Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Basket 0
(max 400 entries)x

Your basket is currently empty.

Select item(s) and click on "Add to basket" to create your own collection here
(400 entries max)

Q46822

- IDI_ECOLI

UniProt

Q46822 - IDI_ECOLI

Protein

Isopentenyl-diphosphate Delta-isomerase

Gene

idi

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
    • BLAST
    • Align
    • Format
    • Add to basket
    • History
      Entry version 131 (01 Oct 2014)
      Sequence version 1 (01 Nov 1996)
      Previous versions | rss
    • Help video
    • Feedback
    • Comment

    Functioni

    Catalyzes the 1,3-allylic rearrangement of the homoallylic substrate isopentenyl (IPP) to its highly electrophilic allylic isomer, dimethylallyl diphosphate (DMAPP).2 Publications

    Catalytic activityi

    Isopentenyl diphosphate = dimethylallyl diphosphate.

    Cofactori

    Binds 1 magnesium ion per subunit. The magnesium ion binds only when substrate is bound.
    Binds 1 manganese ion per subunit.

    Kineticsi

    1. KM=9.5 µM for Isopentenyl diphosphate1 Publication

    Vmax=260 mmol/h/mg enzyme1 Publication

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei21 – 211Substrate
    Metal bindingi25 – 251Manganese2 Publications
    Metal bindingi32 – 321Manganese2 Publications
    Binding sitei51 – 511Substrate
    Binding sitei55 – 551Substrate
    Active sitei67 – 671
    Metal bindingi67 – 671Magnesium; via carbonyl oxygen
    Metal bindingi69 – 691Manganese2 Publications
    Binding sitei69 – 691Substrate
    Binding sitei83 – 831Substrate
    Metal bindingi87 – 871Magnesium
    Binding sitei87 – 871Substrate
    Sitei104 – 1041Essential for catalytic activity
    Metal bindingi114 – 1141Manganese2 Publications
    Active sitei116 – 1161
    Metal bindingi116 – 1161Manganese2 Publications

    GO - Molecular functioni

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

    GO - Biological processi

    1. cellular response to DNA damage stimulus Source: EcoliWiki
    2. dimethylallyl diphosphate biosynthetic process Source: UniProtKB-UniPathway
    3. isoprenoid biosynthetic process Source: EcoCyc
    4. ubiquinone biosynthetic process Source: EcoCyc

    Keywords - Molecular functioni

    Isomerase

    Keywords - Biological processi

    Isoprene biosynthesis

    Keywords - Ligandi

    Magnesium, Manganese, Metal-binding

    Enzyme and pathway databases

    BioCyciEcoCyc:IPPISOM-MONOMER.
    ECOL316407:JW2857-MONOMER.
    MetaCyc:IPPISOM-MONOMER.
    SABIO-RKQ46822.
    UniPathwayiUPA00059; UER00104.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Isopentenyl-diphosphate Delta-isomerase (EC:5.3.3.2)
    Short name:
    IPP isomerase
    Alternative name(s):
    IPP:DMAPP isomerase
    Isopentenyl pyrophosphate isomerase
    Gene namesi
    Name:idi
    Synonyms:ygfV
    Ordered Locus Names:b2889, JW2857
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG13072. idi.

    Subcellular locationi

    GO - Cellular componenti

    1. cytoplasm Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi104 – 1041Y → A: Reduces activity by 99%.
    Mutagenesisi104 – 1041Y → F: Reduces activity by 97%.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 182182Isopentenyl-diphosphate Delta-isomerasePRO_0000205249Add
    BLAST

    Expressioni

    Gene expression databases

    GenevestigatoriQ46822.

    Interactioni

    Subunit structurei

    Homodimer.7 Publications

    Protein-protein interaction databases

    IntActiQ46822. 4 interactions.
    STRINGi511145.b2889.

    Structurei

    Secondary structure

    1
    182
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi5 – 95
    Beta strandi11 – 133
    Beta strandi15 – 206
    Helixi21 – 244
    Beta strandi35 – 406
    Beta strandi46 – 516
    Beta strandi56 – 583
    Beta strandi62 – 687
    Helixi76 – 8813
    Beta strandi96 – 994
    Beta strandi103 – 1075
    Beta strandi113 – 1175
    Beta strandi120 – 1256
    Turni133 – 1353
    Beta strandi136 – 1427
    Helixi144 – 15310
    Helixi155 – 1573
    Helixi160 – 1678
    Helixi169 – 1779

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1HX3X-ray2.10A/B1-182[»]
    1HZTX-ray1.45A1-182[»]
    1I9AX-ray2.50A/B1-182[»]
    1NFSX-ray1.96A/B1-182[»]
    1NFZX-ray1.97A/B1-182[»]
    1OW2X-ray2.00A/B1-182[»]
    1PPVX-ray1.70A/B1-182[»]
    1PPWX-ray2.21A/B1-182[»]
    1PVFX-ray1.78A/B1-182[»]
    1Q54X-ray1.93A/B1-182[»]
    1R67X-ray1.77A1-182[»]
    1X83X-ray1.80A/B1-182[»]
    1X84X-ray1.78A/B1-182[»]
    2B2KX-ray1.97A/B1-182[»]
    2G73X-ray1.97A/B1-182[»]
    2G74X-ray1.96A/B1-182[»]
    2VNPX-ray2.19A/B1-182[»]
    2VNQX-ray2.20A/B1-182[»]
    ProteinModelPortaliQ46822.
    SMRiQ46822. Positions 4-182.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ46822.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini30 – 164135Nudix hydrolaseAdd
    BLAST

    Sequence similaritiesi

    Belongs to the IPP isomerase type 1 family.Curated
    Contains 1 nudix hydrolase domain.Curated

    Phylogenomic databases

    eggNOGiCOG1443.
    HOGENOMiHOG000274107.
    KOiK01823.
    OMAiFRYRATA.
    OrthoDBiEOG6MSS4M.
    PhylomeDBiQ46822.

    Family and domain databases

    Gene3Di3.90.79.10. 1 hit.
    HAMAPiMF_00202. Idi.
    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.

    Q46822-1 [UniParc]FASTAAdd to Basket

    « Hide

    MQTEHVILLN AQGVPTGTLE KYAAHTADTR LHLAFSSWLF NAKGQLLVTR    50
    RALSKKAWPG VWTNSVCGHP QLGESNEDAV IRRCRYELGV EITPPESIYP 100
    DFRYRATDPS GIVENEVCPV FAARTTSALQ INDDEVMDYQ WCDLADVLHG 150
    IDATPWAFSP WMVMQATNRE ARKRLSAFTQ LK 182
    Length:182
    Mass (Da):20,508
    Last modified:November 1, 1996 - v1
    Checksum:iAEAE3EF8254ECC2D
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF119715 Genomic DNA. Translation: AAD26812.1.
    U28375 Genomic DNA. Translation: AAA83070.1.
    U00096 Genomic DNA. Translation: AAC75927.1.
    AP009048 Genomic DNA. Translation: BAE76954.1.
    PIRiA65073.
    RefSeqiNP_417365.1. NC_000913.3.
    YP_491090.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC75927; AAC75927; b2889.
    BAE76954; BAE76954; BAE76954.
    GeneIDi12930440.
    949020.
    KEGGiecj:Y75_p2821.
    eco:b2889.
    PATRICi32121188. VBIEscCol129921_2982.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF119715 Genomic DNA. Translation: AAD26812.1 .
    U28375 Genomic DNA. Translation: AAA83070.1 .
    U00096 Genomic DNA. Translation: AAC75927.1 .
    AP009048 Genomic DNA. Translation: BAE76954.1 .
    PIRi A65073.
    RefSeqi NP_417365.1. NC_000913.3.
    YP_491090.1. NC_007779.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1HX3 X-ray 2.10 A/B 1-182 [» ]
    1HZT X-ray 1.45 A 1-182 [» ]
    1I9A X-ray 2.50 A/B 1-182 [» ]
    1NFS X-ray 1.96 A/B 1-182 [» ]
    1NFZ X-ray 1.97 A/B 1-182 [» ]
    1OW2 X-ray 2.00 A/B 1-182 [» ]
    1PPV X-ray 1.70 A/B 1-182 [» ]
    1PPW X-ray 2.21 A/B 1-182 [» ]
    1PVF X-ray 1.78 A/B 1-182 [» ]
    1Q54 X-ray 1.93 A/B 1-182 [» ]
    1R67 X-ray 1.77 A 1-182 [» ]
    1X83 X-ray 1.80 A/B 1-182 [» ]
    1X84 X-ray 1.78 A/B 1-182 [» ]
    2B2K X-ray 1.97 A/B 1-182 [» ]
    2G73 X-ray 1.97 A/B 1-182 [» ]
    2G74 X-ray 1.96 A/B 1-182 [» ]
    2VNP X-ray 2.19 A/B 1-182 [» ]
    2VNQ X-ray 2.20 A/B 1-182 [» ]
    ProteinModelPortali Q46822.
    SMRi Q46822. Positions 4-182.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    IntActi Q46822. 4 interactions.
    STRINGi 511145.b2889.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC75927 ; AAC75927 ; b2889 .
    BAE76954 ; BAE76954 ; BAE76954 .
    GeneIDi 12930440.
    949020.
    KEGGi ecj:Y75_p2821.
    eco:b2889.
    PATRICi 32121188. VBIEscCol129921_2982.

    Organism-specific databases

    EchoBASEi EB2883.
    EcoGenei EG13072. idi.

    Phylogenomic databases

    eggNOGi COG1443.
    HOGENOMi HOG000274107.
    KOi K01823.
    OMAi FRYRATA.
    OrthoDBi EOG6MSS4M.
    PhylomeDBi Q46822.

    Enzyme and pathway databases

    UniPathwayi UPA00059 ; UER00104 .
    BioCyci EcoCyc:IPPISOM-MONOMER.
    ECOL316407:JW2857-MONOMER.
    MetaCyc:IPPISOM-MONOMER.
    SABIO-RK Q46822.

    Miscellaneous databases

    EvolutionaryTracei Q46822.
    PROi Q46822.

    Gene expression databases

    Genevestigatori Q46822.

    Family and domain databases

    Gene3Di 3.90.79.10. 1 hit.
    HAMAPi MF_00202. Idi.
    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. "Engineered isoprenoid pathway enhances astaxanthin production in Escherichia coli."
      Wang C.-W., Oh M.-K., Liao J.C.
      Biotechnol. Bioeng. 62:235-241(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION.
      Strain: K12 / MG1655 / ATCC 47076.
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    3. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
      Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
      Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    4. "Identification of genes affecting lycopene formation in Escherichia coli transformed with carotenoid biosynthetic genes: candidates for early genes in isoprenoid biosynthesis."
      Hemmi H., Ohnuma S., Nagaoka K., Nishino T.
      J. Biochem. 123:1088-1096(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    5. "Escherichia coli open reading frame 696 is idi, a nonessential gene encoding isopentenyl diphosphate isomerase."
      Hahn F.M., Hurlburt A.P., Poulter C.D.
      J. Bacteriol. 181:4499-4504(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: CHARACTERIZATION.
    6. "Crystal structure of isopentenyl diphosphate:dimethylallyl diphosphate isomerase."
      Durbecq V., Sainz G., Oudjama Y., Clantin B., Bompard-Gilles C., Tricot C., Caillet J., Stalon V., Droogmans L., Villeret V.
      EMBO J. 20:1530-1537(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.45 ANGSTROMS) IN COMPLEX WITH METAL IONS.
    7. Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) IN COMPLEX WITH METAL IONS.
    8. "Structure and mechanism of action of isopentenylpyrophosphate-dimethylallylpyrophosphate isomerase."
      Wouters J., Oudjama Y., Ghosh S., Stalon V., Droogmans L., Oldfield E.
      J. Am. Chem. Soc. 125:3198-3199(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.93 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOG; MANGANESE AND MAGNESIUM IONS.
    9. "Catalytic mechanism of Escherichia coli isopentenyl diphosphate isomerase involves Cys-67, Glu-116, and Tyr-104 as suggested by crystal structures of complexes with transition state analogues and irreversible inhibitors."
      Wouters J., Oudjama Y., Barkley S.J., Tricot C., Stalon V., Droogmans L., Poulter C.D.
      J. Biol. Chem. 278:11903-11908(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.97 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS.
    10. "Crystal structure of the C67A mutant of isopentenyl diphosphate isomerase complexed with a mechanism-based irreversible inhibitor."
      Wouters J., Oudjama Y., Stalon V., Droogmans L., Poulter C.D.
      Proteins 54:216-221(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF MUTANT ALA-67 IN COMPLEX WITH SUBSTRATE ANALOG.
    11. "A crystallographic investigation of phosphoantigen binding to isopentenyl pyrophosphate/dimethylallyl pyrophosphate isomerase."
      Wouters J., Yin F., Song Y., Zhang Y., Oudjama Y., Stalon V., Droogmans L., Morita C.T., Oldfield E.
      J. Am. Chem. Soc. 127:536-537(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.65 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS; MANGANESE AND MAGNESIUM IONS.
    12. "Structural role for Tyr-104 in Escherichia coli isopentenyl-diphosphate isomerase: site-directed mutagenesis, enzymology, and protein crystallography."
      de Ruyck J., Durisotti V., Oudjama Y., Wouters J.
      J. Biol. Chem. 281:17864-17869(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) OF MUTANT ALA/PHE-104 IN COMPLEX WITH SUBSTRATE ANALOG, BIOPHYSICOCHEMICAL PROPERTIES.

    Entry informationi

    Entry nameiIDI_ECOLI
    AccessioniPrimary (citable) accession number: Q46822
    Secondary accession number(s): Q2M9V2
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 30, 2000
    Last sequence update: November 1, 1996
    Last modified: October 1, 2014
    This is version 131 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3