ID   IDI_ECOLI               Reviewed;         182 AA.
AC   Q46822; Q2M9V2;
DT   30-MAY-2000, integrated into UniProtKB/Swiss-Prot.
DT   01-NOV-1996, sequence version 1.
DT   27-MAR-2024, entry version 181.
DE   RecName: Full=Isopentenyl-diphosphate Delta-isomerase;
DE            Short=IPP isomerase {ECO:0000303|PubMed:10419945};
DE            EC=5.3.3.2 {ECO:0000269|PubMed:10419945};
DE   AltName: Full=IPP:DMAPP isomerase;
DE   AltName: Full=Isopentenyl pyrophosphate isomerase;
GN   Name=idi {ECO:0000303|PubMed:10419945}; Synonyms=ygfV;
GN   OrderedLocusNames=b2889, JW2857;
OS   Escherichia coli (strain K12).
OC   Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
OC   Enterobacteriaceae; Escherichia.
OX   NCBI_TaxID=83333;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND FUNCTION.
RC   STRAIN=K12 / MG1655 / ATCC 47076;
RX   PubMed=10099534;
RX   DOI=10.1002/(sici)1097-0290(19990120)62:2<235::aid-bit14>3.0.co;2-u;
RA   Wang C.-W., Oh M.-K., Liao J.C.;
RT   "Engineered isoprenoid pathway enhances astaxanthin production in
RT   Escherichia coli.";
RL   Biotechnol. Bioeng. 62:235-241(1999).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=K12 / MG1655 / ATCC 47076;
RX   PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA   Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA   Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA   Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA   Shao Y.;
RT   "The complete genome sequence of Escherichia coli K-12.";
RL   Science 277:1453-1462(1997).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX   PubMed=16738553; DOI=10.1038/msb4100049;
RA   Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA   Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT   "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT   and W3110.";
RL   Mol. Syst. Biol. 2:E1-E5(2006).
RN   [4]
RP   FUNCTION.
RX   PubMed=9603997; DOI=10.1093/oxfordjournals.jbchem.a022047;
RA   Hemmi H., Ohnuma S., Nagaoka K., Nishino T.;
RT   "Identification of genes affecting lycopene formation in Escherichia coli
RT   transformed with carotenoid biosynthetic genes: candidates for early genes
RT   in isoprenoid biosynthesis.";
RL   J. Biochem. 123:1088-1096(1998).
RN   [5]
RP   FUNCTION, CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES, AND
RP   PATHWAY.
RX   PubMed=10419945; DOI=10.1128/jb.181.15.4499-4504.1999;
RA   Hahn F.M., Hurlburt A.P., Poulter C.D.;
RT   "Escherichia coli open reading frame 696 is idi, a nonessential gene
RT   encoding isopentenyl diphosphate isomerase.";
RL   J. Bacteriol. 181:4499-4504(1999).
RN   [6]
RP   X-RAY CRYSTALLOGRAPHY (1.45 ANGSTROMS) IN COMPLEX WITH METAL IONS.
RX   PubMed=11285217; DOI=10.1093/emboj/20.7.1530;
RA   Durbecq V., Sainz G., Oudjama Y., Clantin B., Bompard-Gilles C., Tricot C.,
RA   Caillet J., Stalon V., Droogmans L., Villeret V.;
RT   "Crystal structure of isopentenyl diphosphate:dimethylallyl diphosphate
RT   isomerase.";
RL   EMBO J. 20:1530-1537(2001).
RN   [7]
RP   X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) IN COMPLEX WITH METAL IONS.
RX   PubMed=11698677; DOI=10.1073/pnas.181466998;
RA   Bonanno J.B., Edo C., Eswar N., Pieper U., Romanowski M.J., Ilyin V.,
RA   Gerchman S.E., Kycia H., Studier F.W., Sali A., Burley S.K.;
RT   "Structural genomics of enzymes involved in sterol/isoprenoid
RT   biosynthesis.";
RL   Proc. Natl. Acad. Sci. U.S.A. 98:12896-12901(2001).
RN   [8]
RP   X-RAY CRYSTALLOGRAPHY (1.93 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOG;
RP   MANGANESE AND MAGNESIUM IONS.
RX   PubMed=12630859; DOI=10.1021/ja029171p;
RA   Wouters J., Oudjama Y., Ghosh S., Stalon V., Droogmans L., Oldfield E.;
RT   "Structure and mechanism of action of isopentenylpyrophosphate-
RT   dimethylallylpyrophosphate isomerase.";
RL   J. Am. Chem. Soc. 125:3198-3199(2003).
RN   [9]
RP   X-RAY CRYSTALLOGRAPHY (1.97 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS.
RX   PubMed=12540835; DOI=10.1074/jbc.m212823200;
RA   Wouters J., Oudjama Y., Barkley S.J., Tricot C., Stalon V., Droogmans L.,
RA   Poulter C.D.;
RT   "Catalytic mechanism of Escherichia coli isopentenyl diphosphate isomerase
RT   involves Cys-67, Glu-116, and Tyr-104 as suggested by crystal structures of
RT   complexes with transition state analogues and irreversible inhibitors.";
RL   J. Biol. Chem. 278:11903-11908(2003).
RN   [10]
RP   X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF MUTANT ALA-67 IN COMPLEX WITH
RP   SUBSTRATE ANALOG.
RX   PubMed=14696183; DOI=10.1002/prot.10573;
RA   Wouters J., Oudjama Y., Stalon V., Droogmans L., Poulter C.D.;
RT   "Crystal structure of the C67A mutant of isopentenyl diphosphate isomerase
RT   complexed with a mechanism-based irreversible inhibitor.";
RL   Proteins 54:216-221(2004).
RN   [11]
RP   X-RAY CRYSTALLOGRAPHY (1.65 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS;
RP   MANGANESE AND MAGNESIUM IONS.
RX   PubMed=15643873; DOI=10.1021/ja040207i;
RA   Wouters J., Yin F., Song Y., Zhang Y., Oudjama Y., Stalon V., Droogmans L.,
RA   Morita C.T., Oldfield E.;
RT   "A crystallographic investigation of phosphoantigen binding to isopentenyl
RT   pyrophosphate/dimethylallyl pyrophosphate isomerase.";
RL   J. Am. Chem. Soc. 127:536-537(2005).
RN   [12]
RP   X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) OF MUTANT ALA/PHE-104 IN COMPLEX
RP   WITH SUBSTRATE ANALOG, AND BIOPHYSICOCHEMICAL PROPERTIES.
RX   PubMed=16617181; DOI=10.1074/jbc.m601851200;
RA   de Ruyck J., Durisotti V., Oudjama Y., Wouters J.;
RT   "Structural role for Tyr-104 in Escherichia coli isopentenyl-diphosphate
RT   isomerase: site-directed mutagenesis, enzymology, and protein
RT   crystallography.";
RL   J. Biol. Chem. 281:17864-17869(2006).
CC   -!- FUNCTION: Catalyzes the 1,3-allylic rearrangement of the homoallylic
CC       substrate isopentenyl (IPP) to its highly electrophilic allylic isomer,
CC       dimethylallyl diphosphate (DMAPP). {ECO:0000269|PubMed:10099534,
CC       ECO:0000269|PubMed:10419945, ECO:0000269|PubMed:9603997}.
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:0000269|PubMed:10419945};
CC       PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:23285;
CC         Evidence={ECO:0000305|PubMed:10419945};
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC         Evidence={ECO:0000269|PubMed:10419945};
CC       Note=Binds 1 Mg(2+) ion per subunit. The magnesium ion binds only when
CC       substrate is bound.;
CC   -!- COFACTOR:
CC       Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC         Evidence={ECO:0000269|PubMed:10419945};
CC       Note=Binds 1 Mn(2+) ion per subunit.;
CC   -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC       Kinetic parameters:
CC         KM=9.5 uM for isopentenyl diphosphate {ECO:0000269|PubMed:16617181};
CC         KM=7.9 uM for isopentenyl diphosphate {ECO:0000269|PubMed:10419945};
CC         KM=14.3 uM for dimethylallyl diphosphate
CC         {ECO:0000269|PubMed:10419945};
CC         Vmax=260 mmol/h/mg enzyme {ECO:0000269|PubMed:16617181};
CC         Vmax=0.97 umol/min/mg enzyme {ECO:0000269|PubMed:10419945};
CC   -!- PATHWAY: Isoprenoid biosynthesis; dimethylallyl diphosphate
CC       biosynthesis; dimethylallyl diphosphate from isopentenyl diphosphate:
CC       step 1/1. {ECO:0000305|PubMed:10419945}.
CC   -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:11285217,
CC       ECO:0000269|PubMed:11698677, ECO:0000269|PubMed:12540835,
CC       ECO:0000269|PubMed:12630859, ECO:0000269|PubMed:14696183,
CC       ECO:0000269|PubMed:15643873, ECO:0000269|PubMed:16617181}.
CC   -!- SUBCELLULAR LOCATION: Cytoplasm.
CC   -!- SIMILARITY: Belongs to the IPP isomerase type 1 family. {ECO:0000305}.
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DR   EMBL; AF119715; AAD26812.1; -; Genomic_DNA.
DR   EMBL; U28375; AAA83070.1; -; Genomic_DNA.
DR   EMBL; U00096; AAC75927.1; -; Genomic_DNA.
DR   EMBL; AP009048; BAE76954.1; -; Genomic_DNA.
DR   PIR; A65073; A65073.
DR   RefSeq; NP_417365.1; NC_000913.3.
DR   RefSeq; WP_001192820.1; NZ_LN832404.1.
DR   PDB; 1HX3; X-ray; 2.10 A; A/B=1-182.
DR   PDB; 1HZT; X-ray; 1.45 A; A=1-182.
DR   PDB; 1I9A; X-ray; 2.50 A; A/B=1-182.
DR   PDB; 1NFS; X-ray; 1.96 A; A/B=1-182.
DR   PDB; 1NFZ; X-ray; 1.97 A; A/B=1-182.
DR   PDB; 1OW2; X-ray; 2.00 A; A/B=1-182.
DR   PDB; 1PPV; X-ray; 1.70 A; A/B=1-182.
DR   PDB; 1PPW; X-ray; 2.21 A; A/B=1-182.
DR   PDB; 1PVF; X-ray; 1.78 A; A/B=1-182.
DR   PDB; 1Q54; X-ray; 1.93 A; A/B=1-182.
DR   PDB; 1R67; X-ray; 1.77 A; A=1-182.
DR   PDB; 1X83; X-ray; 1.80 A; A/B=1-182.
DR   PDB; 1X84; X-ray; 1.78 A; A/B=1-182.
DR   PDB; 2B2K; X-ray; 1.97 A; A/B=1-182.
DR   PDB; 2G73; X-ray; 1.97 A; A/B=1-182.
DR   PDB; 2G74; X-ray; 1.96 A; A/B=1-182.
DR   PDB; 2VNP; X-ray; 2.19 A; A/B=1-182.
DR   PDB; 2VNQ; X-ray; 2.20 A; A/B=1-182.
DR   PDBsum; 1HX3; -.
DR   PDBsum; 1HZT; -.
DR   PDBsum; 1I9A; -.
DR   PDBsum; 1NFS; -.
DR   PDBsum; 1NFZ; -.
DR   PDBsum; 1OW2; -.
DR   PDBsum; 1PPV; -.
DR   PDBsum; 1PPW; -.
DR   PDBsum; 1PVF; -.
DR   PDBsum; 1Q54; -.
DR   PDBsum; 1R67; -.
DR   PDBsum; 1X83; -.
DR   PDBsum; 1X84; -.
DR   PDBsum; 2B2K; -.
DR   PDBsum; 2G73; -.
DR   PDBsum; 2G74; -.
DR   PDBsum; 2VNP; -.
DR   PDBsum; 2VNQ; -.
DR   AlphaFoldDB; Q46822; -.
DR   SMR; Q46822; -.
DR   BioGRID; 4259434; 130.
DR   IntAct; Q46822; 4.
DR   STRING; 511145.b2889; -.
DR   DrugBank; DB02480; (S)-4-bromo-3-hydroxy-3-methylbutyl diphosphate.
DR   DrugBank; DB03165; 2-Dimethylamino-Ethyl-Diphosphate.
DR   DrugBank; DB04170; 4-bromo-3-hydroxy-3-methyl butyl diphosphate.
DR   DrugBank; DB01799; 4-Hydroxy-3-Methyl Butyl Diphosphate.
DR   DrugBank; DB03366; Imidazole.
DR   jPOST; Q46822; -.
DR   PaxDb; 511145-b2889; -.
DR   EnsemblBacteria; AAC75927; AAC75927; b2889.
DR   GeneID; 949020; -.
DR   KEGG; ecj:JW2857; -.
DR   KEGG; eco:b2889; -.
DR   PATRIC; fig|1411691.4.peg.3845; -.
DR   EchoBASE; EB2883; -.
DR   eggNOG; COG1443; Bacteria.
DR   HOGENOM; CLU_060552_2_0_6; -.
DR   InParanoid; Q46822; -.
DR   OMA; VEQEYNH; -.
DR   OrthoDB; 9809458at2; -.
DR   PhylomeDB; Q46822; -.
DR   BioCyc; EcoCyc:IPPISOM-MONOMER; -.
DR   BioCyc; MetaCyc:IPPISOM-MONOMER; -.
DR   BRENDA; 5.3.3.2; 2026.
DR   SABIO-RK; Q46822; -.
DR   UniPathway; UPA00059; UER00104.
DR   EvolutionaryTrace; Q46822; -.
DR   PRO; PR:Q46822; -.
DR   Proteomes; UP000000318; Chromosome.
DR   Proteomes; UP000000625; Chromosome.
DR   GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR   GO; GO:0004452; F:isopentenyl-diphosphate delta-isomerase activity; IDA:EcoCyc.
DR   GO; GO:0000287; F:magnesium ion binding; IDA:EcoCyc.
DR   GO; GO:0008270; F:zinc ion binding; IDA:EcoCyc.
DR   GO; GO:0050992; P:dimethylallyl diphosphate biosynthetic process; IEA:UniProtKB-UniPathway.
DR   GO; GO:0006974; P:DNA damage response; IEP:EcoliWiki.
DR   GO; GO:0008299; P:isoprenoid biosynthetic process; IMP:EcoCyc.
DR   CDD; cd02885; IPP_Isomerase; 1.
DR   Gene3D; 3.90.79.10; Nucleoside Triphosphate Pyrophosphohydrolase; 1.
DR   HAMAP; MF_00202; Idi; 1.
DR   InterPro; IPR011876; IsopentenylPP_isomerase_typ1.
DR   InterPro; IPR015797; NUDIX_hydrolase-like_dom_sf.
DR   InterPro; IPR000086; NUDIX_hydrolase_dom.
DR   NCBIfam; TIGR02150; IPP_isom_1; 1.
DR   PANTHER; PTHR10885; ISOPENTENYL-DIPHOSPHATE DELTA-ISOMERASE; 1.
DR   PANTHER; PTHR10885:SF23; ISOPENTENYL-DIPHOSPHATE DELTA-ISOMERASE; 1.
DR   Pfam; PF00293; NUDIX; 1.
DR   PIRSF; PIRSF018427; Isopntndiph_ism; 1.
DR   SUPFAM; SSF55811; Nudix; 1.
DR   PROSITE; PS51462; NUDIX; 1.
PE   1: Evidence at protein level;
KW   3D-structure; Cytoplasm; Isomerase; Isoprene biosynthesis; Magnesium;
KW   Manganese; Metal-binding; Reference proteome.
FT   CHAIN           1..182
FT                   /note="Isopentenyl-diphosphate Delta-isomerase"
FT                   /id="PRO_0000205249"
FT   DOMAIN          30..164
FT                   /note="Nudix hydrolase"
FT   ACT_SITE        67
FT   ACT_SITE        116
FT   BINDING         21
FT                   /ligand="substrate"
FT   BINDING         25
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /evidence="ECO:0000269|PubMed:12630859,
FT                   ECO:0000269|PubMed:15643873"
FT   BINDING         32
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /evidence="ECO:0000269|PubMed:12630859,
FT                   ECO:0000269|PubMed:15643873"
FT   BINDING         51
FT                   /ligand="substrate"
FT   BINDING         55
FT                   /ligand="substrate"
FT   BINDING         67
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT   BINDING         69
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /evidence="ECO:0000269|PubMed:12630859,
FT                   ECO:0000269|PubMed:15643873"
FT   BINDING         69
FT                   /ligand="substrate"
FT   BINDING         83
FT                   /ligand="substrate"
FT   BINDING         87
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT   BINDING         87
FT                   /ligand="substrate"
FT   BINDING         114
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /evidence="ECO:0000269|PubMed:12630859,
FT                   ECO:0000269|PubMed:15643873"
FT   BINDING         116
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /evidence="ECO:0000269|PubMed:12630859,
FT                   ECO:0000269|PubMed:15643873"
FT   SITE            104
FT                   /note="Essential for catalytic activity"
FT   MUTAGEN         104
FT                   /note="Y->A: Reduces activity by 99%."
FT   MUTAGEN         104
FT                   /note="Y->F: Reduces activity by 97%."
FT   STRAND          5..9
FT                   /evidence="ECO:0007829|PDB:1PPV"
FT   STRAND          11..13
FT                   /evidence="ECO:0007829|PDB:1PPV"
FT   STRAND          15..20
FT                   /evidence="ECO:0007829|PDB:1PPV"
FT   HELIX           21..24
FT                   /evidence="ECO:0007829|PDB:1PPV"
FT   STRAND          35..40
FT                   /evidence="ECO:0007829|PDB:1HZT"
FT   STRAND          46..51
FT                   /evidence="ECO:0007829|PDB:1HZT"
FT   STRAND          56..58
FT                   /evidence="ECO:0007829|PDB:1HZT"
FT   STRAND          62..68
FT                   /evidence="ECO:0007829|PDB:1HZT"
FT   HELIX           76..88
FT                   /evidence="ECO:0007829|PDB:1HZT"
FT   STRAND          96..99
FT                   /evidence="ECO:0007829|PDB:1HZT"
FT   STRAND          103..107
FT                   /evidence="ECO:0007829|PDB:1HZT"
FT   STRAND          113..117
FT                   /evidence="ECO:0007829|PDB:1HZT"
FT   STRAND          120..125
FT                   /evidence="ECO:0007829|PDB:1HZT"
FT   TURN            133..135
FT                   /evidence="ECO:0007829|PDB:1HZT"
FT   STRAND          136..142
FT                   /evidence="ECO:0007829|PDB:1HZT"
FT   HELIX           144..153
FT                   /evidence="ECO:0007829|PDB:1HZT"
FT   HELIX           155..157
FT                   /evidence="ECO:0007829|PDB:1HZT"
FT   HELIX           160..167
FT                   /evidence="ECO:0007829|PDB:1HZT"
FT   HELIX           169..177
FT                   /evidence="ECO:0007829|PDB:1HZT"
SQ   SEQUENCE   182 AA;  20508 MW;  AEAE3EF8254ECC2D CRC64;
     MQTEHVILLN AQGVPTGTLE KYAAHTADTR LHLAFSSWLF NAKGQLLVTR RALSKKAWPG
     VWTNSVCGHP QLGESNEDAV IRRCRYELGV EITPPESIYP DFRYRATDPS GIVENEVCPV
     FAARTTSALQ INDDEVMDYQ WCDLADVLHG IDATPWAFSP WMVMQATNRE ARKRLSAFTQ
     LK
//