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P41939

- IDHC_YEAST

UniProt

P41939 - IDHC_YEAST

Protein

Isocitrate dehydrogenase [NADP] cytoplasmic

Gene

IDP2

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 122 (01 Oct 2014)
      Sequence version 2 (01 Oct 1996)
      Previous versions | rss
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    Functioni

    May function in the production of NADPH for fatty acid and sterol synthesis.

    Catalytic activityi

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

    Cofactori

    Binds 1 magnesium or manganese ion per subunit.By similarity

    Enzyme regulationi

    By catabolite repression.

    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: SGD
    2. magnesium ion binding Source: InterPro
    3. NAD binding Source: InterPro

    GO - Biological processi

    1. glyoxylate cycle Source: UniProtKB-KW
    2. isocitrate metabolic process Source: SGD
    3. 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

    BioCyciMetaCyc:YLR174W-MONOMER.
    YEAST:YLR174W-MONOMER.
    ReactomeiREACT_207320. Abnormal conversion of 2-oxoglutarate to 2-hydroxyglutarate.
    REACT_227890. NADPH regeneration.
    SABIO-RKP41939.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Isocitrate dehydrogenase [NADP] cytoplasmic (EC:1.1.1.42)
    Short name:
    IDH
    Alternative name(s):
    IDP
    NADP(+)-specific ICDH
    Oxalosuccinate decarboxylase
    Gene namesi
    Name:IDP2
    Ordered Locus Names:YLR174W
    ORF Names:L9470.12
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome XII

    Organism-specific databases

    CYGDiYLR174w.
    SGDiS000004164. IDP2.

    Subcellular locationi

    GO - Cellular componenti

    1. cytosol Source: SGD

    Keywords - Cellular componenti

    Cytoplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 412412Isocitrate dehydrogenase [NADP] cytoplasmicPRO_0000083587Add
    BLAST

    Post-translational modificationi

    The N-terminus is blocked.

    Proteomic databases

    MaxQBiP41939.
    PaxDbiP41939.
    PeptideAtlasiP41939.
    PRIDEiP41939.

    Expressioni

    Gene expression databases

    GenevestigatoriP41939.

    Interactioni

    Subunit structurei

    Homodimer.

    Protein-protein interaction databases

    BioGridi31445. 17 interactions.
    DIPiDIP-4252N.
    IntActiP41939. 1 interaction.
    MINTiMINT-545477.
    STRINGi4932.YLR174W.

    Structurei

    3D structure databases

    ProteinModelPortaliP41939.
    SMRiP41939. Positions 2-408.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

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

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiCOG0538.
    GeneTreeiENSGT00390000012547.
    HOGENOMiHOG000019858.
    KOiK00031.
    OMAiEANWRSK.
    OrthoDBiEOG7G4QQD.

    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.

    P41939-1 [UniParc]FASTAAdd to Basket

    « Hide

    MTKIKVANPI VEMDGDEQTR IIWHLIRDKL VLPYLDVDLK YYDLSVEYRD    50
    QTNDQVTVDS ATATLKYGVA VKCATITPDE ARVEEFHLKK MWKSPNGTIR 100
    NILGGTVFRE PIIIPRIPRL VPQWEKPIII GRHAFGDQYK ATDVIVPEEG 150
    ELRLVYKSKS GTHDVDLKVF DYPEHGGVAM MMYNTTDSIE GFAKASFELA 200
    IERKLPLYST TKNTILKKYD GKFKDVFEAM YARSYKEKFE SLGIWYEHRL 250
    IDDMVAQMLK SKGGYIIAMK NYDGDVESDI VAQGFGSLGL MTSVLITPDG 300
    KTFESEAAHG TVTRHFRQHQ QGKETSTNSI ASIFAWTRGI IQRGKLDNTP 350
    DVVKFGQILE SATVNTVQED GIMTKDLALI LGKSERSAYV TTEEFIDAVE 400
    SRLKKEFEAA AL 412
    Length:412
    Mass (Da):46,562
    Last modified:October 1, 1996 - v2
    Checksum:i83EB54CC56A29857
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti24 – 274HLIR → SFNQ in AAA64516. (PubMed:8068643)Curated
    Sequence conflicti68 – 681G → R in AAA64516. (PubMed:8068643)Curated
    Sequence conflicti185 – 1851T → N in AAA64516. (PubMed:8068643)Curated
    Sequence conflicti232 – 2398ARSYKEKF → LEVIKRSL in AAA64516. (PubMed:8068643)Curated
    Sequence conflicti267 – 2671I → M in AAA64516. (PubMed:8068643)Curated
    Sequence conflicti306 – 3072EA → DR in AAA64516. (PubMed:8068643)Curated
    Sequence conflicti316 – 3238FRQHQQGK → LTDYDKGR in AAA64516. (PubMed:8068643)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    L26312 Genomic DNA. Translation: AAA64516.1.
    U17246 Genomic DNA. Translation: AAB67464.1.
    BK006945 Genomic DNA. Translation: DAA09494.1.
    PIRiS51419.
    RefSeqiNP_013275.1. NM_001182061.1.

    Genome annotation databases

    EnsemblFungiiYLR174W; YLR174W; YLR174W.
    GeneIDi850871.
    KEGGisce:YLR174W.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    L26312 Genomic DNA. Translation: AAA64516.1 .
    U17246 Genomic DNA. Translation: AAB67464.1 .
    BK006945 Genomic DNA. Translation: DAA09494.1 .
    PIRi S51419.
    RefSeqi NP_013275.1. NM_001182061.1.

    3D structure databases

    ProteinModelPortali P41939.
    SMRi P41939. Positions 2-408.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 31445. 17 interactions.
    DIPi DIP-4252N.
    IntActi P41939. 1 interaction.
    MINTi MINT-545477.
    STRINGi 4932.YLR174W.

    Proteomic databases

    MaxQBi P41939.
    PaxDbi P41939.
    PeptideAtlasi P41939.
    PRIDEi P41939.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YLR174W ; YLR174W ; YLR174W .
    GeneIDi 850871.
    KEGGi sce:YLR174W.

    Organism-specific databases

    CYGDi YLR174w.
    SGDi S000004164. IDP2.

    Phylogenomic databases

    eggNOGi COG0538.
    GeneTreei ENSGT00390000012547.
    HOGENOMi HOG000019858.
    KOi K00031.
    OMAi EANWRSK.
    OrthoDBi EOG7G4QQD.

    Enzyme and pathway databases

    BioCyci MetaCyc:YLR174W-MONOMER.
    YEAST:YLR174W-MONOMER.
    Reactomei REACT_207320. Abnormal conversion of 2-oxoglutarate to 2-hydroxyglutarate.
    REACT_227890. NADPH regeneration.
    SABIO-RK P41939.

    Miscellaneous databases

    NextBioi 967206.

    Gene expression databases

    Genevestigatori P41939.

    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. "Isolation, characterization, and disruption of the yeast gene encoding cytosolic NADP-specific isocitrate dehydrogenase."
      Loftus T.M., Hall L.V., Anderson S.L., McAlister-Henn L.
      Biochemistry 33:9661-9667(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PARTIAL PROTEIN SEQUENCE, CHARACTERIZATION.
    2. "The nucleotide sequence of Saccharomyces cerevisiae chromosome XII."
      Johnston M., Hillier L.W., Riles L., Albermann K., Andre B., Ansorge W., Benes V., Brueckner M., Delius H., Dubois E., Duesterhoeft A., Entian K.-D., Floeth M., Goffeau A., Hebling U., Heumann K., Heuss-Neitzel D., Hilbert H.
      , Hilger F., Kleine K., Koetter P., Louis E.J., Messenguy F., Mewes H.-W., Miosga T., Moestl D., Mueller-Auer S., Nentwich U., Obermaier B., Piravandi E., Pohl T.M., Portetelle D., Purnelle B., Rechmann S., Rieger M., Rinke M., Rose M., Scharfe M., Scherens B., Scholler P., Schwager C., Schwarz S., Underwood A.P., Urrestarazu L.A., Vandenbol M., Verhasselt P., Vierendeels F., Voet M., Volckaert G., Voss H., Wambutt R., Wedler E., Wedler H., Zimmermann F.K., Zollner A., Hani J., Hoheisel J.D.
      Nature 387:87-90(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    3. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    4. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
    5. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

    Entry informationi

    Entry nameiIDHC_YEAST
    AccessioniPrimary (citable) accession number: P41939
    Secondary accession number(s): D6VYH8
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1995
    Last sequence update: October 1, 1996
    Last modified: October 1, 2014
    This is version 122 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Present with 2620 molecules/cell in log phase SD medium.1 Publication

    Keywords - Technical termi

    Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. SIMILARITY comments
      Index of protein domains and families
    2. Yeast
      Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
    3. Yeast chromosome XII
      Yeast (Saccharomyces cerevisiae) chromosome XII: entries and gene names

    External Data

    Dasty 3