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Expression|

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Standard Name	nagC
Gene Synonym(s)	ECK0664, b0676, JW0662, nagR^[1], nagR
Product Desc.	NagC transcriptional dual regulator^[2]^[3] Transcriptional regulator of nag operon^[4]
Product Synonyms(s)	DNA-binding transcriptional dual regulator, repressor of N-acetylglucosamine^[1], B0676^[2]^[1], NagR^[2]^[1], NagC^[2]^[1], transcriptional repressor of nag (N-acetylglucosamine) operon^[2]^[1] , ECK0664, JW0662, nagR, b0676
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): nagBACD^[2], OP00058, nagB
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	nagC
Mnemonic	N-Acetylglucosamine
Synonyms	ECK0664, b0676, JW0662, nagR^[1], nagR
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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	15.08 minutes	MG1655: 700817..699597 <gbrowseImage> name=NC_000913:699597..700817 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 683689..682469 <gbrowseImage> name=NC_012967:682469..683689 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 602357..603577 <gbrowseImage> name=NC_012759:602357..603577 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 702016..700796 <gbrowseImage> name=NC_007779:700796..702016 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 753409..752189 <gbrowseImage> name=NC_010473:752189..753409 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
nagC(del) (Keio:JW0662)	deletion	deletion			PMID:16738554	Shigen CGSC8753^[5]
nagC(del)::kan	deletion		Biolog:respiration	unable to respire a-Ketoglutarate	PMID:16095938
nagC(del)::kan	deletion		Biolog:respiration	unable to respire Succinate	PMID:16095938
nagC(del)::kan	deletion		Biolog:respiration	unable to respire Bromosuccinate	PMID:16095938
nagC(del)::kan	deletion		Biolog:respiration	unable to respire L-Asparagine	PMID:16095938
nagC(del)::kan	deletion		Biolog:respiration	unable to respire L-Aspartate	PMID:16095938
nagC725(del)::kan					PMID:16738554	CGSC:101992
nagC725(del)::FRTKanFRT	deletion		Mutagenesis Rate	Decrease in stress induced mutagenesis (SIM).	PMID:23224554	Parent Strain: SMR4562 Experimental Strain: SMR4562	The mutation caused a significant decrease in SIM with a reduction of mutant frequency over 90 %. See table S3 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
JW0662	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCACACCAGGCGGACAAGCTCA Primer 2:CCATTTTCCAGCAAATGCTGGAG
16A8	Kohara Phage	Genobase	PMID:3038334
3A6	Kohara Phage	Genobase	PMID:3038334
crcA280::Tn10	Linked marker	CAG12077 = CGSC7347^[5]	est. P1 cotransduction: 13% ^[6] Synonyms:zbe-280::Tn10
asnB3057::Tn10	Linked marker	CAG18433 = CGSC7349^[5]	est. P1 cotransduction: 97% ^[6] Synonyms:zbf-3057::Tn10 nnnThe Tn10 in CAG18433 is inserted in the asnB regulatory region, 4 bp before the start of the asnB ORF.
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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:EG10636	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10636	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000629	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945285	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0630	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0002299	Escherichia coli str. K-12 substr. MG1655
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Notes

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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	NagC
Synonyms	DNA-binding transcriptional dual regulator, repressor of N-acetylglucosamine^[1], B0676^[2]^[1], NagR^[2]^[1], NagC^[2]^[1], transcriptional repressor of nag (N-acetylglucosamine) operon^[2]^[1] , ECK0664, JW0662, nagR, b0676
Product description	NagC transcriptional dual regulator^[2]^[3] Transcriptional regulator of nag 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: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:IPR000835	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005622	intracellular	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000835	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005975	carbohydrate metabolic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0119	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:IPR000835	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	rpmB	PMID:16606699	Experiment(s):EBI-1137661
Protein	groL	PMID:16606699	Experiment(s):EBI-1137661
Protein	nagB	PMID:16606699	Experiment(s):EBI-1137661
Protein	tatE	PMID:16606699	Experiment(s):EBI-1137661
Protein	rsuA	PMID:16606699	Experiment(s):EBI-1137661
Protein	gpmA	PMID:19402753	LCMS(ID Probability):99.6
Protein	minD	PMID:19402753	MALDI(Z-score):32.026756
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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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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 MTPGGQAQIG NVDLVKQLNS AAVYRLIDQY GPISRIQIAE QSQLAPASVT KITRQLIERG LIKEVDQQAS TGGRRAISIV TETRNFHAIG VRLGRHDATI TLFDLSSKVL AEEHYPLPER TQQTLEHALL NAIAQFIDSY QRKLRELIAI SVILPGLVDP DSGKIHYMPH IQVENWGLVE ALEERFKVTC FVGHDIRSLA LAEHYFGASQ DCEDSILVRV HRGTGAGIIS NGRIFIGRNG NVGEIGHIQV EPLGERCHCG NFGCLETIAA NAAIEQRVLN LLKQGYQSRV PLDDCTIKTI CKAANKGDSL ASEVIEYVGR HLGKTIAIAI NLFNPQKIVI AGEITEADKV LLPAIESCIN TQALKAFRTN LPVVRSELDH RSAIGAFALV KRAMLNGILL QHLLEN
Length	406
Mol. Wt	44.541 kDa
pI	7.4 (calculated)
Extinction coefficient	17,420 - 18,420 (calc based on 8 Y, 1 W, and 8 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	18..67	PF01047 MarR family	PMID:19920124
Domain	90..274	PF00480 ROK 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=nagC 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:16128652	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945285	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0002299	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0AF20	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10636	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10636	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945285	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000629	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0630	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	37.702+/-0.253	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.049180328	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	505	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	224	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	379	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)
nagBACD
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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_000913:700797..700837 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:b0676 (EcoliWiki Page)	NCBI GEO profiles for nagC
microarray	GenExpDB:b0676 (EcoliWiki Page)	Summary of data for nagC 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 nagC Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10636	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0630	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0676
EcoGene	EcoGene:EG10636	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000629	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0002299	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	ENSANGP00000028845 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Bos taurus	ENSBTAP00000001520 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000003351 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Danio rerio	ZDB-GENE-040426-1848 (score: 1.000; bootstrap: 100%) ZDB-CDNA-040425-2788 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000024699 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Homo sapiens	ENSP00000340770 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000008062 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000003196 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Mus musculus	MGI:1354951 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000035798 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000019532 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000157294 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00033530001 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000015559 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	NAGC	From SHIGELLACYC
E. coli O157	NAGC	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)	PF01047 MarR family
Pfam (EcoliWiki Page)	PF00480 ROK 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.

↑ ^1.00 ^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 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 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).

nagC:On One Page

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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 nagC Expression

Notes

Links

Evolution

Homologs in Other Organisms

Notes

Families

Notes

Links

References

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