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Gene |

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Expression|

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Standard Name	ytfE
Gene Synonym(s)	ECK4205, b4209, JW4167^[1], dnrN, JW4167
Product Desc.	iron metabolism protein^[2]; protein involved in repair of stress-damaged iron-sulfur clusters^[3] Iron-sulfur cluster repair protein; confers resistance to nitric oxide and hydrogen peroxide; di-iron center^[4]
Product Synonyms(s)	predicted regulator of cell morphogenesis and cell wall metabolism^[1], B4209^[2]^[1], YtfE^[2]^[1] , dnrN, ECK4205, JW4167, b4209
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): ytfE^[2]
Regulation/Activity
Quick Links
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Notes

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ytfE is induced by NO as part of the NsrR regulon. YtfE can regenerate damaged AcnB and FumA in vitro (Justino, 2007). A ytfE mutant grows poorly under anaerobic respiratory conditions and has an increased sensitivity to iron starvation. ytfE is homologous to S. aureus scdA. ytfE expression is increased in fnr and fur mutants, but no obvious Fnr or Fur binding sites were found.^[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	ytfE
Mnemonic	Systematic nomenclature
Synonyms	ECK4205, b4209, JW4167^[1], dnrN, JW4167
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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	95.47 minutes	MG1655: 4430006..4429344 <gbrowseImage> name=NC_000913:4429344..4430006 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 4416982..4416320 <gbrowseImage> name=NC_012967:4416320..4416982 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 4368079..4368741 <gbrowseImage> name=NC_012759:4368079..4368741 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 4436663..4436001 <gbrowseImage> name=NC_007779:4436001..4436663 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 4530368..4529706 <gbrowseImage> name=NC_010473:4529706..4530368 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)	Reference	Availability
ΔytfE (Keio:JW4167)	deletion	deletion	PMID:16738554	Shigen CGSC11001^[5]
ΔytfE758::kan			PMID:16738554	CGSC:106068
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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
JW4167	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCGCTTATCGCGACCAACCTTT Primer 2:CCtTCACCCGCCAGCGCGCGTGG
7E9	Kohara Phage	Genobase	PMID:3038334
5B5	Kohara Phage	Genobase	PMID:3038334
cycA30::Tn10	Linked marker	CAG12073 = CGSC7482^[5]	est. P1 cotransduction: 90% ^[6]
zjf-920::Tn10	Linked marker	CAG12019 = CGSC7484^[5]	est. P1 cotransduction: 58% ^[6] Synonyms:zjh-901::Tn10, zjg-920::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:G7866	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12505	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004361	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948724	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2398	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013766	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	YtfE
Synonyms	predicted regulator of cell morphogenesis and cell wall metabolism^[1], B4209^[2]^[1], YtfE^[2]^[1] , dnrN, ECK4205, JW4167, b4209
Product description	iron metabolism protein^[2]; protein involved in repair of stress-damaged iron-sulfur clusters^[3] Iron-sulfur cluster repair protein; confers resistance to nitric oxide and hydrogen peroxide; di-iron center^[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:0005737	cytoplasm	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01606	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
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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	rplD		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 MAYRDQPLGE LALSIPRASA LFRKYDMDYC CGGKQTLARA AARKELDVEV IEAELAKLAE QPIEKDWRSA PLAEIIDHII VRYHDRHREQ LPELILQATK VERVHADKPS VPKGLTKYLT MLHEELSSHM MKEEQILFPM IKQGMGSQAM GPISVMESEH DEAGELLEVI KHTTNNVTPP PEACTTWKAM YNGINELIDD LMDHISLENN VLFPRALAGE
Length	220
Mol. Wt	24.882 kDa
pI	5.2 (calculated)
Extinction coefficient	19,940 - 20,315 (calc based on 6 Y, 2 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	76..140	PF01814 Hemerythrin HHE cation binding domain	PMID:19920124
Domain	152..215	PF01814 Hemerythrin HHE cation binding domain	PMID:19920124
Domain	4..59	PF04405 Domain of Unknown function (DUF542)	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=ytfE 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:16132031	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948724	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013766	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P69506	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G7866	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12505	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948724	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004361	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2398	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	5.519+/-0.164	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.006042296	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	70	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	11	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	23^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)
ytfE
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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_000913:4429986..4430026 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:b4209 (EcoliWiki Page)	NCBI GEO profiles for ytfE
microarray	GenExpDB:b4209 (EcoliWiki Page)	Summary of data for ytfE 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 (4429464..4429708) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ03; Well:H3^[7]
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Notes

Accessions Related to ytfE Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G7866	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2398	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b4209
EcoGene	EcoGene:EG12505	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004361	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013766	Escherichia coli str. K-12 substr. MG1655
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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	YTFE	From SHIGELLACYC
E. coli O157	YTFE	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)	PF01814 Hemerythrin HHE cation binding domain
Pfam (EcoliWiki Page)	PF01814 Hemerythrin HHE cation binding domain
Pfam (EcoliWiki Page)	PF04405 Domain of Unknown function (DUF542)
EcoCyc	EcoCyc:G7866	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12505	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004361	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2398	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013766	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 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).
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

ytfE: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 ytfE Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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