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P15496

- IDI1_YEAST

UniProt

P15496 - IDI1_YEAST

Protein

Isopentenyl-diphosphate Delta-isomerase

Gene

IDI1

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 146 (01 Oct 2014)
      Sequence version 2 (23 Jan 2007)
      Previous versions | rss
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    Functioni

    Catalyzes the 1,3-allylic rearrangement of the homoallylic substrate isopentenyl (IPP) to its highly electrophilic allylic isomer, dimethylallyl diphosphate (DMAPP).

    Catalytic activityi

    Isopentenyl diphosphate = dimethylallyl diphosphate.

    Cofactori

    Binds 1 magnesium ion per subunit.By similarity

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei89 – 891SubstrateBy similarity
    Metal bindingi93 – 931MagnesiumBy similarity
    Metal bindingi104 – 1041MagnesiumBy similarity
    Binding sitei123 – 1231SubstrateBy similarity
    Binding sitei127 – 1271SubstrateBy similarity
    Active sitei139 – 1391By similarity
    Binding sitei140 – 1401SubstrateBy similarity
    Metal bindingi205 – 2051MagnesiumBy similarity
    Active sitei207 – 2071By similarity
    Metal bindingi207 – 2071MagnesiumBy similarity

    GO - Molecular functioni

    1. hydrolase activity Source: InterPro
    2. isopentenyl-diphosphate delta-isomerase activity Source: SGD
    3. metal ion binding Source: UniProtKB-KW

    GO - Biological processi

    1. dimethylallyl diphosphate biosynthetic process Source: UniProtKB-UniPathway
    2. farnesyl diphosphate biosynthetic process Source: SGD
    3. sterol biosynthetic process Source: UniProtKB-KW

    Keywords - Molecular functioni

    Isomerase

    Keywords - Biological processi

    Isoprene biosynthesis, Lipid biosynthesis, Lipid metabolism, Steroid biosynthesis, Steroid metabolism, Sterol biosynthesis, Sterol metabolism

    Keywords - Ligandi

    Magnesium, Metal-binding

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-654.
    YEAST:YPL117C-MONOMER.
    UniPathwayiUPA00059; UER00104.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Isopentenyl-diphosphate Delta-isomerase (EC:5.3.3.2)
    Alternative name(s):
    Isopentenyl pyrophosphate isomerase
    Short name:
    IPP isomerase
    Gene namesi
    Name:IDI1
    Synonyms:BOT2
    Ordered Locus Names:YPL117C
    ORF Names:LPH10C
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome XVI

    Organism-specific databases

    SGDiS000006038. IDI1.

    Subcellular locationi

    GO - Cellular componenti

    1. cytoplasm Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi138 – 1381C → S or V: 10-fold reduction in activity. 1 Publication
    Mutagenesisi139 – 1391C → A or V: Inactive. 1 Publication
    Mutagenesisi139 – 1391C → S: Reduces activity over 100000-fold. 1 Publication
    Mutagenesisi207 – 2071E → Q or V: Inactive. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed1 Publication
    Chaini2 – 288287Isopentenyl-diphosphate Delta-isomerasePRO_0000205231Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei7 – 71Phosphoserine1 Publication

    Keywords - PTMi

    Phosphoprotein

    Proteomic databases

    MaxQBiP15496.
    PaxDbiP15496.
    PeptideAtlasiP15496.

    Expressioni

    Gene expression databases

    GenevestigatoriP15496.

    Interactioni

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    itself1EBI-8902,EBI-8902
    ARO8P530901EBI-8902,EBI-2042933
    COX7P101741EBI-8902,EBI-2050505
    ESS1P226961EBI-8902,EBI-6679
    GLN1P322881EBI-8902,EBI-7665
    HEF3P539781EBI-8902,EBI-6345
    IPP1P008171EBI-8902,EBI-9338
    PRP40P332031EBI-8902,EBI-701
    RFT1P382061EBI-8902,EBI-15028
    RNR1P215241EBI-8902,EBI-15234
    RNR2P099381EBI-8902,EBI-15240
    RSC58Q079791EBI-8902,EBI-36549
    RSP5P399401EBI-8902,EBI-16219
    TAF6P530401EBI-8902,EBI-18876
    TFC7Q124151EBI-8902,EBI-33456
    USO1P253861EBI-8902,EBI-20157

    Protein-protein interaction databases

    BioGridi36064. 45 interactions.
    IntActiP15496. 14 interactions.
    MINTiMINT-642308.
    STRINGi4932.YPL117C.

    Structurei

    3D structure databases

    ProteinModelPortaliP15496.
    SMRiP15496. Positions 66-287.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini102 – 259158Nudix hydrolasePROSITE-ProRule annotationAdd
    BLAST

    Sequence similaritiesi

    Belongs to the IPP isomerase type 1 family.Curated
    Contains 1 nudix hydrolase domain.PROSITE-ProRule annotation

    Phylogenomic databases

    eggNOGiCOG1443.
    GeneTreeiENSGT00390000008527.
    HOGENOMiHOG000274106.
    KOiK01823.
    OMAiELLWANT.
    OrthoDBiEOG7Z0K7M.

    Family and domain databases

    Gene3Di3.90.79.10. 1 hit.
    InterProiIPR011876. IsopentenylPP_isomerase_typ1.
    IPR000086. NUDIX_hydrolase_dom.
    IPR015797. NUDIX_hydrolase_dom-like.
    [Graphical view]
    PANTHERiPTHR10885. PTHR10885. 1 hit.
    PfamiPF00293. NUDIX. 1 hit.
    [Graphical view]
    PIRSFiPIRSF018427. Isopntndiph_ism. 1 hit.
    SUPFAMiSSF55811. SSF55811. 1 hit.
    TIGRFAMsiTIGR02150. IPP_isom_1. 1 hit.
    PROSITEiPS51462. NUDIX. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

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

    P15496-1 [UniParc]FASTAAdd to Basket

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    MTADNNSMPH GAVSSYAKLV QNQTPEDILE EFPEIIPLQQ RPNTRSSETS    50
    NDESGETCFS GHDEEQIKLM NENCIVLDWD DNAIGAGTKK VCHLMENIEK 100
    GLLHRAFSVF IFNEQGELLL QQRATEKITF PDLWTNTCCS HPLCIDDELG 150
    LKGKLDDKIK GAITAAVRKL DHELGIPEDE TKTRGKFHFL NRIHYMAPSN 200
    EPWGEHEIDY ILFYKINAKE NLTVNPNVNE VRDFKWVSPN DLKTMFADPS 250
    YKFTPWFKII CENYLFNWWE QLDDLSEVEN DRQIHRML 288
    Length:288
    Mass (Da):33,352
    Last modified:January 23, 2007 - v2
    Checksum:i44A373A62EAE1C70
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    J05090 Genomic DNA. Translation: AAA34708.1.
    U43503 Genomic DNA. Translation: AAB68245.1.
    BK006949 Genomic DNA. Translation: DAA11317.1.
    PIRiA34440.
    RefSeqiNP_015208.1. NM_001183931.1.

    Genome annotation databases

    EnsemblFungiiYPL117C; YPL117C; YPL117C.
    GeneIDi855986.
    KEGGisce:YPL117C.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    J05090 Genomic DNA. Translation: AAA34708.1 .
    U43503 Genomic DNA. Translation: AAB68245.1 .
    BK006949 Genomic DNA. Translation: DAA11317.1 .
    PIRi A34440.
    RefSeqi NP_015208.1. NM_001183931.1.

    3D structure databases

    ProteinModelPortali P15496.
    SMRi P15496. Positions 66-287.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 36064. 45 interactions.
    IntActi P15496. 14 interactions.
    MINTi MINT-642308.
    STRINGi 4932.YPL117C.

    Proteomic databases

    MaxQBi P15496.
    PaxDbi P15496.
    PeptideAtlasi P15496.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YPL117C ; YPL117C ; YPL117C .
    GeneIDi 855986.
    KEGGi sce:YPL117C.

    Organism-specific databases

    SGDi S000006038. IDI1.

    Phylogenomic databases

    eggNOGi COG1443.
    GeneTreei ENSGT00390000008527.
    HOGENOMi HOG000274106.
    KOi K01823.
    OMAi ELLWANT.
    OrthoDBi EOG7Z0K7M.

    Enzyme and pathway databases

    UniPathwayi UPA00059 ; UER00104 .
    BioCyci MetaCyc:MONOMER-654.
    YEAST:YPL117C-MONOMER.

    Miscellaneous databases

    NextBioi 980831.
    PROi P15496.

    Gene expression databases

    Genevestigatori P15496.

    Family and domain databases

    Gene3Di 3.90.79.10. 1 hit.
    InterProi IPR011876. IsopentenylPP_isomerase_typ1.
    IPR000086. NUDIX_hydrolase_dom.
    IPR015797. NUDIX_hydrolase_dom-like.
    [Graphical view ]
    PANTHERi PTHR10885. PTHR10885. 1 hit.
    Pfami PF00293. NUDIX. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF018427. Isopntndiph_ism. 1 hit.
    SUPFAMi SSF55811. SSF55811. 1 hit.
    TIGRFAMsi TIGR02150. IPP_isom_1. 1 hit.
    PROSITEi PS51462. NUDIX. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Isopentenyl diphosphate:dimethylallyl diphosphate isomerase. An improved purification of the enzyme and isolation of the gene from Saccharomyces cerevisiae."
      Anderson M.S., Muehlbacher M., Street I.P., Proffitt J., Poulter C.D.
      J. Biol. Chem. 264:19169-19175(1989) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-36.
    2. "The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI."
      Bussey H., Storms R.K., Ahmed A., Albermann K., Allen E., Ansorge W., Araujo R., Aparicio A., Barrell B.G., Badcock K., Benes V., Botstein D., Bowman S., Brueckner M., Carpenter J., Cherry J.M., Chung E., Churcher C.M.
      , Coster F., Davis K., Davis R.W., Dietrich F.S., Delius H., DiPaolo T., Dubois E., Duesterhoeft A., Duncan M., Floeth M., Fortin N., Friesen J.D., Fritz C., Goffeau A., Hall J., Hebling U., Heumann K., Hilbert H., Hillier L.W., Hunicke-Smith S., Hyman R.W., Johnston M., Kalman S., Kleine K., Komp C., Kurdi O., Lashkari D., Lew H., Lin A., Lin D., Louis E.J., Marathe R., Messenguy F., Mewes H.-W., Mirtipati S., Moestl D., Mueller-Auer S., Namath A., Nentwich U., Oefner P., Pearson D., Petel F.X., Pohl T.M., Purnelle B., Rajandream M.A., Rechmann S., Rieger M., Riles L., Roberts D., Schaefer M., Scharfe M., Scherens B., Schramm S., Schroeder M., Sdicu A.-M., Tettelin H., Urrestarazu L.A., Ushinsky S., Vierendeels F., Vissers S., Voss H., Walsh S.V., Wambutt R., Wang Y., Wedler E., Wedler H., Winnett E., Zhong W.-W., Zollner A., Vo D.H., Hani J.
      Nature 387:103-105(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. "Isopentenyldiphosphate:dimethylallyldiphosphate isomerase: construction of a high-level heterologous expression system for the gene from Saccharomyces cerevisiae and identification of an active-site nucleophile."
      Street I.P., Poulter C.D.
      Biochemistry 29:7531-7538(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 124-154, ACTIVE SITE.
    5. "Identification of Cys139 and Glu207 as catalytically important groups in the active site of isopentenyl diphosphate:dimethylallyl diphosphate isomerase."
      Street I.P., Coffman H.R., Baker J.A., Poulter C.D.
      Biochemistry 33:4212-4217(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 196-215, ACTIVE SITE, MUTAGENESIS OF CYS-138; CYS-139 AND GLU-207.
    6. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
    7. "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae."
      Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J., Elias J.E., Gygi S.P.
      J. Proteome Res. 6:1190-1197(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Strain: ADR376.
    8. "A multidimensional chromatography technology for in-depth phosphoproteome analysis."
      Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.
      Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-7, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    9. "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution."
      Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.
      Science 325:1682-1686(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

    Entry informationi

    Entry nameiIDI1_YEAST
    AccessioniPrimary (citable) accession number: P15496
    Secondary accession number(s): D6W3Q1
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: April 1, 1990
    Last sequence update: January 23, 2007
    Last modified: October 1, 2014
    This is version 146 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 25500 molecules/cell in log phase SD medium.1 Publication

    Keywords - Technical termi

    Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    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 XVI
      Yeast (Saccharomyces cerevisiae) chromosome XVI: entries and gene names

    External Data

    Dasty 3