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Product(s) |

Expression|

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Standard Name	iclR
Gene Synonym(s)	ECK4010, b4018, JW3978^[1], JW3978
Product Desc.	IclR transcriptional repressor^[2]^[3] Repressor of aceBA operon^[4]
Product Synonyms(s)	DNA-binding transcriptional repressor^[1], B4018^[2]^[1], IclR^[2]^[1], acetate operon repressor^[2]^[1] , ECK4010, JW3978, b4018
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): iclR^[2]
Regulation/Activity
Quick Links
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Notes

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Tetrameric IclR binds to the aceBA operator and dimeric IclR is inactive. Glyoxylate dissociates IclR and favors dimers; pyruvate promotes binding and favors tetramers (Lorca, 2007).^[4]

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	iclR
Mnemonic	Isocitrate lyase
Synonyms	ECK4010, b4018, JW3978^[1], JW3978
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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	90.97 minutes	MG1655: 4221651..4220827 <gbrowseImage> name=NC_000913:4220827..4221651 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 4202559..4201735 <gbrowseImage> name=NC_012967:4201735..4202559 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 4110507..4111331 <gbrowseImage> name=NC_012759:4110507..4111331 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 4227218..4226394 <gbrowseImage> name=NC_007779:4226394..4227218 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 4321347..4320523 <gbrowseImage> name=NC_010473:4320523..4321347 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
Coding Start (SO:0000323)	MG1655	4220830	Edman degradation	PMID:8844850
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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
ΔiclR (Keio:JW3978)	deletion	deletion		PMID:16738554	Shigen CGSC10861^[5]
iclRM146D		M146D	Strongly reduced promoter binding and tetramerization			seeded from UniProt:P16528
iclRL143D		L143D	Strongly reduced promoter binding and tetramerization			seeded from UniProt:P16528
iclRL220D		L220D	Loss of promoter binding and tetramerization			seeded from UniProt:P16528
iclRL154D		L154D	Strongly reduced promoter binding and tetramerization			seeded from UniProt:P16528
iclR7(Const)			constitutive		CGSC:5053
iclR17(Const)			constitutive		CGSC:7371
iclR13					CGSC:9104
iclR15(Const)			constitutive		CGSC:14484
ΔiclR785::kan				PMID:16738554	CGSC:101524
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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
JW3978	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCGTCGCACCCATTCCCGCGAA Primer 2:CCGCGCATTCCACCGTACGCCAG
6G10	Kohara Phage	Genobase	PMID:3038334
4E5	Kohara Phage	Genobase	PMID:3038334
thiC39::Tn10	Linked marker	CAG18500 = CGSC7472^[5]	est. P1 cotransduction: 36% ^[6] Synonyms:thi-39::Tn10
malF3089::Tn10	Linked marker	CAG12164 = CGSC7476^[5]	est. P1 cotransduction: 49% ^[6]
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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:EG10491	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10491	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000484	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948524	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0486	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013136	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	IclR
Synonyms	DNA-binding transcriptional repressor^[1], B4018^[2]^[1], IclR^[2]^[1], acetate operon repressor^[2]^[1] , ECK4010, JW3978, b4018
Product description	IclR transcriptional repressor^[2]^[3] Repressor of aceBA operon^[4]
EC number (for enzymes)
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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:0003677	DNA binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005471	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003677	DNA binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0238	F	Seeded from EcoCyc (v14.0)	complete
	GO:0006097	glyoxylate cycle	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0329	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006350	transcription	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0804	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006355	regulation of transcription, DNA-dependent	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005471	P	Seeded from EcoCyc (v14.0)	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	Notes	References	Evidence
Protein	hldD		PMID:15690043	Experiment(s):EBI-885803
Protein	rpsC		PMID:16606699	Experiment(s):EBI-1147301
Protein	aceF		PMID:15690043	Experiment(s):EBI-892341
Protein	rplA		PMID:15690043	Experiment(s):EBI-892341
Protein	rplD		PMID:15690043	Experiment(s):EBI-892341
Protein	rplM		PMID:15690043	Experiment(s):EBI-892341
Protein	rplT		PMID:15690043	Experiment(s):EBI-892341
Protein	rplU		PMID:15690043	Experiment(s):EBI-892341
Protein	rplV		PMID:15690043	Experiment(s):EBI-892341
Protein	rplX		PMID:15690043	Experiment(s):EBI-892341
Protein	rpsB		PMID:15690043	Experiment(s):EBI-892341
Protein	rpsE		PMID:15690043	Experiment(s):EBI-892341
Protein	rpsF		PMID:15690043	Experiment(s):EBI-892341
Protein	rpsG		PMID:15690043	Experiment(s):EBI-892341
Protein	rpsH		PMID:15690043	Experiment(s):EBI-892341
Protein	rpsM		PMID:15690043	Experiment(s):EBI-892341
Protein	rpsN		PMID:15690043	Experiment(s):EBI-892341
Protein	rpsF		PMID:19402753	LCMS(ID Probability):99.6
Protein	rplT		PMID:19402753	LCMS(ID Probability):99.6
Protein	rpsH		PMID:19402753	LCMS(ID Probability):99.6
Protein	rplX		PMID:19402753	LCMS(ID Probability):99.6
Protein	rplM		PMID:19402753	LCMS(ID Probability):99.6
Protein	rplA		PMID:19402753	LCMS(ID Probability):99.6
Protein	rpsM		PMID:19402753	LCMS(ID Probability):99.6
Protein	rfaD		PMID:19402753	MALDI(Z-score):21.217150
Protein	fadR	when fadR and iclR are acting together, they cause full repression of the ace operon	PMID:7033207
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Notes

Localization

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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 MKMISTIQKK ETVMVAPIPA KRGRKPAVAT APATGQVQSL TRGLKLLEWI AESNGSVALT ELAQQAGLPN STTHRLLTTM QQQGFVRQVG ELGHWAIGAH AFMVGSSFLQ SRNLLAIVHP ILRNLMEESG ETVNMAVLDQ SDHEAIIIDQ VQCTHLMRMS APIGGKLPMH ASGAGKAFLA QLSEEQVTKL LHRKGLHAYT HATLVSPVHL KEDLAQTRKR GYSFDDEEHA LGLRCLAACI FDEHREPFAA ISISGPISRI TDDRVTEFGA MVIKAAKEVT LAYGGMR
Length	287
Mol. Wt	31.257 kDa
pI	8.8 (calculated)
Extinction coefficient	15,470 - 15,845 (calc based on 3 Y, 2 W, and 3 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	References
Domain	143..269	PF01614 Bacterial transcriptional regulator	PMID:19920124
Domain	26..77	PF09339 IclR helix-turn-helix 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=iclR 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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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:90111675	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948524	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013136	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P16528	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10491	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10491	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948524	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000484	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0486	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	Reference(s)
Protein	E. coli K-12 MC4100	1.67E+02	molecules/cell	Medium: median data from rich and minimal media Temperature (°C): 37 Doubling time (min): Growth Rate(min): Growth phase: other:	emPAI	PMID:18304323
Protein	E. coli K-12 MG1655	519	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	147	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	353	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	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)
iclR
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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_000913:4221631..4221671 source=MG1655 flip=1 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:b4018 (EcoliWiki Page)	NCBI GEO profiles for iclR
microarray	GenExpDB:b4018 (EcoliWiki Page)	Summary of data for iclR 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
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Notes

Accessions Related to iclR Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10491	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0486	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b4018
EcoGene	EcoGene:EG10491	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000484	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013136	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
Xenopus tropicalis	ENSXETP00000047490 (score: 1.000; bootstrap: 84%) ENSXETP00000050568 (score: 0.064)	From Inparanoid:20070104
Shigella flexneri	ICLR	From SHIGELLACYC
E. coli O157	ICLR	From ECOO157CYC
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Notes

Families

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<protect> See Help:Evolution_families for help entering or editing information in this section of EcoliWiki.

Database	Accession	Notes
Pfam (EcoliWiki Page)	PF01614 Bacterial transcriptional regulator
Pfam (EcoliWiki Page)	PF09339 IclR helix-turn-helix domain
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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.

↑ ^1.0 ^1.1 ^1.2 ^1.3 ^1.4 ^1.5 ^1.6 ^1.7 ^1.8 ^1.9 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.0 ^2.1 ^2.2 ^2.3 ^2.4 ^2.5 ^2.6 ^2.7 ^2.8 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 ^4.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^5.0 ^5.1 ^5.2 CGSC: The Coli Genetics Stock Center
↑ ^6.0 ^6.1 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).

iclR: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 iclR Expression

Notes

Links

Evolution

Homologs in Other Organisms

Notes

Families

Notes

Links

References

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