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Protein

Isopentenyl-diphosphate delta-isomerase

Gene

fni

Organism
Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Involved in the biosynthesis of isoprenoids. Catalyzes the 1,3-allylic rearrangement of the homoallylic substrate isopentenyl (IPP) to its allylic isomer, dimethylallyl diphosphate (DMAPP).UniRule annotation1 Publication

Catalytic activityi

Isopentenyl diphosphate = dimethylallyl diphosphate.UniRule annotation1 Publication

Cofactori

Protein has several cofactor binding sites:
  • FMNUniRule annotation1 Publication
  • NADPHUniRule annotation1 Publication
  • Mg2+UniRule annotation1 Publication

Enzyme regulationi

Competitively inhibited by N,N-dimethyl-2-amino-1-ethyl diphosphate (NIPP) and isopentyl diphosphate.1 Publication

Kineticsi

Kcat is 17.9 sec(-1) for isomerase activity with IPP (at pH 7.6 and 37 degrees Celsius).

  1. KM=5.6 µM for IPP (at pH 7.6 and 37 degrees Celsius)1 Publication

    Temperature dependencei

    Optimum temperature is 60 degrees Celsius.1 Publication

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Binding sitei95FMN; via amide nitrogenUniRule annotation2 Publications1
    Binding sitei123FMNUniRule annotation2 Publications1
    Binding sitei157SubstrateUniRule annotation1
    Metal bindingi158MagnesiumUniRule annotation1
    Binding sitei187FMNUniRule annotation2 Publications1
    Binding sitei217FMNUniRule annotation2 Publications1
    Binding sitei285FMN; via amide nitrogenUniRule annotation2 Publications1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi65 – 67FMNUniRule annotation2 Publications3
    Nucleotide bindingi264 – 266FMNUniRule annotation2 Publications3
    Nucleotide bindingi285 – 286FMN2 Publications2

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Isomerase

    Keywords - Biological processi

    Isoprene biosynthesis

    Keywords - Ligandi

    Cadmium, Flavoprotein, FMN, Magnesium, Metal-binding, NADP, Nucleotide-binding

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Isopentenyl-diphosphate delta-isomeraseUniRule annotation (EC:5.3.3.2UniRule annotation)
    Short name:
    IPP isomeraseUniRule annotation
    Alternative name(s):
    Isopentenyl diphosphate:dimethylallyl diphosphate isomeraseUniRule annotation
    Isopentenyl pyrophosphate isomeraseUniRule annotation
    Type 2 isopentenyl diphosphate isomeraseUniRule annotation
    Short name:
    IDI-2UniRule annotation
    Gene namesi
    Name:fniUniRule annotation
    Ordered Locus Names:TT_P0067
    Encoded oniPlasmid pTT271 Publication
    OrganismiThermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
    Taxonomic identifieri262724 [NCBI]
    Taxonomic lineageiBacteriaDeinococcus-ThermusDeinococciThermalesThermaceaeThermus
    Proteomesi
    • UP000000592 Componenti: Plasmid pTT27

    Subcellular locationi

    • Cytoplasm UniRule annotation

    GO - Cellular componenti

    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00004303501 – 332Isopentenyl-diphosphate delta-isomeraseAdd BLAST332

    Interactioni

    Subunit structurei

    Homooctamer. Dimer of tetramers.UniRule annotation2 Publications

    Protein-protein interaction databases

    STRINGi262724.TT_P0067.

    Structurei

    Secondary structure

    1332
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Helixi10 – 16Combined sources7
    Helixi28 – 30Combined sources3
    Beta strandi31 – 33Combined sources3
    Helixi43 – 45Combined sources3
    Beta strandi50 – 52Combined sources3
    Beta strandi55 – 63Combined sources9
    Helixi73 – 87Combined sources15
    Beta strandi90 – 95Combined sources6
    Helixi97 – 101Combined sources5
    Turni103 – 105Combined sources3
    Helixi106 – 109Combined sources4
    Turni112 – 114Combined sources3
    Beta strandi116 – 118Combined sources3
    Beta strandi120 – 125Combined sources6
    Helixi126 – 130Combined sources5
    Helixi134 – 144Combined sources11
    Beta strandi147 – 152Combined sources6
    Helixi155 – 160Combined sources6
    Helixi170 – 177Combined sources8
    Beta strandi184 – 187Combined sources4
    Beta strandi189 – 191Combined sources3
    Helixi195 – 201Combined sources7
    Beta strandi207 – 210Combined sources4
    Helixi219 – 224Combined sources6
    Helixi234 – 237Combined sources4
    Helixi243 – 253Combined sources11
    Beta strandi255 – 257Combined sources3
    Beta strandi259 – 264Combined sources6
    Helixi268 – 277Combined sources10
    Beta strandi280 – 284Combined sources5
    Helixi286 – 288Combined sources3
    Helixi289 – 292Combined sources4
    Helixi296 – 317Combined sources22
    Helixi322 – 325Combined sources4
    Beta strandi329 – 331Combined sources3

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1VCFX-ray2.60A/B1-332[»]
    1VCGX-ray3.02A/B/C/D1-332[»]
    ProteinModelPortaliQ746I8.
    SMRiQ746I8.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ746I8.

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni6 – 7Substrate bindingUniRule annotation2
    Regioni95 – 97Substrate bindingUniRule annotation3

    Sequence similaritiesi

    Belongs to the IPP isomerase type 2 family.UniRule annotation

    Phylogenomic databases

    eggNOGiENOG4106UJV. Bacteria.
    COG1304. LUCA.
    HOGENOMiHOG000072126.
    KOiK01823.
    OMAiGSQRVML.

    Family and domain databases

    CDDicd02811. IDI-2_FMN. 1 hit.
    Gene3Di3.20.20.70. 1 hit.
    HAMAPiMF_00354. Idi_2. 1 hit.
    InterProiIPR013785. Aldolase_TIM.
    IPR000262. FMN-dep_DH.
    IPR011179. IPdP_isomerase.
    [Graphical view]
    PANTHERiPTHR10578:SF3. PTHR10578:SF3. 2 hits.
    PfamiPF01070. FMN_dh. 2 hits.
    [Graphical view]
    PIRSFiPIRSF003314. IPP_isomerase. 1 hit.
    TIGRFAMsiTIGR02151. IPP_isom_2. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Q746I8-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MNIRERKRKH LEACLEGEVA YQKTTTGLEG FRLRYQALAG LALGEVDLTT
    60 70 80 90 100
    PFLGKTLKAP FLIGAMTGGE ENGERINLAL AEAAEALGVG MMLGSGRILL
    110 120 130 140 150
    ERPEALRSFR VRKVAPKALL IANLGLAQLR RYGRDDLLRL VEALEADALA
    160 170 180 190 200
    FHVNPLQEAV QRGDTDFRGL VERLAELLPL PFPVMVKEVG HGLSREAALA
    210 220 230 240 250
    LRDLPLAAVD VAGAGGTSWA RVEEWVRFGE VRHPELCEIG IPTARAILEV
    260 270 280 290 300
    REVLPHLPLV ASGGVYTGTD GAKALALGAD LLAVARPLLR PALEGAERVA
    310 320 330
    AWIGDYLEEL RTALFAIGAK NPKEARGRVE RV
    Length:332
    Mass (Da):35,901
    Last modified:July 5, 2004 - v1
    Checksum:i842EC8FDD2BA9551
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AE017222 Genomic DNA. Translation: AAS82397.1.
    RefSeqiWP_011174493.1. NC_005838.1.

    Genome annotation databases

    EnsemblBacteriaiAAS82397; AAS82397; TT_P0067.
    KEGGitth:TT_P0067.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AE017222 Genomic DNA. Translation: AAS82397.1.
    RefSeqiWP_011174493.1. NC_005838.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1VCFX-ray2.60A/B1-332[»]
    1VCGX-ray3.02A/B/C/D1-332[»]
    ProteinModelPortaliQ746I8.
    SMRiQ746I8.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi262724.TT_P0067.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAS82397; AAS82397; TT_P0067.
    KEGGitth:TT_P0067.

    Phylogenomic databases

    eggNOGiENOG4106UJV. Bacteria.
    COG1304. LUCA.
    HOGENOMiHOG000072126.
    KOiK01823.
    OMAiGSQRVML.

    Miscellaneous databases

    EvolutionaryTraceiQ746I8.

    Family and domain databases

    CDDicd02811. IDI-2_FMN. 1 hit.
    Gene3Di3.20.20.70. 1 hit.
    HAMAPiMF_00354. Idi_2. 1 hit.
    InterProiIPR013785. Aldolase_TIM.
    IPR000262. FMN-dep_DH.
    IPR011179. IPdP_isomerase.
    [Graphical view]
    PANTHERiPTHR10578:SF3. PTHR10578:SF3. 2 hits.
    PfamiPF01070. FMN_dh. 2 hits.
    [Graphical view]
    PIRSFiPIRSF003314. IPP_isomerase. 1 hit.
    TIGRFAMsiTIGR02151. IPP_isom_2. 1 hit.
    ProtoNetiSearch...

    Entry informationi

    Entry nameiIDI2_THET2
    AccessioniPrimary (citable) accession number: Q746I8
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 1, 2014
    Last sequence update: July 5, 2004
    Last modified: November 2, 2016
    This is version 99 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, Plasmid

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.