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Protein

Isocitrate dehydrogenase [NADP] cytoplasmic

Gene

Idh1

Organism
Mus musculus (Mouse)
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

GO - Biological processi

  • 2-oxoglutarate metabolic process Source: UniProtKB
  • female gonad development Source: Ensembl
  • glutathione metabolic process Source: MGI
  • glyoxylate cycle Source: UniProtKB-KW
  • isocitrate metabolic process Source: UniProtKB
  • regulation of phospholipid biosynthetic process Source: MGI
  • regulation of phospholipid catabolic process Source: MGI
  • response to oxidative stress Source: MGI
  • response to steroid hormone Source: Ensembl
  • 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. 3474.
ReactomeiREACT_298351. 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
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
ProteomesiUP000000589 Componenti: Chromosome 1

Organism-specific databases

MGIiMGI:96413. Idh1.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: MGI
  • cytosol Source: MGI
  • extracellular exosome Source: MGI
  • mitochondrion Source: MGI
  • peroxisome Source: MGI
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_0000083578Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylserineBy similarity
Modified residuei42 – 421PhosphotyrosineBy similarity
Modified residuei81 – 811N6-acetyllysine1 Publication
Modified residuei126 – 1261N6-succinyllysine1 Publication
Modified residuei224 – 2241N6-acetyllysine1 Publication
Modified residuei233 – 2331N6-acetyllysine1 Publication
Modified residuei243 – 2431N6-acetyllysine1 Publication
Modified residuei321 – 3211N6-acetyllysineBy similarity
Modified residuei400 – 4001N6-succinyllysine1 Publication

Post-translational modificationi

Acetylation at Lys-374 dramatically reduces catalytic activity.By similarity

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

MaxQBiO88844.
PaxDbiO88844.
PRIDEiO88844.

2D gel databases

COMPLUYEAST-2DPAGEO88844.
REPRODUCTION-2DPAGEO88844.
SWISS-2DPAGEO88844.

PTM databases

PhosphoSiteiO88844.

Expressioni

Gene expression databases

BgeeiO88844.
CleanExiMM_IDH1.
ExpressionAtlasiO88844. baseline and differential.
GenevisibleiO88844. MM.

Interactioni

Subunit structurei

Homodimer.By similarity

Protein-protein interaction databases

IntActiO88844. 5 interactions.
MINTiMINT-1859161.
STRINGi10090.ENSMUSP00000095316.

Structurei

Secondary structure

1
414
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi5 – 1410Combined sources
Helixi17 – 3014Combined sources
Turni31 – 344Combined sources
Beta strandi35 – 439Combined sources
Helixi46 – 516Combined sources
Turni52 – 543Combined sources
Helixi55 – 6713Combined sources
Beta strandi68 – 725Combined sources
Helixi80 – 867Combined sources
Helixi95 – 1039Combined sources
Beta strandi106 – 1116Combined sources
Beta strandi128 – 1336Combined sources
Helixi137 – 1404Combined sources
Beta strandi142 – 1465Combined sources
Beta strandi148 – 16215Combined sources
Beta strandi165 – 1728Combined sources
Beta strandi177 – 1859Combined sources
Helixi186 – 20318Combined sources
Beta strandi207 – 2115Combined sources
Turni213 – 2153Combined sources
Helixi219 – 23416Combined sources
Helixi236 – 2416Combined sources
Beta strandi246 – 2505Combined sources
Helixi251 – 26010Combined sources
Beta strandi265 – 2695Combined sources
Helixi271 – 28515Combined sources
Beta strandi290 – 2967Combined sources
Beta strandi303 – 3064Combined sources
Helixi313 – 3208Combined sources
Helixi330 – 34718Combined sources
Helixi350 – 36819Combined sources
Helixi374 – 3818Combined sources
Helixi383 – 3853Combined sources
Helixi388 – 3903Combined sources
Helixi394 – 41219Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2CMJX-ray1.99A/B4-413[»]
2CMVX-ray2.52A/B4-413[»]
ProteinModelPortaliO88844.
SMRiO88844. Positions 4-413.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO88844.

Family & Domainsi

Region

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

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0538.
GeneTreeiENSGT00390000012547.
HOGENOMiHOG000019858.
HOVERGENiHBG006119.
InParanoidiO88844.
KOiK00031.
OMAiHNFESCG.
OrthoDBiEOG7QNVKS.
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.

O88844-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSRKIQGGSV 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 GTQKVTYMVH DFEEGGGVAM GMYNQDKSIE DFAHSSFQMA
210 220 230 240 250
LSKGWPLYLS TKNTILKKYD GRFKDIFQEI YDKKYKSQFE AQKICYEHRL
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
ELSFFAKALE DVCIETIEAG FMTKDLAACI KGLPNVQRSD YLNTFEFMDK
410
LGENLKAKLA QAKL
Length:414
Mass (Da):46,674
Last modified:July 27, 2011 - v2
Checksum:iC7FEF315D042C44C
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti243 – 2431K → N in AAD02919 (PubMed:9866202).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF020039 mRNA. Translation: AAD02919.1.
AK149019 mRNA. Translation: BAE28720.1.
AK151212 mRNA. Translation: BAE30207.1.
AK159173 mRNA. Translation: BAE34873.1.
AK160896 mRNA. Translation: BAE36075.1.
AK167158 mRNA. Translation: BAE39299.1.
CH466548 Genomic DNA. Translation: EDL00223.1.
CH466548 Genomic DNA. Translation: EDL00225.1.
CCDSiCCDS15016.1.
RefSeqiNP_001104790.1. NM_001111320.1.
NP_034627.3. NM_010497.3.
UniGeneiMm.9925.

Genome annotation databases

EnsembliENSMUST00000097709; ENSMUSP00000095316; ENSMUSG00000025950.
ENSMUST00000169032; ENSMUSP00000127307; ENSMUSG00000025950.
GeneIDi15926.
KEGGimmu:15926.
UCSCiuc007bhn.2. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF020039 mRNA. Translation: AAD02919.1.
AK149019 mRNA. Translation: BAE28720.1.
AK151212 mRNA. Translation: BAE30207.1.
AK159173 mRNA. Translation: BAE34873.1.
AK160896 mRNA. Translation: BAE36075.1.
AK167158 mRNA. Translation: BAE39299.1.
CH466548 Genomic DNA. Translation: EDL00223.1.
CH466548 Genomic DNA. Translation: EDL00225.1.
CCDSiCCDS15016.1.
RefSeqiNP_001104790.1. NM_001111320.1.
NP_034627.3. NM_010497.3.
UniGeneiMm.9925.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2CMJX-ray1.99A/B4-413[»]
2CMVX-ray2.52A/B4-413[»]
ProteinModelPortaliO88844.
SMRiO88844. Positions 4-413.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiO88844. 5 interactions.
MINTiMINT-1859161.
STRINGi10090.ENSMUSP00000095316.

PTM databases

PhosphoSiteiO88844.

2D gel databases

COMPLUYEAST-2DPAGEO88844.
REPRODUCTION-2DPAGEO88844.
SWISS-2DPAGEO88844.

Proteomic databases

MaxQBiO88844.
PaxDbiO88844.
PRIDEiO88844.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000097709; ENSMUSP00000095316; ENSMUSG00000025950.
ENSMUST00000169032; ENSMUSP00000127307; ENSMUSG00000025950.
GeneIDi15926.
KEGGimmu:15926.
UCSCiuc007bhn.2. mouse.

Organism-specific databases

CTDi3417.
MGIiMGI:96413. Idh1.

Phylogenomic databases

eggNOGiCOG0538.
GeneTreeiENSGT00390000012547.
HOGENOMiHOG000019858.
HOVERGENiHBG006119.
InParanoidiO88844.
KOiK00031.
OMAiHNFESCG.
OrthoDBiEOG7QNVKS.
TreeFamiTF300428.

Enzyme and pathway databases

BRENDAi1.1.1.42. 3474.
ReactomeiREACT_298351. NADPH regeneration.

Miscellaneous databases

EvolutionaryTraceiO88844.
NextBioi288640.
PROiO88844.
SOURCEiSearch...

Gene expression databases

BgeeiO88844.
CleanExiMM_IDH1.
ExpressionAtlasiO88844. baseline and differential.
GenevisibleiO88844. MM.

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. "Cytosolic isocitrate dehydrogenase in humans, mice, and voles and phylogenetic analysis of the enzyme family."
    Nekrutenko A., Hillis D.M., Patton J.C., Bradley R.D., Baker R.J.
    Mol. Biol. Evol. 15:1674-1684(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
  2. "The transcriptional landscape of the mammalian genome."
    Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.
    , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
    Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: C57BL/6J.
    Tissue: Bone marrow, Embryo and Sympathetic ganglion.
  3. Mural R.J., Adams M.D., Myers E.W., Smith H.O., Venter J.C.
    Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  4. Lubec G., Yang J.W., Zigmond M.
    Submitted (JUL-2007) to UniProtKB
    Cited for: PROTEIN SEQUENCE OF 30-49.
    Tissue: Brain.
  5. "SIRT5-mediated lysine desuccinylation impacts diverse metabolic pathways."
    Park J., Chen Y., Tishkoff D.X., Peng C., Tan M., Dai L., Xie Z., Zhang Y., Zwaans B.M., Skinner M.E., Lombard D.B., Zhao Y.
    Mol. Cell 50:919-930(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUCCINYLATION [LARGE SCALE ANALYSIS] AT LYS-126 AND LYS-400, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Embryonic fibroblast and Liver.
  6. "Label-free quantitative proteomics of the lysine acetylome in mitochondria identifies substrates of SIRT3 in metabolic pathways."
    Rardin M.J., Newman J.C., Held J.M., Cusack M.P., Sorensen D.J., Li B., Schilling B., Mooney S.D., Kahn C.R., Verdin E., Gibson B.W.
    Proc. Natl. Acad. Sci. U.S.A. 110:6601-6606(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-81; LYS-224; LYS-233 AND LYS-243, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Liver.

Entry informationi

Entry nameiIDHC_MOUSE
AccessioniPrimary (citable) accession number: O88844
Secondary accession number(s): Q3UAV7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: July 27, 2011
Last modified: June 24, 2015
This is version 122 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. 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.