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Protein

Isopentenyl-diphosphate Delta-isomerase

Gene

idi

Organism
Escherichia coli (strain ATCC 8739 / DSM 1576 / Crooks)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

Functioni

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

Catalytic activityi

Isopentenyl diphosphate = dimethylallyl diphosphate.UniRule annotation

Cofactori

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

Pathwayi: dimethylallyl diphosphate biosynthesis

This protein is involved in step 1 of the subpathway that synthesizes dimethylallyl diphosphate from isopentenyl diphosphate.UniRule annotation
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)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi25 – 251ManganeseUniRule annotation
Metal bindingi32 – 321ManganeseUniRule annotation
Active sitei67 – 671UniRule annotation
Metal bindingi69 – 691ManganeseUniRule annotation
Metal bindingi87 – 871MagnesiumUniRule annotation
Metal bindingi114 – 1141ManganeseUniRule annotation
Active sitei116 – 1161UniRule annotation
Metal bindingi116 – 1161ManganeseUniRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Isomerase

Keywords - Biological processi

Isoprene biosynthesis

Keywords - Ligandi

Magnesium, Manganese, Metal-binding

Enzyme and pathway databases

BioCyciECOL481805:GI3G-835-MONOMER.
UniPathwayiUPA00059; UER00104.

Names & Taxonomyi

Protein namesi
Recommended name:
Isopentenyl-diphosphate Delta-isomeraseUniRule annotation (EC:5.3.3.2UniRule annotation)
Short name:
IPP isomeraseUniRule annotation
Alternative name(s):
IPP:DMAPP isomeraseUniRule annotation
Isopentenyl pyrophosphate isomeraseUniRule annotation
Gene namesi
Name:idiUniRule annotation
Ordered Locus Names:EcolC_0820
OrganismiEscherichia coli (strain ATCC 8739 / DSM 1576 / Crooks)
Taxonomic identifieri481805 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 182182Isopentenyl-diphosphate Delta-isomerasePRO_1000077742Add
BLAST

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi481805.EcolC_0820.

Structurei

3D structure databases

ProteinModelPortaliB1ITB3.
SMRiB1ITB3. Positions 4-178.
ModBaseiSearch...
MobiDBiSearch...

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.UniRule annotation
Contains 1 nudix hydrolase domain.Curated

Phylogenomic databases

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

Family and domain databases

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.

B1ITB3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MQTEHVILLN AQGVPTGTLE KYAAHTADTL 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 WMVMQAANSE ARKLLSAFAQ HN
Length:182
Mass (Da):20,303
Last modified:April 29, 2008 - v1
Checksum:i2D5C3E25AB4F96DC
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000946 Genomic DNA. Translation: ACA76492.1.
RefSeqiWP_001192794.1. NC_010468.1.

Genome annotation databases

EnsemblBacteriaiACA76492; ACA76492; EcolC_0820.
KEGGiecl:EcolC_0820.
PATRICi18224229. VBIEscCol82905_0870.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000946 Genomic DNA. Translation: ACA76492.1.
RefSeqiWP_001192794.1. NC_010468.1.

3D structure databases

ProteinModelPortaliB1ITB3.
SMRiB1ITB3. Positions 4-178.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi481805.EcolC_0820.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACA76492; ACA76492; EcolC_0820.
KEGGiecl:EcolC_0820.
PATRICi18224229. VBIEscCol82905_0870.

Phylogenomic databases

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

Enzyme and pathway databases

UniPathwayiUPA00059; UER00104.
BioCyciECOL481805:GI3G-835-MONOMER.

Family and domain databases

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_ECOLC
AccessioniPrimary (citable) accession number: B1ITB3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 20, 2008
Last sequence update: April 29, 2008
Last modified: September 7, 2016
This is version 58 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. 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.