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P21954

- IDHP_YEAST

UniProt

P21954 - IDHP_YEAST

Protein

Isocitrate dehydrogenase [NADP], mitochondrial

Gene

IDP1

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 137 (01 Oct 2014)
      Sequence version 1 (01 Aug 1991)
      Previous versions | rss
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    Functioni

    Mitochondrial IDP1 may regulate flux through the tricarboxylic acid cycle and respiration. Its probably critical function is the production of NADPH.

    Catalytic activityi

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

    Cofactori

    Binds 1 magnesium or manganese ion per subunit.By similarity

    Enzyme regulationi

    The enzyme is subject to end product inhibition by NADPH and 2-oxoglutarate.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei93 – 931SubstrateBy similarity
    Binding sitei98 – 981NADPBy similarity
    Binding sitei125 – 1251SubstrateBy similarity
    Binding sitei148 – 1481SubstrateBy similarity
    Sitei155 – 1551Critical for catalysisBy similarity
    Sitei229 – 2291Critical for catalysisBy similarity
    Metal bindingi269 – 2691Magnesium or manganeseBy similarity
    Binding sitei277 – 2771NADPBy similarity
    Metal bindingi292 – 2921Magnesium or manganeseBy similarity
    Binding sitei345 – 3451NADP; via amide nitrogen and carbonyl oxygenBy similarity

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi91 – 933NADPBy similarity
    Nucleotide bindingi327 – 3326NADPBy similarity

    GO - Molecular functioni

    1. isocitrate dehydrogenase (NADP+) activity Source: SGD
    2. magnesium ion binding Source: InterPro
    3. NAD binding Source: InterPro
    4. protein binding Source: IntAct

    GO - Biological processi

    1. glutamate biosynthetic process Source: SGD
    2. glyoxylate cycle Source: UniProtKB-KW
    3. isocitrate metabolic process Source: InterPro
    4. 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

    BioCyciYEAST:YDL066W-MONOMER.
    ReactomeiREACT_207320. Abnormal conversion of 2-oxoglutarate to 2-hydroxyglutarate.
    REACT_227890. NADPH regeneration.
    SABIO-RKP21954.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Isocitrate dehydrogenase [NADP], mitochondrial (EC:1.1.1.42)
    Short name:
    IDH
    Alternative name(s):
    IDP
    NADP(+)-specific ICDH
    Oxalosuccinate decarboxylase
    Gene namesi
    Name:IDP1
    Ordered Locus Names:YDL066W
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome IV

    Organism-specific databases

    CYGDiYDL066w.
    SGDiS000002224. IDP1.

    Subcellular locationi

    GO - Cellular componenti

    1. mitochondrial nucleoid Source: SGD
    2. mitochondrion Source: SGD

    Keywords - Cellular componenti

    Mitochondrion

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Transit peptidei1 – 1616Mitochondrion1 PublicationAdd
    BLAST
    Chaini17 – 428412Isocitrate dehydrogenase [NADP], mitochondrialPRO_0000014426Add
    BLAST

    Proteomic databases

    MaxQBiP21954.
    PaxDbiP21954.
    PeptideAtlasiP21954.
    PRIDEiP21954.

    Expressioni

    Inductioni

    By growth with glucose as a carbon source.

    Gene expression databases

    GenevestigatoriP21954.

    Interactioni

    Subunit structurei

    Homodimer.

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    KAR2P164742EBI-8898,EBI-7876

    Protein-protein interaction databases

    BioGridi31993. 40 interactions.
    DIPiDIP-4494N.
    IntActiP21954. 18 interactions.
    MINTiMINT-510681.
    STRINGi4932.YDL066W.

    Structurei

    Secondary structure

    1
    428
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi26 – 305
    Helixi33 – 4614
    Turni47 – 504
    Beta strandi55 – 595
    Helixi62 – 676
    Turni68 – 703
    Helixi71 – 8313
    Beta strandi84 – 885
    Helixi96 – 1016
    Helixi111 – 1199
    Beta strandi121 – 1277
    Beta strandi142 – 1498
    Helixi153 – 1564
    Beta strandi158 – 1625
    Beta strandi164 – 17512
    Turni177 – 1793
    Beta strandi183 – 19210
    Beta strandi194 – 2029
    Helixi203 – 22018
    Beta strandi224 – 2285
    Turni230 – 2323
    Helixi236 – 25116
    Helixi253 – 2597
    Beta strandi263 – 2675
    Helixi268 – 27710
    Beta strandi280 – 2867
    Helixi288 – 30215
    Beta strandi307 – 3137
    Beta strandi315 – 3184
    Beta strandi320 – 3234
    Helixi330 – 3378
    Helixi347 – 36418
    Helixi367 – 38519
    Helixi392 – 3976
    Helixi403 – 4053
    Helixi409 – 42618

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2QFVX-ray2.30A/B/C/D16-428[»]
    2QFWX-ray2.60A/B/C/D/E/F16-428[»]
    2QFXX-ray2.70A/B/C/D/E/F16-428[»]
    2QFYX-ray2.10A/B/C/D/E/F16-428[»]
    ProteinModelPortaliP21954.
    SMRiP21954. Positions 17-427.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP21954.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni110 – 1167Substrate bindingBy similarity

    Sequence similaritiesi

    Keywords - Domaini

    Transit peptide

    Phylogenomic databases

    eggNOGiCOG0538.
    GeneTreeiENSGT00390000012547.
    HOGENOMiHOG000019858.
    KOiK00031.
    OMAiTRIIWDK.
    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.

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

    P21954-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSMLSRRLFS TSRLAAFSKI KVKQPVVELD GDEMTRIIWD KIKKKLILPY    50
    LDVDLKYYDL SVESRDATSD KITQDAAEAI KKYGVGIKCA TITPDEARVK 100
    EFNLHKMWKS PNGTIRNILG GTVFREPIVI PRIPRLVPRW EKPIIIGRHA 150
    HGDQYKATDT LIPGPGSLEL VYKPSDPTTA QPQTLKVYDY KGSGVAMAMY 200
    NTDESIEGFA HSSFKLAIDK KLNLFLSTKN TILKKYDGRF KDIFQEVYEA 250
    QYKSKFEQLG IHYEHRLIDD MVAQMIKSKG GFIMALKNYD GDVQSDIVAQ 300
    GFGSLGLMTS ILVTPDGKTF ESEAAHGTVT RHYRKYQKGE ETSTNSIASI 350
    FAWSRGLLKR GELDNTPALC KFANILESAT LNTVQQDGIM TKDLALACGN 400
    NERSAYVTTE EFLDAVEKRL QKEIKSIE 428
    Length:428
    Mass (Da):48,190
    Last modified:August 1, 1991 - v1
    Checksum:i7F885785B8682416
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M57229 Genomic DNA. Translation: AAA34703.1.
    Z74114 Genomic DNA. Translation: CAA98631.1.
    BK006938 Genomic DNA. Translation: DAA11791.1.
    PIRiA38610. DCBYIS.
    RefSeqiNP_010217.1. NM_001180125.1.

    Genome annotation databases

    EnsemblFungiiYDL066W; YDL066W; YDL066W.
    GeneIDi851493.
    KEGGisce:YDL066W.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M57229 Genomic DNA. Translation: AAA34703.1 .
    Z74114 Genomic DNA. Translation: CAA98631.1 .
    BK006938 Genomic DNA. Translation: DAA11791.1 .
    PIRi A38610. DCBYIS.
    RefSeqi NP_010217.1. NM_001180125.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2QFV X-ray 2.30 A/B/C/D 16-428 [» ]
    2QFW X-ray 2.60 A/B/C/D/E/F 16-428 [» ]
    2QFX X-ray 2.70 A/B/C/D/E/F 16-428 [» ]
    2QFY X-ray 2.10 A/B/C/D/E/F 16-428 [» ]
    ProteinModelPortali P21954.
    SMRi P21954. Positions 17-427.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 31993. 40 interactions.
    DIPi DIP-4494N.
    IntActi P21954. 18 interactions.
    MINTi MINT-510681.
    STRINGi 4932.YDL066W.

    Proteomic databases

    MaxQBi P21954.
    PaxDbi P21954.
    PeptideAtlasi P21954.
    PRIDEi P21954.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YDL066W ; YDL066W ; YDL066W .
    GeneIDi 851493.
    KEGGi sce:YDL066W.

    Organism-specific databases

    CYGDi YDL066w.
    SGDi S000002224. IDP1.

    Phylogenomic databases

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

    Enzyme and pathway databases

    BioCyci YEAST:YDL066W-MONOMER.
    Reactomei REACT_207320. Abnormal conversion of 2-oxoglutarate to 2-hydroxyglutarate.
    REACT_227890. NADPH regeneration.
    SABIO-RK P21954.

    Miscellaneous databases

    EvolutionaryTracei P21954.
    NextBioi 968825.
    PROi P21954.

    Gene expression databases

    Genevestigatori P21954.

    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, nucleotide sequence, and disruption of the Saccharomyces cerevisiae gene encoding mitochondrial NADP(H)-specific isocitrate dehydrogenase."
      Haselbeck R.J., McAlister-Henn L.
      J. Biol. Chem. 266:2339-2345(1991) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 17-36.
    2. "The nucleotide sequence of Saccharomyces cerevisiae chromosome IV."
      Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G., Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C., Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F., Delaveau T.
      , del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M., Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T., Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C., Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S., Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L., Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H., Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M., Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M., Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A., Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G., Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E., Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S., Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D., Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V., Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E., Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M., Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X., Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A., Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T., Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L., Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E., Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L., Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M., Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K., Mewes H.-W., Zollner A., Zaccaria P.
      Nature 387:75-78(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.

    Entry informationi

    Entry nameiIDHP_YEAST
    AccessioniPrimary (citable) accession number: P21954
    Secondary accession number(s): D6VRT1
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: August 1, 1991
    Last sequence update: August 1, 1991
    Last modified: October 1, 2014
    This is version 137 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

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

    Documents

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

    External Data

    Dasty 3