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Standard Name	trpR
Gene Synonym(s)	ECK4385, b4393, JW4356, rtrY^[1]
Product Desc.	TrpR^[2]^[3]; Component of TrpR transcriptional repressor^[2]^[3]; TrpR-Tryptophan transcriptional repressor^[2]^[3] Autogenously regulated tryptophan repressor protein; regulator of trp operon, aroH, and other members of the TrpR regulon; 5-Methyltryptophan resistance^[4]
Product Synonyms(s)	DNA-binding transcriptional repressor, tryptophan-binding ^[1], B4393 ^[2]^[1], RtrY ^[2]^[1], TrpR ^[2]^[1], regulator for trp operon and aroH; trp aporepressor ^[2]^[1] , ECK4385, JW4356, b4393
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): trpR^[2], OP00310
Regulation/Activity
Quick Links
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Notes

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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	trpR
Mnemonic	Tryptophan
Synonyms	ECK4385, b4393, JW4356, rtrY^[1]
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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	99.81 minutes	MG1655: 4630783..4631109 <gbrowseImage> name=NC_000913:4630783..4631109 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 4620973..4621299 <gbrowseImage> name=NC_012967:4620973..4621299 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 4569267..4569593 <gbrowseImage> name=NC_012759:4569267..4569593 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 4637440..4637766 <gbrowseImage> name=NC_007779:4637440..4637766 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 4677245..4677571 <gbrowseImage> name=NC_010473:4677245..4677571 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	4630786	Edman degradation	PMID:2415531 PMID:6338493 PMID:7012834
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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: Type	Phenotype: Description	Reference	Availability	Comments
trpR(del) (Keio:JW4356)	deletion	deletion			PMID:16738554	Shigen CGSC11110^[5]
trpR55					PMID:6233264	CGSC:4525
trpR72(Am)						CGSC:5054	amber (UAG) mutation
trpR80						CGSC:7370
trpR47						CGSC:11093
trpR789(del)::kan					PMID:16738554	CGSC:103234
SP361(lamGB2)(ptrpS13)	Deletion of trpR and insertion of extra trpS gene.		Resistant to	Increase resistance toward Indolmycin.	PMID:6337120		See figure 2 for experimental results.
SP361(lamGB2)	Deletion of trpR gene.		Resistant to	Increase resistance toward Indolmycin	PMID:6337120		See figure 2 for full experimental results.
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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
JW4356	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCGCCCAACAATCACCCTATTC Primer 2:CCATCGCTTTTCAGCAACACCTC
12A4	Kohara Phage	Genobase	PMID:3038334
15A5	Kohara Phage	Genobase	PMID:3038334
mdoB202::Tn10	Linked marker	CAG18430 = CGSC7488^[5]	est. P1 cotransduction: 21% ^[6] Synonyms:zjj-202::Tn10, zji-202::Tn10
thrA34::Tn10	Linked marker	CAG18442 = CGSC7320^[5]	est. P1 cotransduction: 74% ^[6] Synonyms:thr-34::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:EG11029	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11029	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001018	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948917	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1022	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0014408	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	TrpR
Synonyms	DNA-binding transcriptional repressor, tryptophan-binding ^[1], B4393 ^[2]^[1], RtrY ^[2]^[1], TrpR ^[2]^[1], regulator for trp operon and aroH; trp aporepressor ^[2]^[1] , ECK4385, JW4356, b4393
Product description	TrpR^[2]^[3]; Component of TrpR transcriptional repressor^[2]^[3]; TrpR-Tryptophan transcriptional repressor^[2]^[3] Autogenously regulated tryptophan repressor protein; regulator of trp operon, aroH, and other members of the TrpR regulon; 5-Methyltryptophan resistance^[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:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00475	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:0003700	transcription factor activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000831	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003700	transcription factor activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR013318	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005622	intracellular	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR013318	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00475	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: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:IPR000831	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:IPR013318	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:IPR013335	P	Seeded from EcoCyc (v14.0)	complete
	GO:0016564	transcription repressor activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00475	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016564	transcription repressor activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR013335	F	Seeded from EcoCyc (v14.0)	complete
	GO:0043565	sequence-specific DNA binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR010921	F	Seeded from EcoCyc (v14.0)	complete
	GO:0045892	negative regulation of transcription, DNA-dependent	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00475	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	Subunits of TrpR transcriptional repressor	could be indirect
Protein	rpsC		PMID:16606699	Experiment(s):EBI-1147985
Protein	rnc		PMID:16606699	Experiment(s):EBI-1147985
Protein	Subunits of TrpR-Tryptophan transcriptional repressor	could be indirect
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Notes

trpR55 is synonymous with trpR2, as studied by Yanofsky, et al, in 1984. ^[7]

trpR2 acts as a frameshift mutation within the trp repressor. As a result, the repressor remains inactive and is unable to bind to the operator of the trp operon, allowing transcription on the trp operon to proceed with tryptophan synthesis, instead of inhibiting production as it normally would in high levels of tryptophan.

trpR2 does not target a specific functional repressor, since levels of trp enzymes in strains with trpR2 mutations do not differ from levels found within strains undergoing trpR amber and trpR deletion mutations. ^[8]

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 MAQQSPYSAA MAEQRHQEWL RFVDLLKNAY QNDLHLPLLN LMLTPDEREA LGTRVRIVEE LLRGEMSQRE LKNELGAGIA TITRGSNSLK AAPVELRQWL EEVLLKSD
Length	108
Mol. Wt	12.355 kDa
pI	5.3 (calculated)
Extinction coefficient	13,980 (calc based on 2 Y, 2 W, and 0 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
Initiator Methionine	1	Removed	UniProt:P0A881
Domain	17..104	PF01371 Trp repressor protein		PMID:19920124
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<motif_map/>

Structure
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Structures

<beststructure> gene=trpR 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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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:16132210	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948917	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0014408	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0A881	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11029	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11029	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948917	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001018	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1022	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 MG1655	924	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	549	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	513	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)
trpR
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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_000913:4630763..4630803 source=MG1655 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

</protect>

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:b4393 (EcoliWiki Page)	NCBI GEO profiles for trpR
microarray	GenExpDB:b4393 (EcoliWiki Page)	Summary of data for trpR 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 (4630143..4630347) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ01; Well:C9^[9]
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Notes

Accessions Related to trpR Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11029	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1022	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b4393
EcoGene	EcoGene:EG11029	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001018	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0014408	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
Shigella flexneri	TRPR	From SHIGELLACYC
E. coli O157	TRPR	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
Superfamily (EcoliWiki Page)	SUPERFAMILY:48295
Pfam (EcoliWiki Page)	PF01371 Trp repressor protein
EcoCyc	EcoCyc:EG11029	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11029	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001018	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1022	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0014408	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 ^1.11 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.00 ^2.01 ^2.02 ^2.03 ^2.04 ^2.05 ^2.06 ^2.07 ^2.08 ^2.09 ^2.10 ^2.11 ^2.12 ^2.13 ^2.14 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 ^3.2 ^3.3 ^3.4 ^3.5 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 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).
↑ http://cgsc2.biology.yale.edu/Mutation.php?ID=4525
↑ Yanofsky, C et al. (1984) Repression is relieved before attenuation in the trp operon of Escherichia coli as tryptophan starvation becomes increasingly severe. J. Bacteriol. 158 1018-24 PubMed
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

trpR:On One Page

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Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

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Genetic Interactions

Notes

Genetic Resources

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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 trpR Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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