Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Isopentenyl-diphosphate delta-isomerase

Gene

fni

Organism
Sulfolobus shibatae
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 annotation3 Publications

Catalytic activityi

Isopentenyl diphosphate = dimethylallyl diphosphate.UniRule annotation1 Publication

Cofactori

Protein has several cofactor binding sites:

Kineticsi

Kcat is 29.9 sec(-1) for isomerase activity with IPP (at pH 6 and 60 degrees Celsius).

  1. KM=7.39 µM for IPP (at pH 6 and 60 degrees Celsius)1 Publication

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Binding sitei65FMNUniRule annotation2 Publications1
    Binding sitei96FMN; via amide nitrogenUniRule annotation2 Publications1
    Binding sitei125FMNUniRule annotation2 Publications1
    Binding sitei160Substrate1
    Metal bindingi161MagnesiumUniRule annotation2 Publications1
    Binding sitei193FMNUniRule annotation2 Publications1
    Binding sitei218FMNUniRule annotation2 Publications1
    Binding sitei223FMN; via amide nitrogenUniRule annotation2 Publications1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi66 – 68FMNUniRule annotation2 Publications3
    Nucleotide bindingi275 – 277FMNUniRule annotation2 Publications3
    Nucleotide bindingi296 – 297FMNUniRule annotation2 Publications2

    GO - Molecular functioni

    • FMN binding Source: UniProtKB
    • isopentenyl-diphosphate delta-isomerase activity Source: UniProtKB
    • magnesium ion binding Source: UniProtKB
    • NADPH binding Source: UniProtKB
    • oxidoreductase activity Source: InterPro

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Isomerase

    Keywords - Biological processi

    Isoprene biosynthesis

    Keywords - Ligandi

    Flavoprotein, FMN, Magnesium, Metal-binding, NADP

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-14625.
    BRENDAi5.3.3.2. 6162.
    SABIO-RKP61615.

    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
    Synonyms:idi
    OrganismiSulfolobus shibatae
    Taxonomic identifieri2286 [NCBI]
    Taxonomic lineageiArchaeaCrenarchaeotaThermoproteiSulfolobalesSulfolobaceaeSulfolobus

    Subcellular locationi

    • Cytoplasm UniRule annotation

    GO - Cellular componenti

    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi7R → A: Does not affect the proper folding of the enzyme, but it shows significant loss of isomerase activity. 1 Publication1
    Mutagenesisi8K → A: Does not affect the proper folding of the enzyme, but it shows significant loss of isomerase activity. 1 Publication1
    Mutagenesisi11H → A: Does not affect the proper folding of the enzyme, but it shows significant reduction of isomerase activity. 1 Publication1
    Mutagenesisi13E → R: This mutant is heat stable and its affinity binding for IPP is smaller than that of the wild-type. It is in the tetrameric state even at a concentration where the wild-type enzyme dominantly formed an octamer; when associated with E-235. 1 Publication1
    Mutagenesisi68T → A: Does not affect the proper folding of the enzyme, but it shows significant reduction of isomerase activity. 1 Publication1
    Mutagenesisi96S → A: Does not affect the proper folding of the enzyme, but it shows significant reduction of isomerase activity. 1 Publication1
    Mutagenesisi125N → A: Does not affect the proper folding of the enzyme, but it shows significant reduction of isomerase activity. 1 Publication1
    Mutagenesisi155H → A: Does not affect the proper folding of the enzyme, but it shows significant reduction of isomerase activity. 1 Publication1
    Mutagenesisi157N → A: Does not affect the proper folding of the enzyme, but it shows significant loss of isomerase activity. 1 Publication1
    Mutagenesisi160Q → A: Does not affect the proper folding of the enzyme, but it shows significant loss of isomerase activity. 2 Publications1
    Mutagenesisi160Q → E: 10-fold decrease in the catalytic efficiency. 2 Publications1
    Mutagenesisi160Q → H: 23-fold decrease in the catalytic efficiency. 2 Publications1
    Mutagenesisi160Q → L: 28-fold decrease in the catalytic efficiency and 5-fold decrease in the affinity binding for IPP. 2 Publications1
    Mutagenesisi160Q → N: 150-fold decrease in the catalytic efficiency and 2-fold decrease in the affinity binding for IPP. 2 Publications1
    Mutagenesisi161E → A: Does not affect the proper folding of the enzyme, but it shows significant loss of isomerase activity. 1 Publication1
    Mutagenesisi193K → A: Shows significant loss of isomerase activity. Binds FMN with very low affinity, but the global structure of the mutant has not been altered by the mutation. 1 Publication1
    Mutagenesisi194E → A: Does not affect the proper folding of the enzyme, but it shows significant reduction of isomerase activity. 1 Publication1
    Mutagenesisi216D → A: Does not affect the proper folding of the enzyme, but it shows significant reduction of isomerase activity. 1 Publication1
    Mutagenesisi229E → A: Does not affect the proper folding of the enzyme, but it shows significant reduction of isomerase activity. 1 Publication1
    Mutagenesisi232R → A: Does not affect the proper folding of the enzyme, but it shows significant reduction of isomerase activity. 1 Publication1
    Mutagenesisi235R → E: This mutant is heat stable and its affinity binding for IPP is smaller than that of the wild-type. It is in the tetrameric state even at a concentration where the wild-type enzyme dominantly formed an octamer; when associated with R-13. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00001344541 – 368Isopentenyl-diphosphate delta-isomeraseAdd BLAST368

    Interactioni

    Subunit structurei

    Homooctamer. Dimer of tetramers.UniRule annotation3 Publications

    Structurei

    Secondary structure

    1368
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Helixi10 – 17Combined sources8
    Helixi29 – 31Combined sources3
    Beta strandi32 – 34Combined sources3
    Beta strandi41 – 43Combined sources3
    Helixi44 – 46Combined sources3
    Beta strandi51 – 53Combined sources3
    Beta strandi56 – 64Combined sources9
    Helixi72 – 88Combined sources17
    Helixi98 – 102Combined sources5
    Helixi104 – 106Combined sources3
    Helixi108 – 116Combined sources9
    Beta strandi118 – 120Combined sources3
    Beta strandi122 – 127Combined sources6
    Helixi128 – 132Combined sources5
    Helixi137 – 146Combined sources10
    Beta strandi150 – 155Combined sources6
    Helixi158 – 163Combined sources6
    Beta strandi164 – 166Combined sources3
    Helixi174 – 183Combined sources10
    Beta strandi190 – 193Combined sources4
    Beta strandi195 – 197Combined sources3
    Helixi201 – 209Combined sources9
    Beta strandi214 – 216Combined sources3
    Helixi225 – 235Combined sources11
    Helixi240 – 246Combined sources7
    Turni247 – 249Combined sources3
    Helixi254 – 264Combined sources11
    Beta strandi269 – 275Combined sources7
    Helixi279 – 288Combined sources10
    Beta strandi291 – 295Combined sources5
    Helixi297 – 305Combined sources9
    Helixi307 – 327Combined sources21
    Helixi333 – 337Combined sources5
    Beta strandi341 – 343Combined sources3
    Helixi345 – 354Combined sources10
    Helixi358 – 365Combined sources8

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    2ZRUX-ray2.00A/B/C/D1-368[»]
    2ZRVX-ray2.30A/B/C/D1-368[»]
    2ZRWX-ray2.40A/B/C/D1-368[»]
    2ZRXX-ray3.00A/B/C/D1-368[»]
    2ZRYX-ray2.64A/B/C/D1-368[»]
    2ZRZX-ray2.90A/B/C/D1-368[»]
    3B03X-ray2.20A/B/C/D1-368[»]
    3B04X-ray2.30A/B/C/D1-368[»]
    3B05X-ray2.20A/B/C/D1-368[»]
    3B06X-ray2.29A/B/C/D1-368[»]
    3VKJX-ray1.70A/B/C/D1-368[»]
    ProteinModelPortaliP61615.
    SMRiP61615.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP61615.

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni7 – 8Substrate binding2
    Regioni96 – 98Substrate binding3

    Sequence similaritiesi

    Belongs to the IPP isomerase type 2 family.UniRule annotation

    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. 1 hit.
    [Graphical view]
    PIRSFiPIRSF003314. IPP_isomerase. 1 hit.
    TIGRFAMsiTIGR02151. IPP_isom_2. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P61615-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MPDIVNRKVE HVEIAAFENV DGLSSSTFLN DVILVHQGFP GISFSEINTK
    60 70 80 90 100
    TKFFRKEISV PVMVTGMTGG RNELGRINKI IAEVAEKFGI PMGVGSQRVA
    110 120 130 140 150
    IEKAEARESF AIVRKVAPTI PIIANLGMPQ LVKGYGLKEF QDAIQMIEAD
    160 170 180 190 200
    AIAVHLNPAQ EVFQPEGEPE YQIYALEKLR DISKELSVPI IVKESGNGIS
    210 220 230 240 250
    METAKLLYSY GIKNFDTSGQ GGTNWIAIEM IRDIRRGNWK AESAKNFLDW
    260 270 280 290 300
    GVPTAASIME VRYSVPDSFL VGSGGIRSGL DAAKAIALGA DIAGMALPVL
    310 320 330 340 350
    KSAIEGKESL EQFFRKIIFE LKAAMMLTGS KDVDALKKTS IVILGKLKEW
    360
    AEYRGINLSI YEKVRKRE
    Length:368
    Mass (Da):40,427
    Last modified:May 24, 2004 - v1
    Checksum:i062245BEB52924BC
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AB118244 Genomic DNA. Translation: BAC82424.1.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AB118244 Genomic DNA. Translation: BAC82424.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    2ZRUX-ray2.00A/B/C/D1-368[»]
    2ZRVX-ray2.30A/B/C/D1-368[»]
    2ZRWX-ray2.40A/B/C/D1-368[»]
    2ZRXX-ray3.00A/B/C/D1-368[»]
    2ZRYX-ray2.64A/B/C/D1-368[»]
    2ZRZX-ray2.90A/B/C/D1-368[»]
    3B03X-ray2.20A/B/C/D1-368[»]
    3B04X-ray2.30A/B/C/D1-368[»]
    3B05X-ray2.20A/B/C/D1-368[»]
    3B06X-ray2.29A/B/C/D1-368[»]
    3VKJX-ray1.70A/B/C/D1-368[»]
    ProteinModelPortaliP61615.
    SMRiP61615.
    ModBaseiSearch...
    MobiDBiSearch...

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-14625.
    BRENDAi5.3.3.2. 6162.
    SABIO-RKP61615.

    Miscellaneous databases

    EvolutionaryTraceiP61615.

    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. 1 hit.
    [Graphical view]
    PIRSFiPIRSF003314. IPP_isomerase. 1 hit.
    TIGRFAMsiTIGR02151. IPP_isom_2. 1 hit.
    ProtoNetiSearch...

    Entry informationi

    Entry nameiIDI2_SULSH
    AccessioniPrimary (citable) accession number: P61615
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 24, 2004
    Last sequence update: May 24, 2004
    Last modified: November 2, 2016
    This is version 64 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

    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.