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On One Page

Quickview |

Gene |

Product(s) |

Expression|

Evolution |

References |

Quickview

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Standard Name	idi
Gene Synonym(s)	ECK2884, b2889, JW2857, ygfV^[1], ygfV
Product Desc.	Isopentenyl diphosphate isomerase, isoprenoid biosynthesis; interconverts isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP)^[2]
Product Synonyms(s)	isopentenyl diphosphate isomerase^[1], B2889^[3]^[1], YgfV^[3]^[1], Idi^[3]^[1] , ECK2884, JW2857, ygfV, b2889
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): idi^[3]
Regulation/Activity
Quick Links
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Notes

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The idi gene is nonessential.^[2]

Gene

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Nomenclature

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name	idi
Mnemonic	Isopentenyl diphosphate isomerase
Synonyms	ECK2884, b2889, JW2857, ygfV^[1], ygfV
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Notes

Location(s) and DNA Sequence

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<protect> See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

Strain	Map location	Genome coordinates	Genome browsers	Sequence links
MG1655	65.33 minutes	MG1655: 3031087..3031635 <gbrowseImage> name=NC_000913:3031087..3031635 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2918819..2919367 <gbrowseImage> name=NC_012967:2918819..2919367 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 2918235..2918783 <gbrowseImage> name=NC_012759:2918235..2918783 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3031721..3032269 <gbrowseImage> name=NC_007779:3031721..3032269 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3124957..3125505 <gbrowseImage> name=NC_010473:3124957..3125505 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
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Notes

Sequence Features

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See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type	Strain	Genomic Location	Evidence	Reference	Notes
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Notes

Alleles and Phenotypes

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See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Allele	Nt change(s)	AA change(s)	Phenotype: Description	Reference	Availability	Comments
Δidi (Keio:JW2857)	deletion	deletion		PMID:16738554	Shigen CGSC10215^[4]
idiY104A		Y104A	Reduces activity by 99%			seeded from UniProt:Q46822
idiY104F		Y104F	Reduces activity by 97%			seeded from UniProt:Q46822
Δidi-740::kan				PMID:16738554	CGSC:101526
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Notes

Genetic Interactions

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Interactor	Interaction	Allele	Score(s)	Reference(s)	Accessions	Notes
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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource	Resource Type	Source	Notes/Reference
JW2857	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCCAAACGGAACACGTCATTTT Primer 2:CCTTTAAGCTGGGTAAATGCAGA
5B4	Kohara Phage	Genobase	PMID:3038334
22H4	Kohara Phage	Genobase	PMID:3038334
recD1901::Tn10	Linked marker	CAG12135 = CGSC7429^[4]	est. P1 cotransduction: % ^[5]
speA210::Tn10	Linked marker	CAG12168 = CGSC7431^[4]	est. P1 cotransduction: 7% ^[5] Synonyms:zgd-210::Tn10, zgf-210::Tn10
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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
EcoCyc	EcoCyc:G7508	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13072	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004070	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:949020	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2883	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009484	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Product(s)

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Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name	Idi
Synonyms	isopentenyl diphosphate isomerase^[1], B2889^[3]^[1], YgfV^[3]^[1], Idi^[3]^[1] , ECK2884, JW2857, ygfV, b2889
Product description	Isopentenyl diphosphate isomerase, isoprenoid biosynthesis; interconverts isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP)^[2]
EC number (for enzymes)	5.3.3.2^[1]
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Notes

Function

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<protect> Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Qualifier	GO ID	GO term name	Reference	Evidence Code	with/from	Aspect	Notes	Status
	GO:0000287	magnesium ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0460	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004452	isopentenyl-diphosphate delta-isomerase activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00202	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004452	isopentenyl-diphosphate delta-isomerase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011876	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004452	isopentenyl-diphosphate delta-isomerase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:5.3.3.2	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00202	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0963	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-0086	C	Seeded from EcoCyc (v14.0)	complete
	GO:0008299	isoprenoid biosynthetic process	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00202	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008299	isoprenoid biosynthetic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011876	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008299	isoprenoid biosynthetic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0414	P	Seeded from EcoCyc (v14.0)	complete
	GO:0016787	hydrolase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000086	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016787	hydrolase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR015797	F	Seeded from EcoCyc (v14.0)	complete
	GO:0030145	manganese ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0464	F	Seeded from EcoCyc (v14.0)	complete
	GO:0046872	metal ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0479	F	Seeded from EcoCyc (v14.0)	complete
	GO:0006974	response to DNA damage stimulus	PMID:11967071	IEP: Inferred from Expression Pattern		P		complete
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Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type	Partner	References	Evidence
Protein	yhiL	PMID:16606699	Experiment(s):EBI-1144191
Protein	lacZ	PMID:16606699	Experiment(s):EBI-1144191
Protein	pepD	PMID:16606699	Experiment(s):EBI-1144191
Protein	ydbH	PMID:16606699	Experiment(s):EBI-1144191
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Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment	Description	Evidence	Reference/Source	Notes
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Notes

Structure and Physical Properties

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<protect> Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Name
Sequence	at EcoCyc MQTEHVILLN AQGVPTGTLE KYAAHTADTR LHLAFSSWLF NAKGQLLVTR RALSKKAWPG VWTNSVCGHP QLGESNEDAV IRRCRYELGV EITPPESIYP DFRYRATDPS GIVENEVCPV FAARTTSALQ INDDEVMDYQ WCDLADVLHG IDATPWAFSP WMVMQATNRE ARKRLSAFTQ LK
Length	182
Mol. Wt	20.507 kDa
pI	6.5 (calculated)
Extinction coefficient	40,450 - 40,950 (calc based on 5 Y, 6 W, and 4 C residues)
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Domains/Motifs/Modification Sites

See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

Type	Residues	Description	Notes	References
Domain	31..165	PF00293 NUDIX domain		PMID:19920124
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<motif_map/>

Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=idi taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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Notes

Gene Product Resources

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See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type	Source	Notes/Reference
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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
NCBI (Protein) (EcoliWiki Page)	GI:16130791	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:949020	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009484	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:Q46822	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G7508	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13072	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:949020	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004070	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2883	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Expression

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Overview

This is a placeholder for a summary statement on how expression of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Cellular Levels

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See Help:Cellular levels

Molecule	Organism or Strain	Value	Units	Experimental Conditions	Assay used	Notes	Reference(s)
Protein	E. coli K-12 MG1655	110	molecules/cell/generation	Medium: MOPS Complete Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling		PMID: 24766808
Protein	E. coli K-12 MG1655	96	molecules/cell/generation	Medium: MOPS Minimal Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling		PMID: 24766808
Protein	E. coli K-12 MG1655	57^a	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	PMID: 24766808
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Notes

Transcription and Transcriptional Regulation

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See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)
idi
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Figure courtesy of RegulonDB

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Notes

This is a placeholder for a summary statement about how transcription of this gene is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Translation and Regulation of Translation

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<protect><gbrowseImage> name=NC_000913:3031067..3031107 source=MG1655 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

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Notes

This is a placeholder for a summary statement about how translation of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Turnover and Regulation of Turnover

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Notes

This is a placeholder for a summary statement about turnover of this gene product. You can help EcoliWiki by becoming a user and writing/editing this statement.

Experimental

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<protect> Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name	Mutation	Phenotype	Reference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type	Reference	Notes
microarray	GEO Profiles:b2889 (EcoliWiki Page)	NCBI GEO profiles for idi
microarray	GenExpDB:b2889 (EcoliWiki Page)	Summary of data for idi from multiple microarray studies
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Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource Name	Resource Type	Description	Source	Notes
	GFP Fusion	Intergenic region (3030735..3031113) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ11; Well:B2^[6]
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Notes

Accessions Related to idi Expression

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
EcoCyc	EcoCyc:G7508	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2883	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2889
EcoGene	EcoGene:EG13072	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004070	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009484	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Evolution

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Homologs in Other Organisms

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See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism	Homologs (Statistics)	Comments
Anopheles gambiae	ENSANGP00000011643 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Arabidopsis thaliana	AT5G16440 (score: 1.000; bootstrap: 68%) AT3G02780 (score: 0.795)	From Inparanoid:20070104
Bos taurus	ENSBTAP00000005323 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Caenorhabditis briggsae	WBGene00041409 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Caenorhabditis elegans	WBGene00019460 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Ciona intestinalis	ENSCINP00000004427 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Danio rerio	ZDB-GENE-050913-44 (score: 1.000; bootstrap: 100%) ZDB-CDNA-050612-98 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Dictyostelium discoideum	DDB0191342 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Drosophila melanogaster	FBgn0038876 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Drosophila pseudoobscura	GA19228-PA (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000010861 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Homo sapiens	ENSP00000263151 (score: 1.000; bootstrap: 100%) ENSP00000277517 (score: 0.485)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000022523 (score: 1.000; bootstrap: 100%) ENSMMUP00000014177 (score: 0.250)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000007423 (score: 1.000; bootstrap: 100%) ENSMODP00000011416 (score: 0.867) ENSMODP00000007397 (score: 0.607) ENSMODP00000007408 (score: 0.581)	From Inparanoid:20070104
Mus musculus	MGI:2442264 (score: 1.000; bootstrap: 100%) MGI:2444315 (score: 0.537)	From Inparanoid:20070104
Oryza gramene	Q71RX2 (score: 1.000; bootstrap: 100%) Q9M6K4 (score: 0.939) Q8GVZ0 (score: 0.939) Q6AUB0 (score: 0.839)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000003784 (score: 1.000; bootstrap: 100%) ENSPTRP00000003781 (score: 0.485)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000022389 (score: 1.000; bootstrap: 100%) ENSRNOP00000033936 (score: 0.548) ENSRNOP00000047707 (score: 0.545) ENSRNOP00000048056 (score: 0.543) ENSRNOP00000047209 (score: 0.541) ENSRNOP00000049372 (score: 0.531) ENSRNOP00000045142 (score: 0.474) ENSRNOP00000036656 (score: 0.411)	From Inparanoid:20070104
Saccharomyces cerevisiae	YPL117C (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPBC1065 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000143706 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00016624001 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000039244 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	S3074	From SHIGELLACYC
E. coli O157	Z4227	From ECOO157CYC
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Do-It-Yourself Web Tools

Notes

Families

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
Pfam (EcoliWiki Page)	PF00293 NUDIX domain
Panther (EcoliWiki Page)	PTHR10885:SF0
Superfamily (EcoliWiki Page)	SUPERFAMILY:55811
EcoCyc	EcoCyc:G7508	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13072	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004070	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2883	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009484	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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References

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See Help:References for how to manage references in EcoliWiki.

↑ ^1.00 ^1.01 ^1.02 ^1.03 ^1.04 ^1.05 ^1.06 ^1.07 ^1.08 ^1.09 ^1.10 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.0 ^2.1 ^2.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^3.0 ^3.1 ^3.2 ^3.3 ^3.4 ^3.5 ^3.6 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 ^4.2 CGSC: The Coli Genetics Stock Center
↑ ^5.0 ^5.1 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

idi:On One Page

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Notes

Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

Notes

Alleles and Phenotypes

Notes

Genetic Interactions

Notes

Genetic Resources

Notes

Accessions in Other Databases

Notes

Links

Product(s)

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

Expression

Overview

Cellular Levels

Notes

Transcription and Transcriptional Regulation

Notes

Translation and Regulation of Translation

Notes

Turnover and Regulation of Turnover

Notes

Experimental

Notes

Accessions Related to idi Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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