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Protein

Isopentenyl-diphosphate Delta-isomerase

Gene

idi

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: -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

Protein has several cofactor binding sites:
  • Mg2+Note: Binds 1 Mg2+ ion per subunit. The magnesium ion binds only when substrate is bound.
  • Mn2+Note: Binds 1 Mn2+ ion per subunit.

Kineticsi

  1. KM=9.5 µM for Isopentenyl diphosphate1 Publication
  1. Vmax=260 mmol/h/mg enzyme1 Publication

Pathwayi: dimethylallyl diphosphate biosynthesis

This protein is involved in step 1 of the subpathway that synthesizes dimethylallyl diphosphate from isopentenyl diphosphate.
Proteins known to be involved in this subpathway in this organism are:
  1. Isopentenyl-diphosphate Delta-isomerase (idi)
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 keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei21Substrate1
Metal bindingi25Manganese2 Publications1
Metal bindingi32Manganese2 Publications1
Binding sitei51Substrate1
Binding sitei55Substrate1
Active sitei671
Metal bindingi67Magnesium; via carbonyl oxygen1
Metal bindingi69Manganese2 Publications1
Binding sitei69Substrate1
Binding sitei83Substrate1
Metal bindingi87Magnesium1
Binding sitei87Substrate1
Sitei104Essential for catalytic activity1
Metal bindingi114Manganese2 Publications1
Active sitei1161
Metal bindingi116Manganese2 Publications1

GO - Molecular functioni

GO - Biological processi

  • cellular response to DNA damage stimulus Source: EcoliWiki
  • dimethylallyl diphosphate biosynthetic process Source: UniProtKB-UniPathway
  • isopentenyl diphosphate biosynthetic process Source: GO_Central
  • isoprenoid biosynthetic process Source: EcoCyc

Keywordsi

Molecular functionIsomerase
Biological processIsoprene biosynthesis
LigandMagnesium, Manganese, Metal-binding

Enzyme and pathway databases

BioCyciEcoCyc:IPPISOM-MONOMER
MetaCyc:IPPISOM-MONOMER
BRENDAi5.3.3.2 2026
SABIO-RKiQ46822
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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG13072 idi

Subcellular locationi

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi104Y → A: Reduces activity by 99%. 1
Mutagenesisi104Y → F: Reduces activity by 97%. 1

Chemistry databases

DrugBankiDB02480 (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
DB04160 Diphosphate

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002052491 – 182Isopentenyl-diphosphate Delta-isomeraseAdd BLAST182

Proteomic databases

PaxDbiQ46822
PRIDEiQ46822

Interactioni

Subunit structurei

Homodimer.7 Publications

Protein-protein interaction databases

BioGridi4259434, 130 interactors
IntActiQ46822, 4 interactors
STRINGi316385.ECDH10B_3063

Structurei

Secondary structure

1182
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi5 – 9Combined sources5
Beta strandi11 – 13Combined sources3
Beta strandi15 – 20Combined sources6
Helixi21 – 24Combined sources4
Beta strandi35 – 40Combined sources6
Beta strandi46 – 51Combined sources6
Beta strandi56 – 58Combined sources3
Beta strandi62 – 68Combined sources7
Helixi76 – 88Combined sources13
Beta strandi96 – 99Combined sources4
Beta strandi103 – 107Combined sources5
Beta strandi113 – 117Combined sources5
Beta strandi120 – 125Combined sources6
Turni133 – 135Combined sources3
Beta strandi136 – 142Combined sources7
Helixi144 – 153Combined sources10
Helixi155 – 157Combined sources3
Helixi160 – 167Combined sources8
Helixi169 – 177Combined sources9

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ46822

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini30 – 164Nudix hydrolaseAdd BLAST135

Sequence similaritiesi

Belongs to the IPP isomerase type 1 family.Curated

Phylogenomic databases

eggNOGiENOG4108ZEY Bacteria
COG1443 LUCA
HOGENOMiHOG000274107
InParanoidiQ46822
KOiK01823
OMAiLRLCPWF
PhylomeDBiQ46822

Family and domain databases

CDDicd02885 IPP_Isomerase, 1 hit
HAMAPiMF_00202 Idi, 1 hit
InterProiView protein in InterPro
IPR011876 IsopentenylPP_isomerase_typ1
IPR015797 NUDIX_hydrolase-like_dom_sf
IPR000086 NUDIX_hydrolase_dom
PANTHERiPTHR10885 PTHR10885, 1 hit
PfamiView protein in Pfam
PF00293 NUDIX, 1 hit
PIRSFiPIRSF018427 Isopntndiph_ism, 1 hit
SUPFAMiSSF55811 SSF55811, 1 hit
TIGRFAMsiTIGR02150 IPP_isom_1, 1 hit
PROSITEiView protein in PROSITE
PS51462 NUDIX, 1 hit

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:
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
PIRiA65073
RefSeqiNP_417365.1, NC_000913.3
WP_001192820.1, NZ_LN832404.1

Genome annotation databases

EnsemblBacteriaiAAC75927; AAC75927; b2889
BAE76954; BAE76954; BAE76954
GeneIDi949020
KEGGiecj:JW2857
eco:b2889
PATRICifig|1411691.4.peg.3845

Similar proteinsi

Entry informationi

Entry nameiIDI_ECOLI
AccessioniPrimary (citable) accession number: Q46822
Secondary accession number(s): Q2M9V2
Entry historyiIntegrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: November 1, 1996
Last modified: March 28, 2018
This is version 152 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health