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Expression|

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Standard Name	melR
Gene Synonym(s)	ECK4111, b4118, JW4079^[1], JW4079
Product Desc.	MelR transcriptional dual regulator^[2]^[3] Transcriptional activator for melAB, AraC family; autoregulatory repressor in absence of co-activator melibiose^[4]
Product Synonyms(s)	DNA-binding transcriptional dual regulator^[1], B4118^[2]^[1], MelR^[2]^[1], regulator of melibiose operon^[2]^[1] , ECK4111, JW4079, b4118
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): melR^[2], OP00050
Regulation/Activity
Quick Links
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Notes

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The C-terminal domain of the RNA polymerase alpha subunit is important for MelR-dependent activation of the melAB promoter. An 18 base pair MelR binding site is necessary for MelR transcription activation because it ensures correct interactions with RNA polymerase sigma subunit.^[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	melR
Mnemonic	Melibiose
Synonyms	ECK4111, b4118, JW4079^[1], JW4079
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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	93.51 minutes	MG1655: 4339651..4338743 <gbrowseImage> name=NC_000913:4338743..4339651 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 4320342..4319434 <gbrowseImage> name=NC_012967:4319434..4320342 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 4277478..4278386 <gbrowseImage> name=NC_012759:4277478..4278386 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 4346306..4345398 <gbrowseImage> name=NC_007779:4345398..4346306 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 4440013..4439105 <gbrowseImage> name=NC_010473:4439105..4440013 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
ΔmelR (Keio:JW4079)	deletion	deletion		PMID:16738554	Shigen CGSC10935^[5]
melRN222A		N222A	No effect			seeded from UniProt:P0ACH8
melRS271A		S271A	50% reduced activity			seeded from UniProt:P0ACH8
melRS272N		S272N	75% reduced activity			seeded from UniProt:P0ACH8
melRR269G		R269G	No effect			seeded from UniProt:P0ACH8
ΔmelR744::kan				PMID:16738554	CGSC:101810
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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
JW4079	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAATACAGATACGTTTATGTG Primer 2:CCGCCGGGAAACGTCTGGCGGCG
8H1	Kohara Phage	Genobase	PMID:3038334
5H2	Kohara Phage	Genobase	PMID:3038334
zje-2241::Tn10	Linked marker	CAG18427 = CGSC7481^[5]	est. P1 cotransduction: 27% ^[6]
cadB2231::Tn10	Linked marker	CAG18488 = CGSC7479^[5]	est. P1 cotransduction: 53% ^[6] Synonyms:zjd-2231::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:EG11230	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11230	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001208	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948637	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1212	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013486	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	MelR
Synonyms	DNA-binding transcriptional dual regulator^[1], B4118^[2]^[1], MelR^[2]^[1], regulator of melibiose operon^[2]^[1] , ECK4111, JW4079, b4118
Product description	MelR transcriptional dual regulator^[2]^[3] Transcriptional activator for melAB, AraC family; autoregulatory repressor in absence of co-activator melibiose^[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:IPR008917	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003677	DNA binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR012287	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:IPR000005	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003700	transcription factor activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR020449	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005622	intracellular	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000005	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005622	intracellular	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR020449	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:IPR000005	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:IPR020449	P	Seeded from EcoCyc (v14.0)	complete
	GO:0043565	sequence-specific DNA binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000005	F	Seeded from EcoCyc (v14.0)	complete
	GO:0043565	sequence-specific DNA binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR020449	F	Seeded from EcoCyc (v14.0)	complete
	GO:0045449	regulation of transcription	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR008917	P	Seeded from EcoCyc (v14.0)	complete
	GO:0045449	regulation of transcription	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR012287	P	Seeded from EcoCyc (v14.0)	complete
	GO:0045449	regulation of transcription	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0805	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	References	Evidence
Protein	groL	PMID:16606699	Experiment(s):EBI-1147482
Protein	argK	PMID:16606699	Experiment(s):EBI-1147482
Protein	rpsI	PMID:16606699	Experiment(s):EBI-1147482
Protein	ycgE	PMID:16606699	Experiment(s):EBI-1147482
Protein	rplB	PMID:16606699	Experiment(s):EBI-1147482
Protein	prs	PMID:16606699	Experiment(s):EBI-1147482
Protein	rpsC	PMID:16606699	Experiment(s):EBI-1147482
Protein	phnF	PMID:16606699	Experiment(s):EBI-1147482
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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 MNTDTFMCSS DEKQTRSPLS LYSEYQRMEI EFRAPHIMPT SHWHGQVEVN VPFDGDVEYL INNEKVNINQ GHITLFWACT PHQLTDTGTC QSMAIFNLPM HLFLSWPLDK DLINHVTHGM VIKSLATQQL SPFEVRRWQQ ELNSPNEQIR QLAIDEIGLM LKRFSLSGWE PILVNKTSRT HKNSVSRHAQ FYVSQMLGFI AENYDQALTI NDVAEHVKLN ANYAMGIFQR VMQLTMKQYI TAMRINHVRA LLSDTDKSIL DIALTAGFRS SSRFYSTFGK YVGMSPQQYR KLSQQRRQTF PG
Length	302
Mol. Wt	34.927 kDa
pI	8.4 (calculated)
Extinction coefficient	42,400 - 42,775 (calc based on 10 Y, 5 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	200..241	PF00165 Bacterial regulatory helix-turn-helix proteins, AraC family	PMID:19920124
Domain	252..291	PF00165 Bacterial regulatory helix-turn-helix proteins, AraC family	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=melR 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:16131944	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948637	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013486	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0ACH8	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11230	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11230	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948637	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001208	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1212	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	Ecoli K-12	0.672+/-0.061	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.00660793	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		by RNA_Seq	PMID:20671182
Protein	E. coli K-12 MG1655	16	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	18	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	7^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)
melR
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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_000913:4339631..4339671 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

</protect>

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:b4118 (EcoliWiki Page)	NCBI GEO profiles for melR
microarray	GenExpDB:b4118 (EcoliWiki Page)	Summary of data for melR 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 melR Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11230	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1212	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b4118
EcoGene	EcoGene:EG11230	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001208	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013486	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	MELR	From SHIGELLACYC
E. coli O157	MELR	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)	PF00165 Bacterial regulatory helix-turn-helix proteins, AraC family
Pfam (EcoliWiki Page)	PF00165 Bacterial regulatory helix-turn-helix proteins, AraC family
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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).

melR:On One Page

Quickview

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 melR Expression

Notes

Links

Evolution

Homologs in Other Organisms

Notes

Families

Notes

Links

References

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