Reviewed, UniProtKB/Swiss-Prot Q46822 (IDI_ECOLI)

Names and origin

Protein names

Recommended name:
    Isopentenyl-diphosphate Delta-isomerase
      Short name=IPP isomerase
    EC=5.3.3.2
Alternative name(s):
    Isopentenyl pyrophosphate isomerase
    IPP:DMAPP isomerase

Gene names

Name:	idi
Synonyms:	ygfV
Ordered Locus Names:	b2889, JW2857

Organism

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

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	182 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
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 MF_00202
Cofactor	Binds 1 magnesium ion per subunit. The magnesium ion binds only when substrate is bound. HAMAP MF_00202 Binds 1 manganese ion per subunit. HAMAP MF_00202
Pathway	Isoprenoid biosynthesis; dimethylallyl-PP biosynthesis; dimethylallyl-PP from isopentenyl-PP: step 1/1. HAMAP MF_00202
Subunit structure	Homodimer. HAMAP MF_00202
Subcellular location	Cytoplasm. HAMAP MF_00202
Sequence similarities	Belongs to the IPP isomerase type 1 family.
Biophysicochemical properties	Kinetic parameters: KM=9.5 µM for Isopentenyl diphosphate HAMAP MF_00202 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
Gene Ontology (GO)
Biological process	isoprenoid biosynthetic process Inferred from electronic annotation. Source: HAMAP
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 electronic annotation. Source: HAMAP magnesium ion binding Inferred from electronic annotation. Source: UniProtKB-KW manganese 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 MF_00202

PRO_0000205249

Sites

Active site

67

1

HAMAP MF_00202

Active site

116

1

HAMAP MF_00202

Metal binding

25

1

Manganese HAMAP MF_00202

Metal binding

32

1

Manganese HAMAP MF_00202

Metal binding

67

1

Magnesium; via carbonyl oxygen HAMAP MF_00202

Metal binding

69

1

Manganese HAMAP MF_00202

Metal binding

87

1

Magnesium HAMAP MF_00202

Metal binding

114

1

Manganese HAMAP MF_00202

Metal binding

116

1

Manganese HAMAP MF_00202

Binding site

21

1

Substrate HAMAP MF_00202

Binding site

51

1

Substrate HAMAP MF_00202

Binding site

55

1

Substrate HAMAP MF_00202

Binding site

69

1

Substrate HAMAP MF_00202

Binding site

83

1

Substrate HAMAP MF_00202

Binding site

87

1

Substrate HAMAP MF_00202

Site

104

1

Essential for catalytic activity HAMAP MF_00202

Experimental info

Mutagenesis

104

1

Y → A: Reduces activity by 99%. HAMAP MF_00202

Mutagenesis

104

1

Y → F: Reduces activity by 97%. HAMAP MF_00202

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)
	Q46822-1 [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: 10099534] [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: 9278503] [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: 16738553] [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: 9603997] [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: 10419945] [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: 11285217] [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: 11698677] [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: 12630859] [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: 12540835] [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: 14696183] [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: 15643873] [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: 16617181] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) OF MUTANT ALA/PHE-104 IN COMPLEX WITH SUBSTRATE ANALOG, BIOPHYSICOCHEMICAL PROPERTIES.

Cross-references

Sequence databases

EMBLGenBankDDBJ

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

AP_003448.1.
NP_417365.1.

3D structure databases

PDBPDBe

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	[»]

ModBase

Search...

Genome annotation databases

GeneID

949020.

GenomeReviews

Gene locus JW2857 in contig AP009048_GR.
Gene locus b2889 in contig U00096_GR.

KEGG

ecj:JW2857.
eco:b2889.

Organism-specific databases

EchoBASE

EB2883.

EcoGene

EG13072. idi.

CMR

Search...

Phylogenomic databases

HOGENOM

Q46822.

OMA

Q46822. GKYHTPG.

Enzyme and pathway databases

BioCyc

EcoCyc:IPPISOM-MON.
MetaCyc:IPPISOM-MON.

Family and domain databases

HAMAP

MF_00202.
[Tree]

InterPro

IPR011876. IsopentenylPP_isomerase_typ1.
IPR000086. NUDIX_hydrolase_core.
[Graphical view]

Gene3D

G3DSA:3.90.79.10. NUDIX_hydrolase. 1 hit.

PANTHER

PTHR10885. IPP_isom_1. 1 hit.

Pfam

PF00293. NUDIX. 1 hit.
[Graphical view]

PIRSF

PIRSF018427. Isopntndiph_ism. 1 hit.

ProDom

PD004109. IPP_isomerase. 1 hit.
[Graphical view] [Entries sharing at least one domain]

TIGRFAMs

TIGR02150. IPP_isom_1. 1 hit.

ProtoNet

Search...

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:	June 16, 2009
This is version 83 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)