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Q46822

- IDI_ECOLI

UniProt

Q46822 - IDI_ECOLI

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Protein

Isopentenyl-diphosphate Delta-isomerase

Gene

idi

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

Functioni

Catalyzes the 1,3-allylic rearrangement of the homoallylic substrate isopentenyl (IPP) to its highly electrophilic allylic isomer, dimethylallyl diphosphate (DMAPP).2 Publications

Catalytic activityi

Isopentenyl diphosphate = dimethylallyl diphosphate.

Cofactori

Binds 1 magnesium ion per subunit. The magnesium ion binds only when substrate is bound.
Binds 1 manganese ion per subunit.

Kineticsi

  1. KM=9.5 µM for Isopentenyl diphosphate1 Publication

Vmax=260 mmol/h/mg enzyme1 Publication

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei21 – 211Substrate
Metal bindingi25 – 251Manganese2 Publications
Metal bindingi32 – 321Manganese2 Publications
Binding sitei51 – 511Substrate
Binding sitei55 – 551Substrate
Active sitei67 – 671
Metal bindingi67 – 671Magnesium; via carbonyl oxygen
Metal bindingi69 – 691Manganese2 Publications
Binding sitei69 – 691Substrate
Binding sitei83 – 831Substrate
Metal bindingi87 – 871Magnesium
Binding sitei87 – 871Substrate
Sitei104 – 1041Essential for catalytic activity
Metal bindingi114 – 1141Manganese2 Publications
Active sitei116 – 1161
Metal bindingi116 – 1161Manganese2 Publications

GO - Molecular functioni

  1. hydrolase activity Source: InterPro
  2. isopentenyl-diphosphate delta-isomerase activity Source: EcoCyc
  3. metal ion binding Source: UniProtKB-KW

GO - Biological processi

  1. cellular response to DNA damage stimulus Source: EcoliWiki
  2. dimethylallyl diphosphate biosynthetic process Source: UniProtKB-UniPathway
  3. isoprenoid biosynthetic process Source: EcoCyc
  4. ubiquinone biosynthetic process Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Isomerase

Keywords - Biological processi

Isoprene biosynthesis

Keywords - Ligandi

Magnesium, Manganese, Metal-binding

Enzyme and pathway databases

BioCyciEcoCyc:IPPISOM-MONOMER.
ECOL316407:JW2857-MONOMER.
MetaCyc:IPPISOM-MONOMER.
SABIO-RKQ46822.
UniPathwayiUPA00059; UER00104.

Names & Taxonomyi

Protein namesi
Recommended name:
Isopentenyl-diphosphate Delta-isomerase (EC:5.3.3.2)
Short name:
IPP isomerase
Alternative name(s):
IPP:DMAPP isomerase
Isopentenyl pyrophosphate isomerase
Gene namesi
Name:idi
Synonyms:ygfV
Ordered Locus Names:b2889, JW2857
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

Organism-specific databases

EcoGeneiEG13072. idi.

Subcellular locationi

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-HAMAP
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi104 – 1041Y → A: Reduces activity by 99%.
Mutagenesisi104 – 1041Y → F: Reduces activity by 97%.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 182182Isopentenyl-diphosphate Delta-isomerasePRO_0000205249Add
BLAST

Expressioni

Gene expression databases

GenevestigatoriQ46822.

Interactioni

Subunit structurei

Homodimer.7 Publications

Protein-protein interaction databases

IntActiQ46822. 4 interactions.
STRINGi511145.b2889.

Structurei

Secondary structure

1
182
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi5 – 95
Beta strandi11 – 133
Beta strandi15 – 206
Helixi21 – 244
Beta strandi35 – 406
Beta strandi46 – 516
Beta strandi56 – 583
Beta strandi62 – 687
Helixi76 – 8813
Beta strandi96 – 994
Beta strandi103 – 1075
Beta strandi113 – 1175
Beta strandi120 – 1256
Turni133 – 1353
Beta strandi136 – 1427
Helixi144 – 15310
Helixi155 – 1573
Helixi160 – 1678
Helixi169 – 1779

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1HX3X-ray2.10A/B1-182[»]
1HZTX-ray1.45A1-182[»]
1I9AX-ray2.50A/B1-182[»]
1NFSX-ray1.96A/B1-182[»]
1NFZX-ray1.97A/B1-182[»]
1OW2X-ray2.00A/B1-182[»]
1PPVX-ray1.70A/B1-182[»]
1PPWX-ray2.21A/B1-182[»]
1PVFX-ray1.78A/B1-182[»]
1Q54X-ray1.93A/B1-182[»]
1R67X-ray1.77A1-182[»]
1X83X-ray1.80A/B1-182[»]
1X84X-ray1.78A/B1-182[»]
2B2KX-ray1.97A/B1-182[»]
2G73X-ray1.97A/B1-182[»]
2G74X-ray1.96A/B1-182[»]
2VNPX-ray2.19A/B1-182[»]
2VNQX-ray2.20A/B1-182[»]
ProteinModelPortaliQ46822.
SMRiQ46822. Positions 4-182.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ46822.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini30 – 164135Nudix hydrolaseAdd
BLAST

Sequence similaritiesi

Belongs to the IPP isomerase type 1 family.Curated
Contains 1 nudix hydrolase domain.Curated

Phylogenomic databases

eggNOGiCOG1443.
HOGENOMiHOG000274107.
InParanoidiQ46822.
KOiK01823.
OMAiFRYRATA.
OrthoDBiEOG6MSS4M.
PhylomeDBiQ46822.

Family and domain databases

Gene3Di3.90.79.10. 1 hit.
HAMAPiMF_00202. Idi.
InterProiIPR011876. IsopentenylPP_isomerase_typ1.
IPR000086. NUDIX_hydrolase_dom.
IPR015797. NUDIX_hydrolase_dom-like.
[Graphical view]
PANTHERiPTHR10885. PTHR10885. 1 hit.
PfamiPF00293. NUDIX. 1 hit.
[Graphical view]
PIRSFiPIRSF018427. Isopntndiph_ism. 1 hit.
SUPFAMiSSF55811. SSF55811. 1 hit.
TIGRFAMsiTIGR02150. IPP_isom_1. 1 hit.
PROSITEiPS51462. NUDIX. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q46822-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MQTEHVILLN AQGVPTGTLE KYAAHTADTR LHLAFSSWLF NAKGQLLVTR
60 70 80 90 100
RALSKKAWPG VWTNSVCGHP QLGESNEDAV IRRCRYELGV EITPPESIYP
110 120 130 140 150
DFRYRATDPS GIVENEVCPV FAARTTSALQ INDDEVMDYQ WCDLADVLHG
160 170 180
IDATPWAFSP WMVMQATNRE ARKRLSAFTQ LK
Length:182
Mass (Da):20,508
Last modified:November 1, 1996 - v1
Checksum:iAEAE3EF8254ECC2D
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AF119715 Genomic DNA. Translation: AAD26812.1.
U28375 Genomic DNA. Translation: AAA83070.1.
U00096 Genomic DNA. Translation: AAC75927.1.
AP009048 Genomic DNA. Translation: BAE76954.1.
PIRiA65073.
RefSeqiNP_417365.1. NC_000913.3.
YP_491090.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC75927; AAC75927; b2889.
BAE76954; BAE76954; BAE76954.
GeneIDi12930440.
949020.
KEGGiecj:Y75_p2821.
eco:b2889.
PATRICi32121188. VBIEscCol129921_2982.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AF119715 Genomic DNA. Translation: AAD26812.1 .
U28375 Genomic DNA. Translation: AAA83070.1 .
U00096 Genomic DNA. Translation: AAC75927.1 .
AP009048 Genomic DNA. Translation: BAE76954.1 .
PIRi A65073.
RefSeqi NP_417365.1. NC_000913.3.
YP_491090.1. NC_007779.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1HX3 X-ray 2.10 A/B 1-182 [» ]
1HZT X-ray 1.45 A 1-182 [» ]
1I9A X-ray 2.50 A/B 1-182 [» ]
1NFS X-ray 1.96 A/B 1-182 [» ]
1NFZ X-ray 1.97 A/B 1-182 [» ]
1OW2 X-ray 2.00 A/B 1-182 [» ]
1PPV X-ray 1.70 A/B 1-182 [» ]
1PPW X-ray 2.21 A/B 1-182 [» ]
1PVF X-ray 1.78 A/B 1-182 [» ]
1Q54 X-ray 1.93 A/B 1-182 [» ]
1R67 X-ray 1.77 A 1-182 [» ]
1X83 X-ray 1.80 A/B 1-182 [» ]
1X84 X-ray 1.78 A/B 1-182 [» ]
2B2K X-ray 1.97 A/B 1-182 [» ]
2G73 X-ray 1.97 A/B 1-182 [» ]
2G74 X-ray 1.96 A/B 1-182 [» ]
2VNP X-ray 2.19 A/B 1-182 [» ]
2VNQ X-ray 2.20 A/B 1-182 [» ]
ProteinModelPortali Q46822.
SMRi Q46822. Positions 4-182.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

IntActi Q46822. 4 interactions.
STRINGi 511145.b2889.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAC75927 ; AAC75927 ; b2889 .
BAE76954 ; BAE76954 ; BAE76954 .
GeneIDi 12930440.
949020.
KEGGi ecj:Y75_p2821.
eco:b2889.
PATRICi 32121188. VBIEscCol129921_2982.

Organism-specific databases

EchoBASEi EB2883.
EcoGenei EG13072. idi.

Phylogenomic databases

eggNOGi COG1443.
HOGENOMi HOG000274107.
InParanoidi Q46822.
KOi K01823.
OMAi FRYRATA.
OrthoDBi EOG6MSS4M.
PhylomeDBi Q46822.

Enzyme and pathway databases

UniPathwayi UPA00059 ; UER00104 .
BioCyci EcoCyc:IPPISOM-MONOMER.
ECOL316407:JW2857-MONOMER.
MetaCyc:IPPISOM-MONOMER.
SABIO-RK Q46822.

Miscellaneous databases

EvolutionaryTracei Q46822.
PROi Q46822.

Gene expression databases

Genevestigatori Q46822.

Family and domain databases

Gene3Di 3.90.79.10. 1 hit.
HAMAPi MF_00202. Idi.
InterProi IPR011876. IsopentenylPP_isomerase_typ1.
IPR000086. NUDIX_hydrolase_dom.
IPR015797. NUDIX_hydrolase_dom-like.
[Graphical view ]
PANTHERi PTHR10885. PTHR10885. 1 hit.
Pfami PF00293. NUDIX. 1 hit.
[Graphical view ]
PIRSFi PIRSF018427. Isopntndiph_ism. 1 hit.
SUPFAMi SSF55811. SSF55811. 1 hit.
TIGRFAMsi TIGR02150. IPP_isom_1. 1 hit.
PROSITEi PS51462. NUDIX. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Engineered isoprenoid pathway enhances astaxanthin production in Escherichia coli."
    Wang C.-W., Oh M.-K., Liao J.C.
    Biotechnol. Bioeng. 62:235-241(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION.
    Strain: K12 / MG1655 / ATCC 47076.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  3. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  4. "Identification of genes affecting lycopene formation in Escherichia coli transformed with carotenoid biosynthetic genes: candidates for early genes in isoprenoid biosynthesis."
    Hemmi H., Ohnuma S., Nagaoka K., Nishino T.
    J. Biochem. 123:1088-1096(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  5. "Escherichia coli open reading frame 696 is idi, a nonessential gene encoding isopentenyl diphosphate isomerase."
    Hahn F.M., Hurlburt A.P., Poulter C.D.
    J. Bacteriol. 181:4499-4504(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: CHARACTERIZATION.
  6. "Crystal structure of isopentenyl diphosphate:dimethylallyl diphosphate isomerase."
    Durbecq V., Sainz G., Oudjama Y., Clantin B., Bompard-Gilles C., Tricot C., Caillet J., Stalon V., Droogmans L., Villeret V.
    EMBO J. 20:1530-1537(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.45 ANGSTROMS) IN COMPLEX WITH METAL IONS.
  7. Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) IN COMPLEX WITH METAL IONS.
  8. "Structure and mechanism of action of isopentenylpyrophosphate-dimethylallylpyrophosphate isomerase."
    Wouters J., Oudjama Y., Ghosh S., Stalon V., Droogmans L., Oldfield E.
    J. Am. Chem. Soc. 125:3198-3199(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.93 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOG; MANGANESE AND MAGNESIUM IONS.
  9. "Catalytic mechanism of Escherichia coli isopentenyl diphosphate isomerase involves Cys-67, Glu-116, and Tyr-104 as suggested by crystal structures of complexes with transition state analogues and irreversible inhibitors."
    Wouters J., Oudjama Y., Barkley S.J., Tricot C., Stalon V., Droogmans L., Poulter C.D.
    J. Biol. Chem. 278:11903-11908(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.97 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS.
  10. "Crystal structure of the C67A mutant of isopentenyl diphosphate isomerase complexed with a mechanism-based irreversible inhibitor."
    Wouters J., Oudjama Y., Stalon V., Droogmans L., Poulter C.D.
    Proteins 54:216-221(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF MUTANT ALA-67 IN COMPLEX WITH SUBSTRATE ANALOG.
  11. "A crystallographic investigation of phosphoantigen binding to isopentenyl pyrophosphate/dimethylallyl pyrophosphate isomerase."
    Wouters J., Yin F., Song Y., Zhang Y., Oudjama Y., Stalon V., Droogmans L., Morita C.T., Oldfield E.
    J. Am. Chem. Soc. 127:536-537(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.65 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS; MANGANESE AND MAGNESIUM IONS.
  12. "Structural role for Tyr-104 in Escherichia coli isopentenyl-diphosphate isomerase: site-directed mutagenesis, enzymology, and protein crystallography."
    de Ruyck J., Durisotti V., Oudjama Y., Wouters J.
    J. Biol. Chem. 281:17864-17869(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) OF MUTANT ALA/PHE-104 IN COMPLEX WITH SUBSTRATE ANALOG, BIOPHYSICOCHEMICAL PROPERTIES.

Entry informationi

Entry nameiIDI_ECOLI
AccessioniPrimary (citable) accession number: Q46822
Secondary accession number(s): Q2M9V2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: November 1, 1996
Last modified: October 29, 2014
This is version 132 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, Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3