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O88844

- IDHC_MOUSE

UniProt

O88844 - IDHC_MOUSE

Protein

Isocitrate dehydrogenase [NADP] cytoplasmic

Gene

Idh1

Organism
Mus musculus (Mouse)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 114 (01 Oct 2014)
      Sequence version 2 (27 Jul 2011)
      Previous versions | rss
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    Functioni

    Catalytic activityi

    Isocitrate + NADP+ = 2-oxoglutarate + CO2 + NADPH.

    Cofactori

    Binds 1 magnesium or manganese 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: Ensembl

    GO - Biological processi

    1. 2-oxoglutarate metabolic process Source: UniProtKB
    2. female gonad development Source: Ensembl
    3. glutathione metabolic process Source: MGI
    4. glyoxylate cycle Source: UniProtKB-KW
    5. isocitrate metabolic process Source: UniProtKB
    6. response to oxidative stress Source: MGI
    7. response to steroid hormone Source: Ensembl
    8. tricarboxylic acid cycle Source: UniProtKB-KW

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    Glyoxylate bypass, Tricarboxylic acid cycle

    Keywords - Ligandi

    Magnesium, Manganese, Metal-binding, NADP

    Enzyme and pathway databases

    ReactomeiREACT_198632. Abnormal conversion of 2-oxoglutarate to 2-hydroxyglutarate.

    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: Chromosome 1

    Organism-specific databases

    MGIiMGI:96413. Idh1.

    Subcellular locationi

    GO - Cellular componenti

    1. cytosol Source: MGI
    2. mitochondrion Source: MGI
    3. peroxisome Source: Ensembl

    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 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

    Proteomic databases

    MaxQBiO88844.
    PaxDbiO88844.
    PRIDEiO88844.

    2D gel databases

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

    PTM databases

    PhosphoSiteiO88844.

    Expressioni

    Gene expression databases

    ArrayExpressiO88844.
    BgeeiO88844.
    CleanExiMM_IDH1.
    GenevestigatoriO88844.

    Interactioni

    Subunit structurei

    Homodimer.By similarity

    Protein-protein interaction databases

    IntActiO88844. 5 interactions.
    MINTiMINT-1859161.

    Structurei

    Secondary structure

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

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    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.
    KOiK00031.
    OMAiSCGGVAM.
    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

    MSRKIQGGSV VEMQGDEMTR IIWELIKEKL ILPYVELDLH SYDLGIENRD    50
    ATNDQVTKDA AEAIKKYNVG VKCATITPDE KRVEEFKLKQ MWKSPNGTIR 100
    NILGGTVFRE AIICKNIPRL VTGWVKPIII GRHAYGDQYR ATDFVVPGPG 150
    KVEITYTPKD GTQKVTYMVH DFEEGGGVAM GMYNQDKSIE DFAHSSFQMA 200
    LSKGWPLYLS TKNTILKKYD GRFKDIFQEI YDKKYKSQFE AQKICYEHRL 250
    IDDMVAQAMK SEGGFIWACK NYDGDVQSDS VAQGYGSLGM MTSVLICPDG 300
    KTVEAEAAHG TVTRHYRMYQ KGQETSTNPI ASIFAWSRGL AHRAKLDNNT 350
    ELSFFAKALE DVCIETIEAG FMTKDLAACI KGLPNVQRSD YLNTFEFMDK 400
    LGENLKAKLA QAKL 414
    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:
    EMBL
    GenBank
    DDBJ
    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:
    EMBL
    GenBank
    DDBJ
    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 .
    CCDSi CCDS15016.1.
    RefSeqi NP_001104790.1. NM_001111320.1.
    NP_034627.3. NM_010497.3.
    UniGenei Mm.9925.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2CMJ X-ray 1.99 A/B 4-413 [» ]
    2CMV X-ray 2.52 A/B 4-413 [» ]
    ProteinModelPortali O88844.
    SMRi O88844. Positions 4-413.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    IntActi O88844. 5 interactions.
    MINTi MINT-1859161.

    PTM databases

    PhosphoSitei O88844.

    2D gel databases

    COMPLUYEAST-2DPAGE O88844.
    REPRODUCTION-2DPAGE O88844.
    SWISS-2DPAGE O88844.

    Proteomic databases

    MaxQBi O88844.
    PaxDbi O88844.
    PRIDEi O88844.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENSMUST00000097709 ; ENSMUSP00000095316 ; ENSMUSG00000025950 .
    ENSMUST00000169032 ; ENSMUSP00000127307 ; ENSMUSG00000025950 .
    GeneIDi 15926.
    KEGGi mmu:15926.
    UCSCi uc007bhn.2. mouse.

    Organism-specific databases

    CTDi 3417.
    MGIi MGI:96413. Idh1.

    Phylogenomic databases

    eggNOGi COG0538.
    GeneTreei ENSGT00390000012547.
    HOGENOMi HOG000019858.
    HOVERGENi HBG006119.
    KOi K00031.
    OMAi SCGGVAM.
    OrthoDBi EOG7QNVKS.
    TreeFami TF300428.

    Enzyme and pathway databases

    Reactomei REACT_198632. Abnormal conversion of 2-oxoglutarate to 2-hydroxyglutarate.

    Miscellaneous databases

    EvolutionaryTracei O88844.
    NextBioi 288640.
    PROi O88844.
    SOURCEi Search...

    Gene expression databases

    ArrayExpressi O88844.
    Bgeei O88844.
    CleanExi MM_IDH1.
    Genevestigatori O88844.

    Family and domain databases

    Gene3Di 3.40.718.10. 1 hit.
    InterProi IPR019818. IsoCit/isopropylmalate_DH_CS.
    IPR004790. Isocitrate_DH_NADP.
    IPR024084. IsoPropMal-DH-like_dom.
    [Graphical view ]
    PANTHERi PTHR11822. PTHR11822. 1 hit.
    Pfami PF00180. Iso_dh. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF000108. IDH_NADP. 1 hit.
    TIGRFAMsi TIGR00127. nadp_idh_euk. 1 hit.
    PROSITEi PS00470. IDH_IMDH. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    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: October 1, 2014
    This is version 114 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