modified residuei413 – 4131N6-acetyllysineBy similarity
Modified residuei442 – 4421N6-acetyllysineBy similarity

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

PhosphoSiteiP56574.

Expressioni

Gene expression databases

GenevisibleiP56574. RN.

Interactioni

Subunit structurei

Homodimer.By similarity

Protein-protein interaction databases

BioGridi262802. 1 interaction.
IntActiP56574. 1 interaction.
MINTiMINT-1794004.
STRINGi10116.ENSRNOP00000019059.

Structurei

3D structure databases

ProteinModelPortaliP56574.
SMRiP56574. Positions 40-452.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni134 – 1407Substrate bindingBy similarity

Sequence similaritiesi

Keywords - Domaini

Transit peptide

Phylogenomic databases

eggNOGiCOG0538.
GeneTreeiENSGT00390000012547.
HOGENOMiHOG000019858.
HOVERGENiHBG006119.
InParanoidiP56574.
KOiK00031.
OMAiQVIEHDV.
OrthoDBiEOG7QNVKS.
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.
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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti49 – 491P → K AA sequence (Ref. 2) Curated
Sequence conflicti52 – 521E → V AA sequence (Ref. 2) Curated

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.
SMRiP56574. Positions 40-452.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi262802. 1 interaction.
IntActiP56574. 1 interaction.
MINTiMINT-1794004.
STRINGi10116.ENSRNOP00000019059.

PTM databases

PhosphoSiteiP56574.

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

eggNOGiCOG0538.
GeneTreeiENSGT00390000012547.
HOGENOMiHOG000019858.
HOVERGENiHBG006119.
InParanoidiP56574.
KOiK00031.
OMAiQVIEHDV.
OrthoDBiEOG7QNVKS.
PhylomeDBiP56574.
TreeFamiTF300428.

Enzyme and pathway databases

BRENDAi1.1.1.42. 5301.
ReactomeiREACT_338796. Citric acid cycle (TCA cycle).
SABIO-RKP56574.

Miscellaneous databases

NextBioi676849.
PROiP56574.

Gene expression databases

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

Publicationsi

« Hide 'large scale' publications
  1. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Kidney.
  2. Cited for: PROTEIN SEQUENCE OF 40-52, SUBCELLULAR LOCATION.
    Strain: Wistar.
    Tissue: Heart.
  3. Lubec G., Chen W.-Q.
    Submitted (APR-2007) to UniProtKB
    Cited for: PROTEIN SEQUENCE OF 61-67; 70-89; 113-122; 141-149; 181-188; 244-251; 262-272; 289-299; 341-353 AND 414-426, IDENTIFICATION BY MASS SPECTROMETRY.
    Strain: Sprague-Dawley.
    Tissue: Hippocampus.

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: June 24, 2015
This is version 100 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

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.