Q46822 (IDI_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended 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

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia › Escherichia coli

Protein attributes

Sequence length	182 AA.
Sequence status	Complete.
Protein existence	Evidence 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

Ontologies

Keywords
Biological process	Isoprene biosynthesis
Cellular component	Cytoplasm
Ligand	Magnesium Manganese Metal-binding
Molecular function	Isomerase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	chlorophyll biosynthetic process Inferred from electronic annotation. Source: HAMAP dimethylallyl diphosphate biosynthetic process Inferred from electronic annotation. Source: UniProtKB-UniPathway isoprenoid biosynthetic process Inferred from electronic annotation. Source: HAMAP photosynthesis Inferred from electronic annotation. Source: HAMAP response to DNA damage stimulus Inferred from expression pattern PubMed 11967071. Source: EcoliWiki ubiquinone biosynthetic process Inferred from direct assay Ref.5. Source: EcoCyc
Cellular_component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	hydrolase activity Inferred from electronic annotation. Source: InterPro isopentenyl-diphosphate delta-isomerase activity Inferred from direct assay Ref.5. Source: EcoCyc metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 182

182

Isopentenyl-diphosphate Delta-isomerase HAMAP-Rule MF_00202

PRO_0000205249

Regions

Domain

30 – 164

135

Nudix hydrolase

Sites

Active site

67

1

Active site

116

1

Metal binding

25

1

Manganese

Metal binding

32

1

Manganese

Metal binding

67

1

Magnesium; via carbonyl oxygen

Metal binding

69

1

Manganese

Metal binding

87

1

Magnesium

Metal binding

114

1

Manganese

Metal binding

116

1

Manganese

Binding site

21

1

Substrate

Binding site

51

1

Substrate

Binding site

55

1

Substrate

Binding site

69

1

Substrate

Binding site

83

1

Substrate

Binding site

87

1

Substrate

Site

104

1

Essential for catalytic activity

Experimental info

Mutagenesis

104

1

Y → A: Reduces activity by 99%.

Mutagenesis

104

1

Y → F: Reduces activity by 97%.

Secondary structure

1

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182

Helix Strand Turn

Details...

Beta strand

5 – 9

5

Beta strand

11 – 13

3

Beta strand

15 – 20

6

Helix

21 – 24

4

Beta strand

35 – 40

6

Beta strand

46 – 51

6

Beta strand

56 – 58

3

Beta strand

62 – 68

7

Helix

76 – 88

13

Beta strand

96 – 99

4

Beta strand

103 – 107

5

Beta strand

113 – 117

5

Beta strand

120 – 125

6

Turn

133 – 135

3

Beta strand

136 – 142

7

Helix

144 – 153

10

Helix

155 – 157

3

Helix

160 – 167

8

Helix

169 – 177

9

Sequences

	Sequence		Length	Mass (Da)
	Q46822 [UniParc]. Last modified November 1, 1996. Version 1. Checksum: AEAE3EF8254ECC2D	FASTA	182	20,508
	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

References

	« Hide 'large scale' referencesShow '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 277:1453-1474(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.

PIR

A65073.

RefSeq

NP_417365.1. NC_000913.2.
YP_491090.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

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	[»]

ProteinModelPortal

Q46822.

SMR

Q46822. Positions 4-182.

ModBase

Search...

Protein-protein interaction databases

IntAct

Q46822. 4 interactions.

STRING

511145.b2889.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC75927; AAC75927; b2889.
BAE76954; BAE76954; BAE76954.

GeneID

12930440.
949020.

KEGG

ecj:Y75_p2821.
eco:b2889.

PATRIC

32121188. VBIEscCol129921_2982.

Organism-specific databases

EchoBASE

EB2883.

EcoGene

EG13072. idi.

Phylogenomic databases

eggNOG

COG1443.

HOGENOM

HOG000274107.

KO

K01823.

OMA

SKKTWPG.

ProtClustDB

PRK03759.

Enzyme and pathway databases

BioCyc

EcoCyc:IPPISOM-MONOMER.
ECOL316407:JW2857-MONOMER.
MetaCyc:IPPISOM-MONOMER.

SABIO-RK

Q46822.

UniPathway

UPA00059; UER00104.

Gene expression databases

Genevestigator

Q46822.

Family and domain databases

Gene3D

3.90.79.10. 1 hit.

HAMAP

MF_00202. Idi.

InterPro

IPR011876. IsopentenylPP_isomerase_typ1.
IPR000086. NUDIX_hydrolase_dom.
IPR015797. NUDIX_hydrolase_dom-like.
[Graphical view]

PANTHER

PTHR10885. PTHR10885. 1 hit.

Pfam

PF00293. NUDIX. 1 hit.
[Graphical view]

PIRSF

PIRSF018427. Isopntndiph_ism. 1 hit.

SUPFAM

SSF55811. NUDIX_hydrolase. 1 hit.

TIGRFAMs

TIGR02150. IPP_isom_1. 1 hit.

PROSITE

PS51462. NUDIX. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

Q46822.

Entry information

Entry name

IDI_ECOLI

Accession

Primary (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:	May 1, 2013
This is version 120 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program