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Protein

Isopentenyl-diphosphate Delta-isomerase

Gene

idi

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

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
  • isoprenoid 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.
BRENDAi5.3.3.2. 2026.
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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG13072. idi.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

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

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.
STRINGi511145.b2889.

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
Contains 1 nudix hydrolase domain.Curated

Phylogenomic databases

eggNOGiENOG4108ZEY. Bacteria.
COG1443. LUCA.
HOGENOMiHOG000274107.
InParanoidiQ46822.
KOiK01823.
OMAiSPWMVLQ.
PhylomeDBiQ46822.

Family and domain databases

CDDicd02885. IPP_Isomerase. 1 hit.
Gene3Di3.90.79.10. 1 hit.
HAMAPiMF_00202. Idi. 1 hit.
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:
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.
PATRICi32121188. VBIEscCol129921_2982.

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.
PIRiA65073.
RefSeqiNP_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 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...

Protein-protein interaction databases

BioGridi4259434. 130 interactors.
IntActiQ46822. 4 interactors.
STRINGi511145.b2889.

Proteomic databases

PaxDbiQ46822.
PRIDEiQ46822.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75927; AAC75927; b2889.
BAE76954; BAE76954; BAE76954.
GeneIDi949020.
KEGGiecj:JW2857.
eco:b2889.
PATRICi32121188. VBIEscCol129921_2982.

Organism-specific databases

EchoBASEiEB2883.
EcoGeneiEG13072. idi.

Phylogenomic databases

eggNOGiENOG4108ZEY. Bacteria.
COG1443. LUCA.
HOGENOMiHOG000274107.
InParanoidiQ46822.
KOiK01823.
OMAiSPWMVLQ.
PhylomeDBiQ46822.

Enzyme and pathway databases

UniPathwayiUPA00059; UER00104.
BioCyciEcoCyc:IPPISOM-MONOMER.
ECOL316407:JW2857-MONOMER.
MetaCyc:IPPISOM-MONOMER.
BRENDAi5.3.3.2. 2026.
SABIO-RKQ46822.

Miscellaneous databases

EvolutionaryTraceiQ46822.
PROiQ46822.

Family and domain databases

CDDicd02885. IPP_Isomerase. 1 hit.
Gene3Di3.90.79.10. 1 hit.
HAMAPiMF_00202. Idi. 1 hit.
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]
ProtoNetiSearch...

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: November 2, 2016
This is version 144 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.