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UniProtKB - Q46822 (IDI_ECOLI)
Protein
Isopentenyl-diphosphate Delta-isomerase
Gene
idi
Organism
Escherichia coli (strain K12)
Status
Functioni
Catalyzes the 1,3-allylic rearrangement of the homoallylic substrate isopentenyl (IPP) to its highly electrophilic allylic isomer, dimethylallyl diphosphate (DMAPP).
3 PublicationsCatalytic activityi
Cofactori
Protein has several cofactor binding sites:- Mg2+1 PublicationNote: Binds 1 Mg2+ ion per subunit. The magnesium ion binds only when substrate is bound.
- Mn2+1 PublicationNote: Binds 1 Mn2+ ion per subunit.
Kineticsi
- KM=9.5 µM for isopentenyl diphosphate1 Publication
- KM=7.9 µM for isopentenyl diphosphate1 Publication
- KM=14.3 µM for dimethylallyl diphosphate1 Publication
- Vmax=260 mmol/h/mg enzyme1 Publication
- Vmax=0.97 µmol/min/mg enzyme1 Publication
: dimethylallyl diphosphate biosynthesis Pathwayi
This protein is involved in step 1 of the subpathway that synthesizes dimethylallyl diphosphate from isopentenyl diphosphate.1 Publication This subpathway is part of the pathway dimethylallyl diphosphate biosynthesis, which is itself part of Isoprenoid biosynthesis.View all proteins of this organism that are known to be involved in the subpathway that synthesizes dimethylallyl diphosphate from isopentenyl diphosphate, the pathway dimethylallyl diphosphate biosynthesis and in Isoprenoid biosynthesis.
Sites
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Binding sitei | 21 | Substrate | 1 | |
Metal bindingi | 25 | Manganese2 Publications | 1 | |
Metal bindingi | 32 | Manganese2 Publications | 1 | |
Binding sitei | 51 | Substrate | 1 | |
Binding sitei | 55 | Substrate | 1 | |
Active sitei | 67 | 1 | ||
Metal bindingi | 67 | Magnesium; via carbonyl oxygen | 1 | |
Metal bindingi | 69 | Manganese2 Publications | 1 | |
Binding sitei | 69 | Substrate | 1 | |
Binding sitei | 83 | Substrate | 1 | |
Metal bindingi | 87 | Magnesium | 1 | |
Binding sitei | 87 | Substrate | 1 | |
Sitei | 104 | Essential for catalytic activity | 1 | |
Metal bindingi | 114 | Manganese2 Publications | 1 | |
Active sitei | 116 | 1 | ||
Metal bindingi | 116 | Manganese2 Publications | 1 |
GO - Molecular functioni
- isopentenyl-diphosphate delta-isomerase activity Source: EcoCyc
- magnesium ion binding Source: EcoCyc
- zinc ion binding Source: EcoCyc
GO - Biological processi
- cellular response to DNA damage stimulus Source: EcoliWiki
- dimethylallyl diphosphate biosynthetic process Source: UniProtKB-UniPathway
- isoprenoid biosynthetic process Source: EcoCyc
Keywordsi
Molecular function | Isomerase |
Biological process | Isoprene biosynthesis |
Ligand | Magnesium, Manganese, Metal-binding |
Enzyme and pathway databases
BioCyci | EcoCyc:IPPISOM-MONOMER |
BRENDAi | 5.3.3.2, 2026 |
SABIO-RKi | Q46822 |
UniPathwayi | UPA00059;UER00104 |
Names & Taxonomyi
Protein namesi | Recommended name: Isopentenyl-diphosphate Delta-isomerase (EC:5.3.3.21 Publication)Short name: IPP isomerase1 Publication Alternative name(s): IPP:DMAPP isomerase Isopentenyl pyrophosphate isomerase |
Gene namesi | Name:idi1 Publication Synonyms:ygfV Ordered Locus Names:b2889, JW2857 |
Organismi | Escherichia coli (strain K12) |
Taxonomic identifieri | 83333 [NCBI] |
Taxonomic lineagei | Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacterales › Enterobacteriaceae › Escherichia › |
Proteomesi |
|
Subcellular locationi
Cytoplasm and Cytosol
Other locations
- cytoplasm Source: UniProtKB-SubCell
Keywords - Cellular componenti
CytoplasmPathology & Biotechi
Mutagenesis
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Mutagenesisi | 104 | Y → A: Reduces activity by 99%. | 1 | |
Mutagenesisi | 104 | Y → F: Reduces activity by 97%. | 1 |
Chemistry databases
DrugBanki | DB02480, (S)-4-bromo-3-hydroxy-3-methylbutyl diphosphate DB03165, 2-Dimethylamino-Ethyl-Diphosphate DB04170, 4-bromo-3-hydroxy-3-methyl butyl diphosphate DB01799, 4-Hydroxy-3-Methyl Butyl Diphosphate DB03366, Imidazole |
PTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
ChainiPRO_0000205249 | 1 – 182 | Isopentenyl-diphosphate Delta-isomeraseAdd BLAST | 182 |
Proteomic databases
jPOSTi | Q46822 |
PaxDbi | Q46822 |
PRIDEi | Q46822 |
Interactioni
Subunit structurei
Homodimer.
7 PublicationsProtein-protein interaction databases
BioGRIDi | 4259434, 130 interactors |
IntActi | Q46822, 4 interactors |
STRINGi | 511145.b2889 |
Structurei
Secondary structure
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details3D structure databases
SMRi | Q46822 |
ModBasei | Search... |
PDBe-KBi | Search... |
Miscellaneous databases
EvolutionaryTracei | Q46822 |
Family & Domainsi
Domains and Repeats
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Domaini | 30 – 164 | Nudix hydrolaseAdd BLAST | 135 |
Sequence similaritiesi
Belongs to the IPP isomerase type 1 family.Curated
Phylogenomic databases
eggNOGi | COG1443, Bacteria |
HOGENOMi | CLU_060552_2_0_6 |
InParanoidi | Q46822 |
PhylomeDBi | Q46822 |
Family and domain databases
CDDi | cd02885, IPP_Isomerase, 1 hit |
HAMAPi | MF_00202, Idi, 1 hit |
InterProi | View protein in InterPro IPR011876, IsopentenylPP_isomerase_typ1 IPR015797, NUDIX_hydrolase-like_dom_sf IPR000086, NUDIX_hydrolase_dom |
Pfami | View protein in Pfam PF00293, NUDIX, 1 hit |
PIRSFi | PIRSF018427, Isopntndiph_ism, 1 hit |
SUPFAMi | SSF55811, SSF55811, 1 hit |
TIGRFAMsi | TIGR02150, IPP_isom_1, 1 hit |
PROSITEi | View protein in PROSITE PS51462, NUDIX, 1 hit |
i Sequence
Sequence statusi: Complete.
Q46822-1 [UniParc]FASTAAdd to basket
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
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi 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 WP_001192820.1, NZ_LN832404.1 |
Genome annotation databases
EnsemblBacteriai | AAC75927; AAC75927; b2889 BAE76954; BAE76954; BAE76954 |
GeneIDi | 949020 |
KEGGi | ecj:JW2857 eco:b2889 |
PATRICi | fig|1411691.4.peg.3845 |
Similar proteinsi
Cross-referencesi
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi 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 WP_001192820.1, NZ_LN832404.1 |
3D structure databases
Select the link destinations: PDBei RCSB PDBi PDBji Links Updated | PDB 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 | [»] | |
SMRi | Q46822 | |||||
ModBasei | Search... | |||||
PDBe-KBi | Search... |
Protein-protein interaction databases
BioGRIDi | 4259434, 130 interactors |
IntActi | Q46822, 4 interactors |
STRINGi | 511145.b2889 |
Chemistry databases
DrugBanki | DB02480, (S)-4-bromo-3-hydroxy-3-methylbutyl diphosphate DB03165, 2-Dimethylamino-Ethyl-Diphosphate DB04170, 4-bromo-3-hydroxy-3-methyl butyl diphosphate DB01799, 4-Hydroxy-3-Methyl Butyl Diphosphate DB03366, Imidazole |
Proteomic databases
jPOSTi | Q46822 |
PaxDbi | Q46822 |
PRIDEi | Q46822 |
Genome annotation databases
EnsemblBacteriai | AAC75927; AAC75927; b2889 BAE76954; BAE76954; BAE76954 |
GeneIDi | 949020 |
KEGGi | ecj:JW2857 eco:b2889 |
PATRICi | fig|1411691.4.peg.3845 |
Organism-specific databases
EchoBASEi | EB2883 |
Phylogenomic databases
eggNOGi | COG1443, Bacteria |
HOGENOMi | CLU_060552_2_0_6 |
InParanoidi | Q46822 |
PhylomeDBi | Q46822 |
Enzyme and pathway databases
UniPathwayi | UPA00059;UER00104 |
BioCyci | EcoCyc:IPPISOM-MONOMER |
BRENDAi | 5.3.3.2, 2026 |
SABIO-RKi | Q46822 |
Miscellaneous databases
EvolutionaryTracei | Q46822 |
PROi | PR:Q46822 |
Family and domain databases
CDDi | cd02885, IPP_Isomerase, 1 hit |
HAMAPi | MF_00202, Idi, 1 hit |
InterProi | View protein in InterPro IPR011876, IsopentenylPP_isomerase_typ1 IPR015797, NUDIX_hydrolase-like_dom_sf IPR000086, NUDIX_hydrolase_dom |
Pfami | View protein in Pfam PF00293, NUDIX, 1 hit |
PIRSFi | PIRSF018427, Isopntndiph_ism, 1 hit |
SUPFAMi | SSF55811, SSF55811, 1 hit |
TIGRFAMsi | TIGR02150, IPP_isom_1, 1 hit |
PROSITEi | View protein in PROSITE PS51462, NUDIX, 1 hit |
MobiDBi | Search... |
Entry informationi
Entry namei | IDI_ECOLI | |
Accessioni | Q46822Primary (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: | February 23, 2022 | |
This is version 171 of the entry and version 1 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Prokaryotic Protein Annotation Program |
Miscellaneousi
Keywords - Technical termi
3D-structure, Reference proteomeDocuments
- PATHWAY comments
Index of metabolic and biosynthesis pathways - PDB cross-references
Index of Protein Data Bank (PDB) cross-references - SIMILARITY comments
Index of protein domains and families