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Q46822 (IDI_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 128. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Isopentenyl-diphosphate Delta-isomerase

Short name=IPP isomerase
EC=5.3.3.2
Alternative name(s):
IPP:DMAPP isomerase
Isopentenyl pyrophosphate isomerase
Gene names
Name:idi
Synonyms:ygfV
Ordered Locus Names:b2889, JW2857
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length182 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Catalyzes the 1,3-allylic rearrangement of the homoallylic substrate isopentenyl (IPP) to its highly electrophilic allylic isomer, dimethylallyl diphosphate (DMAPP). Ref.1 Ref.4

Catalytic activity

Isopentenyl diphosphate = dimethylallyl diphosphate. HAMAP-Rule MF_00202

Cofactor

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

Binds 1 manganese ion per subunit.

Pathway

Isoprenoid biosynthesis; dimethylallyl diphosphate biosynthesis; dimethylallyl diphosphate from isopentenyl diphosphate: step 1/1. HAMAP-Rule MF_00202

Subunit structure

Homodimer.

Subcellular location

Cytoplasm HAMAP-Rule MF_00202.

Sequence similarities

Belongs to the IPP isomerase type 1 family.

Contains 1 nudix hydrolase domain.

Biophysicochemical properties

Kinetic parameters:

KM=9.5 µM for Isopentenyl diphosphate Ref.12

Vmax=260 mmol/h/mg enzyme

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 182182Isopentenyl-diphosphate Delta-isomerase HAMAP-Rule MF_00202
PRO_0000205249

Regions

Domain30 – 164135Nudix hydrolase

Sites

Active site671
Active site1161
Metal binding251Manganese
Metal binding321Manganese
Metal binding671Magnesium; via carbonyl oxygen
Metal binding691Manganese
Metal binding871Magnesium
Metal binding1141Manganese
Metal binding1161Manganese
Binding site211Substrate
Binding site511Substrate
Binding site551Substrate
Binding site691Substrate
Binding site831Substrate
Binding site871Substrate
Site1041Essential for catalytic activity

Experimental info

Mutagenesis1041Y → A: Reduces activity by 99%.
Mutagenesis1041Y → F: Reduces activity by 97%.

Secondary structure

..................................... 182
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q46822 [UniParc].

Last modified November 1, 1996. Version 1.
Checksum: AEAE3EF8254ECC2D

FASTA18220,508
        10         20         30         40         50         60 
MQTEHVILLN AQGVPTGTLE KYAAHTADTR LHLAFSSWLF NAKGQLLVTR RALSKKAWPG 

        70         80         90        100        110        120 
VWTNSVCGHP QLGESNEDAV IRRCRYELGV EITPPESIYP DFRYRATDPS GIVENEVCPV 

       130        140        150        160        170        180 
FAARTTSALQ INDDEVMDYQ WCDLADVLHG IDATPWAFSP WMVMQATNRE ARKRLSAFTQ 


LK 

« Hide

References

« Hide 'large scale' references
[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]"The complete genome sequence of Escherichia coli K-12."
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y.
Science 277:1453-1462(1997) [PubMed] [Europe PMC] [Abstract]
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]"Structural genomics of enzymes involved in sterol/isoprenoid biosynthesis."
Bonanno J.B., Edo C., Eswar N., Pieper U., Romanowski M.J., Ilyin V., Gerchman S.E., Kycia H., Studier F.W., Sali A., Burley S.K.
Proc. Natl. Acad. Sci. U.S.A. 98:12896-12901(2001) [PubMed] [Europe PMC] [Abstract]
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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AF119715 Genomic DNA. Translation: AAD26812.1.
U28375 Genomic DNA. Translation: AAA83070.1.
U00096 Genomic DNA. Translation: AAC75927.1.
AP009048 Genomic DNA. Translation: BAE76954.1.
PIRA65073.
RefSeqNP_417365.1. NC_000913.3.
YP_491090.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj
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[»]
ProteinModelPortalQ46822.
SMRQ46822. Positions 4-182.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

IntActQ46822. 4 interactions.
STRING511145.b2889.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC75927; AAC75927; b2889.
BAE76954; BAE76954; BAE76954.
GeneID12930440.
949020.
KEGGecj:Y75_p2821.
eco:b2889.
PATRIC32121188. VBIEscCol129921_2982.

Organism-specific databases

EchoBASEEB2883.
EcoGeneEG13072. idi.

Phylogenomic databases

eggNOGCOG1443.
HOGENOMHOG000274107.
KOK01823.
OMAPFAFSPW.
OrthoDBEOG6MSS4M.
PhylomeDBQ46822.
ProtClustDBPRK03759.

Enzyme and pathway databases

BioCycEcoCyc:IPPISOM-MONOMER.
ECOL316407:JW2857-MONOMER.
MetaCyc:IPPISOM-MONOMER.
SABIO-RKQ46822.
UniPathwayUPA00059; UER00104.

Gene expression databases

GenevestigatorQ46822.

Family and domain databases

Gene3D3.90.79.10. 1 hit.
HAMAPMF_00202. Idi.
InterProIPR011876. IsopentenylPP_isomerase_typ1.
IPR000086. NUDIX_hydrolase_dom.
IPR015797. NUDIX_hydrolase_dom-like.
[Graphical view]
PANTHERPTHR10885. PTHR10885. 1 hit.
PfamPF00293. NUDIX. 1 hit.
[Graphical view]
PIRSFPIRSF018427. Isopntndiph_ism. 1 hit.
SUPFAMSSF55811. SSF55811. 1 hit.
TIGRFAMsTIGR02150. IPP_isom_1. 1 hit.
PROSITEPS51462. NUDIX. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceQ46822.
PROQ46822.

Entry information

Entry nameIDI_ECOLI
AccessionPrimary (citable) accession number: Q46822
Secondary accession number(s): Q2M9V2
Entry history
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: November 1, 1996
Last modified: April 16, 2014
This is version 128 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

PATHWAY comments

Index of metabolic and biosynthesis pathways

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene