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Gene |

Product(s) |

Expression|

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Standard Name	nrfA
Gene Synonym(s)	ECK4063, b4070, JW4031, aidC^[1]
Product Desc.	CYTOCHROMEC552^[2]^[3]; Component of nitrite reductase complex^[2]^[3] Cytochrome c nitrite reductase, cytochrome c552, periplasmic; formate-dependent; required for NO synthesis^[4]
Product Synonyms(s)	nitrite reductase, formate-dependent, cytochrome^[1], B4070^[2]^[1], NrfA^[2]^[1] , ECK4063, JW4031, b4070
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): nrfABCDEFG^[2], OP00279, nrf
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	nrfA
Mnemonic	Nitrite reductase, formate-dependent
Synonyms	ECK4063, b4070, JW4031, aidC^[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	92.37 minutes	MG1655: 4285787..4287223 <gbrowseImage> name=NC_000913:4285787..4287223 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 4266697..4268133 <gbrowseImage> name=NC_012967:4266697..4268133 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 4224633..4226069 <gbrowseImage> name=NC_012759:4224633..4226069 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 4291354..4292790 <gbrowseImage> name=NC_007779:4291354..4292790 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 4385483..4386919 <gbrowseImage> name=NC_010473:4385483..4386919 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	4285865	Edman degradation	PMID:7934939
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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
ΔnrfA (Keio:JW4031)	deletion	deletion		PMID:16738554	Shigen CGSC10899^[5]
nrfAK126H,I,L		K126H,I,L	Almost complete loss of nitrite reductase activity			seeded from UniProt:P0ABK9
ΔnrfA765::kan				PMID:16738554	CGSC:102116
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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
JW4031	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCACAAGGATAAAAATAAACGC Primer 2:CCTTGGCTTAACAGACCGTTTTT
3F12	Kohara Phage	Genobase	PMID:3038334
10G7	Kohara Phage	Genobase	PMID:3038334
malF3089::Tn10	Linked marker	CAG12164 = CGSC7476^[5]	est. P1 cotransduction: 14% ^[6]
zje-2241::Tn10	Linked marker	CAG18427 = CGSC7481^[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:EG11781	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11781	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001715	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948571	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1729	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013342	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	NrfA
Synonyms	nitrite reductase, formate-dependent, cytochrome^[1], B4070^[2]^[1], NrfA^[2]^[1] , ECK4063, JW4031, b4070
Product description	CYTOCHROMEC552^[2]^[3]; Component of nitrite reductase complex^[2]^[3] Cytochrome c nitrite reductase, cytochrome c552, periplasmic; formate-dependent; required for NO synthesis^[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:0005506	iron ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0408	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005509	calcium ion binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR017570	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005509	calcium ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0106	F	Seeded from EcoCyc (v14.0)	complete
	GO:0006807	nitrogen compound metabolic process	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01182	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006807	nitrogen compound metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003321	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006807	nitrogen compound metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR017570	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006810	transport	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0813	P	Seeded from EcoCyc (v14.0)	complete
	GO:0016491	oxidoreductase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0560	F	Seeded from EcoCyc (v14.0)	complete
	GO:0020037	heme binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR017570	F	Seeded from EcoCyc (v14.0)	complete
	GO:0022900	electron transport chain	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0249	P	Seeded from EcoCyc (v14.0)	complete
	GO:0042279	nitrite reductase (cytochrome, ammonia-forming) activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01182	F	Seeded from EcoCyc (v14.0)	complete
	GO:0042279	nitrite reductase (cytochrome, ammonia-forming) activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR017570	F	Seeded from EcoCyc (v14.0)	complete
	GO:0042279	nitrite reductase (cytochrome, ammonia-forming) activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:1.7.2.2	F	Seeded from EcoCyc (v14.0)	complete
	GO:0042597	periplasmic space	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01182	C	Seeded from EcoCyc (v14.0)	complete
	GO:0042597	periplasmic space	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR017570	C	Seeded from EcoCyc (v14.0)	complete
	GO:0042597	periplasmic space	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0574	C	Seeded from EcoCyc (v14.0)	complete
	GO:0042597	periplasmic space	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-0200	C	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
	GO:0055114	oxidation reduction	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01182	P	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003321	P	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR017570	P	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0560	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 nitrite reductase complex	could be indirect
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Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment	Evidence	Reference/Source
Periplasm	PMID:793493	EchoLocation:nrfA
periplasm		From EcoCyc^[3]
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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 MTRIKINARR IFSLLIPFFF FTSVHAEQTA APAKPVTVEA KNETFAPQHP DQYLSWKATS EQSERVDALA EDPRLVILWA GYPFSRDYNK PRGHAFAVTD VRETLRTGAP KNAEDGPLPM ACWSCKSPDV ARLIQKDGED GYFHGKWARG GPEIVNNLGC ADCHNTASPE FAKGKPELTL SRPYAARAME AIGKPFEKAG RFDQQSMVCG QCHVEYYFDG KNKAVKFPWD DGMKVENMEQ YYDKIAFSDW TNSLSKTPML KAQHPEYETW TAGIHGKNNV TCIDCHMPKV QNAEGKLYTD HKIGNPFDNF AQTCANCHTQ DKAALQKVVA ERKQSINDLK IKVEDQLVHA HFEAKAALDA GATEAEMKPI QDDIRHAQWR WDLAIASHGI HMHAPEEGLR MLGTAMDKAA DARTKLARLL ATKGITHEIQ IPDISTKEKA QQAIGLNMEQ IKAEKQDFIK TVIPQWEEQA RKNGLLSQ
Length	478
Mol. Wt	53.703 kDa
pI	7.2 (calculated)
Extinction coefficient	71,390 - 72,640 (calc based on 11 Y, 10 W, and 10 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
motif	1-26	UniProt Manual:Signal Peptides	UniProt:P0ABK9
Domain	41..474	PF02335 Cytochrome c552		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=nrfA 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:16131896	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948571	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013342	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0ABK9	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11781	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11781	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948571	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001715	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1729	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	E. coli K-12 MC4100	1.17E+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	6^a	molecules/cell/generation	Medium: MOPS Complete Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	PMID: 24766808
Protein	E. coli K-12 MG1655	4	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	0^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)
nrfABCDEFG
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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_000913:4285767..4285807 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:b4070 (EcoliWiki Page)	NCBI GEO profiles for nrfA
microarray	GenExpDB:b4070 (EcoliWiki Page)	Summary of data for nrfA 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 (4284874..4285418) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ03; Well:F12^[7]
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Notes

Accessions Related to nrfA Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11781	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1729	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b4070
EcoGene	EcoGene:EG11781	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001715	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013342	Escherichia coli str. K-12 substr. MG1655
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Notes

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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	NRFA	From SHIGELLACYC
E. coli O157	NRFA	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)	PF02335 Cytochrome c552
Superfamily (EcoliWiki Page)	SUPERFAMILY:48695
EcoCyc	EcoCyc:EG11781	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11781	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001715	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1729	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013342	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 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 ^3.2 ^3.3 ^3.4 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).
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

nrfA: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 nrfA Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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