IDI2_METJA
ID IDI2_METJA Reviewed; 359 AA.
AC Q58272;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 117.
DE RecName: Full=Isopentenyl-diphosphate delta-isomerase {ECO:0000255|HAMAP-Rule:MF_00354};
DE Short=IPP isomerase {ECO:0000255|HAMAP-Rule:MF_00354};
DE EC=5.3.3.2 {ECO:0000255|HAMAP-Rule:MF_00354};
DE AltName: Full=Isopentenyl diphosphate:dimethylallyl diphosphate isomerase {ECO:0000255|HAMAP-Rule:MF_00354};
DE AltName: Full=Isopentenyl pyrophosphate isomerase {ECO:0000255|HAMAP-Rule:MF_00354};
DE AltName: Full=Type 2 isopentenyl diphosphate isomerase {ECO:0000255|HAMAP-Rule:MF_00354};
DE Short=IDI-2 {ECO:0000255|HAMAP-Rule:MF_00354};
GN Name=fni {ECO:0000255|HAMAP-Rule:MF_00354}; OrderedLocusNames=MJ0862;
OS Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM
OS 10045 / NBRC 100440) (Methanococcus jannaschii).
OC Archaea; Euryarchaeota; Methanomada group; Methanococci; Methanococcales;
OC Methanocaldococcaceae; Methanocaldococcus.
OX NCBI_TaxID=243232;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440;
RX PubMed=8688087; DOI=10.1126/science.273.5278.1058;
RA Bult C.J., White O., Olsen G.J., Zhou L., Fleischmann R.D., Sutton G.G.,
RA Blake J.A., FitzGerald L.M., Clayton R.A., Gocayne J.D., Kerlavage A.R.,
RA Dougherty B.A., Tomb J.-F., Adams M.D., Reich C.I., Overbeek R.,
RA Kirkness E.F., Weinstock K.G., Merrick J.M., Glodek A., Scott J.L.,
RA Geoghagen N.S.M., Weidman J.F., Fuhrmann J.L., Nguyen D., Utterback T.R.,
RA Kelley J.M., Peterson J.D., Sadow P.W., Hanna M.C., Cotton M.D.,
RA Roberts K.M., Hurst M.A., Kaine B.P., Borodovsky M., Klenk H.-P.,
RA Fraser C.M., Smith H.O., Woese C.R., Venter J.C.;
RT "Complete genome sequence of the methanogenic archaeon, Methanococcus
RT jannaschii.";
RL Science 273:1058-1073(1996).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, ACTIVITY
RP REGULATION, AND COFACTOR.
RC STRAIN=ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440;
RX PubMed=16793276; DOI=10.1016/j.bmc.2006.06.011;
RA Hoshino T., Tamegai H., Kakinuma K., Eguchi T.;
RT "Inhibition of type 2 isopentenyl diphosphate isomerase from
RT Methanocaldococcus jannaschii by a mechanism-based inhibitor of type 1
RT isopentenyl diphosphate isomerase.";
RL Bioorg. Med. Chem. 14:6555-6559(2006).
RN [3]
RP CRYSTALLIZATION.
RX PubMed=21206036; DOI=10.1107/s1744309110046944;
RA Hoshino T., Nango E., Baba S., Eguchi T., Kumasaka T.;
RT "Crystallization and preliminary X-ray analysis of isopentenyl diphosphate
RT isomerase from Methanocaldococcus jannaschii.";
RL Acta Crystallogr. F 67:101-103(2011).
CC -!- FUNCTION: Involved in the biosynthesis of isoprenoids. Catalyzes the
CC 1,3-allylic rearrangement of the homoallylic substrate isopentenyl
CC (IPP) to its allylic isomer, dimethylallyl diphosphate (DMAPP).
CC {ECO:0000255|HAMAP-Rule:MF_00354, ECO:0000269|PubMed:16793276}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=isopentenyl diphosphate = dimethylallyl diphosphate;
CC Xref=Rhea:RHEA:23284, ChEBI:CHEBI:57623, ChEBI:CHEBI:128769;
CC EC=5.3.3.2; Evidence={ECO:0000255|HAMAP-Rule:MF_00354,
CC ECO:0000269|PubMed:16793276};
CC -!- COFACTOR:
CC Name=FMN; Xref=ChEBI:CHEBI:58210;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00354,
CC ECO:0000269|PubMed:16793276};
CC -!- COFACTOR:
CC Name=NADPH; Xref=ChEBI:CHEBI:57783;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00354,
CC ECO:0000269|PubMed:16793276};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00354};
CC -!- ACTIVITY REGULATION: Inhibited by 3,4-epoxy-3-methylbutyl diphosphate
CC (EIPP). {ECO:0000269|PubMed:16793276}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=15.3 mM for IPP {ECO:0000269|PubMed:16793276};
CC Note=kcat is 191 sec(-1) for isomerase activity with IPP.;
CC pH dependence:
CC Optimum pH is between 7 and 7.2. {ECO:0000269|PubMed:16793276};
CC Temperature dependence:
CC Optimum temperature is between 85 and 95 degrees Celsius.
CC {ECO:0000269|PubMed:16793276};
CC -!- SUBUNIT: Homooctamer. Dimer of tetramers. {ECO:0000255|HAMAP-
CC Rule:MF_00354}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00354}.
CC -!- SIMILARITY: Belongs to the IPP isomerase type 2 family.
CC {ECO:0000255|HAMAP-Rule:MF_00354}.
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DR EMBL; L77117; AAB98867.1; -; Genomic_DNA.
DR PIR; F64407; F64407.
DR RefSeq; WP_010870377.1; NC_000909.1.
DR AlphaFoldDB; Q58272; -.
DR SMR; Q58272; -.
DR STRING; 243232.MJ_0862; -.
DR EnsemblBacteria; AAB98867; AAB98867; MJ_0862.
DR GeneID; 1451751; -.
DR KEGG; mja:MJ_0862; -.
DR eggNOG; arCOG00613; Archaea.
DR HOGENOM; CLU_065515_1_0_2; -.
DR InParanoid; Q58272; -.
DR OMA; WDWGIPT; -.
DR OrthoDB; 42330at2157; -.
DR PhylomeDB; Q58272; -.
DR BioCyc; MetaCyc:MON-21126; -.
DR Proteomes; UP000000805; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0010181; F:FMN binding; IEA:UniProtKB-UniRule.
DR GO; GO:0004452; F:isopentenyl-diphosphate delta-isomerase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0070402; F:NADPH binding; IEA:UniProtKB-UniRule.
DR GO; GO:0016491; F:oxidoreductase activity; IEA:InterPro.
DR GO; GO:0008299; P:isoprenoid biosynthetic process; IEA:UniProtKB-UniRule.
DR CDD; cd02811; IDI-2_FMN; 1.
DR Gene3D; 3.20.20.70; -; 1.
DR HAMAP; MF_00354; Idi_2; 1.
DR InterPro; IPR013785; Aldolase_TIM.
DR InterPro; IPR000262; FMN-dep_DH.
DR InterPro; IPR011179; IPdP_isomerase.
DR PANTHER; PTHR43665; PTHR43665; 1.
DR Pfam; PF01070; FMN_dh; 1.
DR PIRSF; PIRSF003314; IPP_isomerase; 1.
DR TIGRFAMs; TIGR02151; IPP_isom_2; 1.
PE 1: Evidence at protein level;
KW Cytoplasm; Flavoprotein; FMN; Isomerase; Isoprene biosynthesis; Magnesium;
KW Metal-binding; NADP; Reference proteome.
FT CHAIN 1..359
FT /note="Isopentenyl-diphosphate delta-isomerase"
FT /id="PRO_0000134444"
FT BINDING 11..12
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00354"
FT BINDING 68
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00354"
FT BINDING 69..71
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00354"
FT BINDING 99..101
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00354"
FT BINDING 99
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00354"
FT BINDING 127
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00354"
FT BINDING 163
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00354"
FT BINDING 164
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00354"
FT BINDING 199
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00354"
FT BINDING 229
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00354"
FT BINDING 278..280
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00354"
FT BINDING 299..300
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00354"
SQ SEQUENCE 359 AA; 39875 MW; 46BDD320262772EA CRC64;
MVNNRNEIEV RKLEHIFLCS YCNVEYEKTT LLEDIELIHK GTCGINFNDI ETEIELFGKK
LSAPIIVSGM TGGHSKAKEI NKNIAKAVEE LGLGMGVGSQ RAAIVNDELI DTYSIVRDYT
NNLVIGNLGA VNFIVDDWDE EIIDKAIEMI DADAIAIHFN PLQEIIQPEG DLNFKNLYKL
KEIISNYKKS YKNIPFIAKQ VGEGFSKEDA LILKDIGFDA IDVQGSGGTS WAKVEIYRVK
EEEIKRLAEK FANWGIPTAA SIFEVKSVYD GIVIGSGGIR GGLDIAKCIA IGCDCCSVAL
PILKASLKGW EEVVKVLESY IKELKIAMFL VGAENIEELK KTSYIVKGTL KEWISQRLK
