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Expression|

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Standard Name	nrdR
Gene Synonym(s)	ybaD, ECK0407, b0413, JW0403^[1]^[2], JW0403, ribX
Product Desc.	conserved protein^[3]^[2] Nrd regulon repressor^[4]
Product Synonyms(s)	conserved protein^[1], B0413^[3]^[1], YbaD^[3]^[1], NrdR^[2]^[1] , ECK0407, JW0403, ribX, ybaD, b0413
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): ybaD^[3]
Regulation/Activity
Quick Links
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Notes

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NrdR has been shown to regulate all three Nrd systems and to bind to the predicted NrdR binding sites (Torrents, 2007). Homologous to S. coelicolor NrdR (Borovok, 2004). Predicted binding sites has been reported for the nrdAB, nrdDG, and nrdHIEF operons (Rodionova, 2005). This corresponds to putative TF Binding SIte Cluster E581 for nrdD and nrdA (Qin, 2003). Binds TrxA (Kumar, 2004). First gene in putative nrdR-ribDE-nusB operon. Also refered to as nrdR in an unpublished comparative analysis (Borovok, 2005, in GenBank AM076828).^[4]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	nrdR
Mnemonic	Nucleotide reductase
Synonyms	ybaD, ECK0407, b0413, JW0403^[1]^[2], JW0403, ribX
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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	9.32 minutes	MG1655: 432226..432675 <gbrowseImage> name=NC_000913:432226..432675 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
BW2952		NC_012759: 334985..335434 <gbrowseImage> name=NC_012759:334985..335434 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 432226..432675 <gbrowseImage> name=NC_007779:432226..432675 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 371557..372006 <gbrowseImage> name=NC_010473:371557..372006 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: Type	Phenotype: Description	Reference	Availability	Comments
ΔnrdR775::kan					PMID:16738554	CGSC:106262
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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
	Plasmid clone	Shigen	PMID:16769691 Status: Primer 1: Primer 2:
4F3	Kohara Phage	Genobase	PMID:3038334
19F6	Kohara Phage	Genobase	PMID:3038334
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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:EG11320	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11320	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001291	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947437	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1296	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001437	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	YbaD
Synonyms	conserved protein^[1], B0413^[3]^[1], YbaD^[3]^[1], NrdR^[2]^[1] , ECK0407, JW0403, ribX, ybaD, b0413
Product description	conserved protein^[3]^[2] Nrd regulon repressor^[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:0000166	nucleotide binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0547	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005524	ATP binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0067	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008270	zinc ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0862	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016564	transcription repressor activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00440	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
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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	yfhM	PMID:15690043	Experiment(s):EBI-892247
Protein	glyS	PMID:15690043	Experiment(s):EBI-892247
Protein	rplL	PMID:15690043	Experiment(s):EBI-892247
Protein	rplU	PMID:15690043	Experiment(s):EBI-892247
Protein	rpsJ	PMID:15690043	Experiment(s):EBI-892247
Protein	ydbK	PMID:15690043	Experiment(s):EBI-892247
Protein	ydcS	PMID:16606699	Experiment(s):EBI-1136500
Protein	ribD	PMID:16606699	Experiment(s):EBI-1136500
Protein	nadE	PMID:16606699	Experiment(s):EBI-1136500
Protein	recF	PMID:16606699	Experiment(s):EBI-1136500
Protein	rplU	PMID:19402753	LCMS(ID Probability):99.6
Protein	glyS	PMID:19402753	LCMS(ID Probability):99.6
Protein	rpsJ	PMID:19402753	LCMS(ID Probability):99.6
Protein	yfhM	PMID:19402753	LCMS(ID Probability):99.6
Protein	rplL	PMID:19402753	LCMS(ID Probability):99.6
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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 MHCPFCFAVD TKVIDSRLVG EGSSVRRRRQ CLVCNERFTT FEVAELVMPR VVKSNDVREP FNEEKLRSGM LRALEKRPVS SDDVEMAINH IKSQLRATGE REVPSKMIGN LVMEQLKKLD KVAYIRFASV YRSFEDIKEF GEEIARLED
Length	149
Mol. Wt	17.228 kDa
pI	7.4 (calculated)
Extinction coefficient	2,980 - 3,480 (calc based on 2 Y, 0 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	49..137	PF03477 ATP cone 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=nrdR taxon=562,83333 </beststructure>

Models

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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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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:16128398	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947437	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001437	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0A8D0	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11320	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11320	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947437	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001291	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1296	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	802	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	354	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	429	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)
ybaD
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File:.jpg

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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_000913:432206..432246 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:b0413 (EcoliWiki Page)	NCBI GEO profiles for nrdR
microarray	GenExpDB:b0413 (EcoliWiki Page)	Summary of data for nrdR 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 (432039..432285) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ13; Well:D6^[5]
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Notes

Accessions Related to nrdR Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11320	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1296	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0413
EcoGene	EcoGene:EG11320	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001291	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001437	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	YBAD	From SHIGELLACYC
E. coli O157	YBAD	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)	PF03477 ATP cone domain
EcoCyc	EcoCyc:EG11320	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11320	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001291	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1296	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001437	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.

↑ ^1.0 ^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 EcoCyc (release 11.1; 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 ^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 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

nrdR: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 nrdR Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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