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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)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei65 – 651FMNUniRule annotation2 Publications
    Binding sitei96 – 961FMN; via amide nitrogenUniRule annotation2 Publications
    Binding sitei125 – 1251FMNUniRule annotation2 Publications
    Binding sitei160 – 1601Substrate
    Metal bindingi161 – 1611MagnesiumUniRule annotation2 Publications
    Binding sitei193 – 1931FMNUniRule annotation2 Publications
    Binding sitei218 – 2181FMNUniRule annotation2 Publications
    Binding sitei223 – 2231FMN; via amide nitrogenUniRule annotation2 Publications

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi66 – 683FMNUniRule annotation2 Publications
    Nucleotide bindingi275 – 2773FMNUniRule annotation2 Publications
    Nucleotide bindingi296 – 2972FMNUniRule annotation2 Publications

    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)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi7 – 71R → A: Does not affect the proper folding of the enzyme, but it shows significant loss of isomerase activity. 1 Publication
    Mutagenesisi8 – 81K → A: Does not affect the proper folding of the enzyme, but it shows significant loss of isomerase activity. 1 Publication
    Mutagenesisi11 – 111H → A: Does not affect the proper folding of the enzyme, but it shows significant reduction of isomerase activity. 1 Publication
    Mutagenesisi13 – 131E → 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 Publication
    Mutagenesisi68 – 681T → A: Does not affect the proper folding of the enzyme, but it shows significant reduction of isomerase activity. 1 Publication
    Mutagenesisi96 – 961S → A: Does not affect the proper folding of the enzyme, but it shows significant reduction of isomerase activity. 1 Publication
    Mutagenesisi125 – 1251N → A: Does not affect the proper folding of the enzyme, but it shows significant reduction of isomerase activity. 1 Publication
    Mutagenesisi155 – 1551H → A: Does not affect the proper folding of the enzyme, but it shows significant reduction of isomerase activity. 1 Publication
    Mutagenesisi157 – 1571N → A: Does not affect the proper folding of the enzyme, but it shows significant loss of isomerase activity. 1 Publication
    Mutagenesisi160 – 1601Q → A: Does not affect the proper folding of the enzyme, but it shows significant loss of isomerase activity. 2 Publications
    Mutagenesisi160 – 1601Q → E: 10-fold decrease in the catalytic efficiency. 2 Publications
    Mutagenesisi160 – 1601Q → H: 23-fold decrease in the catalytic efficiency. 2 Publications
    Mutagenesisi160 – 1601Q → L: 28-fold decrease in the catalytic efficiency and 5-fold decrease in the affinity binding for IPP. 2 Publications
    Mutagenesisi160 – 1601Q → N: 150-fold decrease in the catalytic efficiency and 2-fold decrease in the affinity binding for IPP. 2 Publications
    Mutagenesisi161 – 1611E → A: Does not affect the proper folding of the enzyme, but it shows significant loss of isomerase activity. 1 Publication
    Mutagenesisi193 – 1931K → 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 Publication
    Mutagenesisi194 – 1941E → A: Does not affect the proper folding of the enzyme, but it shows significant reduction of isomerase activity. 1 Publication
    Mutagenesisi216 – 2161D → A: Does not affect the proper folding of the enzyme, but it shows significant reduction of isomerase activity. 1 Publication
    Mutagenesisi229 – 2291E → A: Does not affect the proper folding of the enzyme, but it shows significant reduction of isomerase activity. 1 Publication
    Mutagenesisi232 – 2321R → A: Does not affect the proper folding of the enzyme, but it shows significant reduction of isomerase activity. 1 Publication
    Mutagenesisi235 – 2351R → 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 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 368368Isopentenyl-diphosphate delta-isomerasePRO_0000134454Add
    BLAST

    Interactioni

    Subunit structurei

    Homooctamer. Dimer of tetramers.UniRule annotation3 Publications

    Structurei

    Secondary structure

    1
    368
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi10 – 178Combined sources
    Helixi29 – 313Combined sources
    Beta strandi32 – 343Combined sources
    Beta strandi41 – 433Combined sources
    Helixi44 – 463Combined sources
    Beta strandi51 – 533Combined sources
    Beta strandi56 – 649Combined sources
    Helixi72 – 8817Combined sources
    Helixi98 – 1025Combined sources
    Helixi104 – 1063Combined sources
    Helixi108 – 1169Combined sources
    Beta strandi118 – 1203Combined sources
    Beta strandi122 – 1276Combined sources
    Helixi128 – 1325Combined sources
    Helixi137 – 14610Combined sources
    Beta strandi150 – 1556Combined sources
    Helixi158 – 1636Combined sources
    Beta strandi164 – 1663Combined sources
    Helixi174 – 18310Combined sources
    Beta strandi190 – 1934Combined sources
    Beta strandi195 – 1973Combined sources
    Helixi201 – 2099Combined sources
    Beta strandi214 – 2163Combined sources
    Helixi225 – 23511Combined sources
    Helixi240 – 2467Combined sources
    Turni247 – 2493Combined sources
    Helixi254 – 26411Combined sources
    Beta strandi269 – 2757Combined sources
    Helixi279 – 28810Combined sources
    Beta strandi291 – 2955Combined sources
    Helixi297 – 3059Combined sources
    Helixi307 – 32721Combined sources
    Helixi333 – 3375Combined sources
    Beta strandi341 – 3433Combined sources
    Helixi345 – 35410Combined sources
    Helixi358 – 3658Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    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.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP61615.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni7 – 82Substrate binding
    Regioni96 – 983Substrate binding

    Sequence similaritiesi

    Belongs to the IPP isomerase type 2 family.UniRule annotation

    Family and domain databases

    Gene3Di3.20.20.70. 1 hit.
    HAMAPiMF_00354. Idi_2.
    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
    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.
    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

    Gene3Di3.20.20.70. 1 hit.
    HAMAPiMF_00354. Idi_2.
    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...

    Publicationsi

    1. "Type 2 isopentenyl diphosphate isomerase from a thermoacidophilic archaeon Sulfolobus shibatae."
      Yamashita S., Hemmi H., Ikeda Y., Nakayama T., Nishino T.
      Eur. J. Biochem. 271:1087-1093(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. "New role of flavin as a general acid-base catalyst with no redox function in type 2 isopentenyl-diphosphate isomerase."
      Unno H., Yamashita S., Ikeda Y., Sekiguchi S.Y., Yoshida N., Yoshimura T., Kusunoki M., Nakayama T., Nishino T., Hemmi H.
      J. Biol. Chem. 284:9160-9167(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) IN COMPLEX WITH FMN; SUBSTRATE ANALOGS AND MAGNESIUM, FUNCTION, MUTAGENESIS OF ARG-7; LYS-8; HIS-11; THR-68; SER-96; ASN-125; HIS-155; ASN-157; GLN-160; GLU-161; LYS-193; GLU-194; ASP-216; GLU-229 AND ARG-232, COFACTOR, SUBUNIT.
    3. "Covalent modification of reduced flavin mononucleotide in type-2 isopentenyl diphosphate isomerase by active-site-directed inhibitors."
      Nagai T., Unno H., Janczak M.W., Yoshimura T., Poulter C.D., Hemmi H.
      Proc. Natl. Acad. Sci. U.S.A. 108:20461-20466(2011) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.20 ANGSTROMS) IN COMPLEX WITH FMN; SUBSTRATE ANALOGS AND MAGNESIUM, FUNCTION, CATALYTIC ACTIVITY, MUTAGENESIS OF GLN-160, BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR, SUBUNIT.
    4. "Substrate-induced change in the quaternary structure of type 2 isopentenyl diphosphate isomerase from Sulfolobus shibatae."
      Nakatani H., Goda S., Unno H., Nagai T., Yoshimura T., Hemmi H.
      J. Bacteriol. 194:3216-3224(2012) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS) IN COMPLEX WITH FMN ANALOG, FUNCTION, MUTAGENESIS OF GLU-13 AND ARG-235, COFACTOR, SUBUNIT.

    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 11, 2015
    This is version 62 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.