IDI_ECOLI
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 03-AUG-2022, entry version 173.
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; Proteobacteria; 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; Q46822; -.
DR PRIDE; Q46822; -.
DR EnsemblBacteria; AAC75927; AAC75927; b2889.
DR EnsemblBacteria; BAE76954; BAE76954; BAE76954.
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; FPLRWAN; -.
DR PhylomeDB; Q46822; -.
DR BioCyc; EcoCyc:IPPISOM-MON; -.
DR BioCyc; MetaCyc:IPPISOM-MON; -.
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:0006974; P:cellular response to DNA damage stimulus; IEP:EcoliWiki.
DR GO; GO:0050992; P:dimethylallyl diphosphate biosynthetic process; IEA:UniProtKB-UniPathway.
DR GO; GO:0008299; P:isoprenoid biosynthetic process; IMP:EcoCyc.
DR CDD; cd02885; IPP_Isomerase; 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 Pfam; PF00293; NUDIX; 1.
DR PIRSF; PIRSF018427; Isopntndiph_ism; 1.
DR SUPFAM; SSF55811; SSF55811; 1.
DR TIGRFAMs; TIGR02150; IPP_isom_1; 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
