nfo:On One Page

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Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Quickview | Gene | Product(s) | Expression| Evolution | References |

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Standard Name

nfo

Gene Synonym(s)

ECK2152, b2159, JW2146[1], JW2146

Product Desc.

endonuclease IV[2][3]

AP endodeoxyribonuclease IV; member of soxRS regulon; endonuclease IV[4]

Product Synonyms(s)

endonuclease IV with intrinsic 3'-5' exonuclease activity[1], B2159[2][1], Nfo[2][1] , ECK2152, JW2146, b2159

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): nfo[2], OP00263

Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

dnadisplay.png proteindisplay.png   pubmed.jpg   textpresso.jpg  

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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

nfo

Mnemonic

Endonuclease IV

Synonyms

ECK2152, b2159, JW2146[1], JW2146

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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

48.47 minutes 

MG1655: 2248862..2249719
<gbrowseImage> name=NC_000913:2248862..2249719 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2202078..2202935
<gbrowseImage> name=NC_012967:2202078..2202935 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2141345..2142202
<gbrowseImage> name=NC_012759:2141345..2142202 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2254174..2255031
<gbrowseImage> name=NC_007779:2254174..2255031 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2339851..2340708
<gbrowseImage> name=NC_010473:2339851..2340708 source=DH10B preset=GeneLocation </gbrowseImage>

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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

Δnfo (Keio:JW2146)

deletion

deletion

PMID:16738554

Shigen
CGSC9740[5]

nfo::Tn5KAN-2 (FB20662)

Insertion at nt 453 in Minus orientation

PMID:15262929

E. coli Genome Project:FB20662

contains pKD46

nfo::Tn5KAN-2 (FB20663)

Insertion at nt 453 in Minus orientation

PMID:15262929

E. coli Genome Project:FB20663

does not contain pKD46

nfo-1::kan,ble

CGSC:10923

Δnfo-786::kan

PMID:16738554

CGSC:102052


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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

JW2146

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCAAATACATTGGAGCGCACGT

Primer 2:CCGGCTACCGCTTTTTCAGTTTG

7H12

Kohara Phage

Genobase

PMID:3038334

5H11

Kohara Phage

Genobase

PMID:3038334

4F2

Kohara Phage

Genobase

PMID:3038334

zbd-3104::Tn10

Linked marker

CAG12021 = CGSC7344[5]

est. P1 cotransduction: 1% [6]
Synonyms:zbc-3105::Tn10, zbd-3105::Tn10

napA722::Tn10

Linked marker

CAG12098 = CGSC7400[5]

est. P1 cotransduction: 8% [6]
Synonyms:zeg-722, zei-722::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:EG10651

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10651

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000644

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946669

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0645

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0007146

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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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

Nfo

Synonyms

endonuclease IV with intrinsic 3'-5' exonuclease activity[1], B2159[2][1], Nfo[2][1] , ECK2152, JW2146, b2159

Product description

endonuclease IV[2][3]

AP endodeoxyribonuclease IV; member of soxRS regulon; endonuclease IV[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:0030288

outer membrane-bounded periplasmic space

C

Seeded from Riley et al 2006 [1].

Missing: evidence, reference

GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001719

F

Seeded from EcoCyc (v14.0)

complete

GO:0009314

response to radiation

P

Seeded from Riley et al 2006 [1].

Missing: evidence, reference

GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR018246

F

Seeded from EcoCyc (v14.0)

complete

GO:0004518

nuclease activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0540

F

Seeded from EcoCyc (v14.0)

complete

GO:0004519

endonuclease activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR018246

F

Seeded from EcoCyc (v14.0)

complete

GO:0004519

endonuclease activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0255

F

Seeded from EcoCyc (v14.0)

complete

GO:0005622

intracellular

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001719

C

Seeded from EcoCyc (v14.0)

complete

GO:0005622

intracellular

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR018246

C

Seeded from EcoCyc (v14.0)

complete

GO:0006281

DNA repair

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00152

P

Seeded from EcoCyc (v14.0)

complete

GO:0006281

DNA repair

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001719

P

Seeded from EcoCyc (v14.0)

complete

GO:0006281

DNA repair

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR018246

P

Seeded from EcoCyc (v14.0)

complete

GO:0006281

DNA repair

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0234

P

Seeded from EcoCyc (v14.0)

complete

GO:0006974

response to DNA damage stimulus

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0227

P

Seeded from EcoCyc (v14.0)

complete

GO:0008270

zinc ion binding

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00152

F

Seeded from EcoCyc (v14.0)

complete

GO:0008270

zinc ion binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001719

F

Seeded from EcoCyc (v14.0)

complete

GO:0008270

zinc ion binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR018246

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:0008833

deoxyribonuclease IV (phage-T4-induced) activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00152

F

Seeded from EcoCyc (v14.0)

complete

GO:0008833

deoxyribonuclease IV (phage-T4-induced) activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001719

F

Seeded from EcoCyc (v14.0)

complete

GO:0008833

deoxyribonuclease IV (phage-T4-induced) activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:3.1.21.2

F

Seeded from EcoCyc (v14.0)

complete

GO:0016787

hydrolase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0378

F

Seeded from EcoCyc (v14.0)

complete

GO:0030145

manganese ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0464

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 Notes References Evidence

Protein

aceF

PMID:15690043

Experiment(s):EBI-881109

Protein

lon

PMID:15690043

Experiment(s):EBI-881109

Protein

malP

PMID:15690043

Experiment(s):EBI-881109

Protein

secA

PMID:15690043

Experiment(s):EBI-881109

Protein

lpdA

PMID:15690043

Experiment(s):EBI-881109

Protein

hemD

PMID:16606699

Experiment(s):EBI-1142046

Protein

rpsI

PMID:16606699

Experiment(s):EBI-1142046

Protein

yciK

PMID:16606699

Experiment(s):EBI-1142046

Protein

rplD

PMID:16606699

Experiment(s):EBI-1142046

Protein

lon

PMID:19402753

MALDI(Z-score):19.964235

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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 

MKYIGAHVSA AGGLANAAIR AAEIDATAFA LFTKNQRQWR AAPLTTQTID EFKAACEKYH
YTSAQILPHD SYLINLGHPV TEALEKSRDA FIDEMQRCEQ LGLSLLNFHP GSHLMQISEE
DCLARIAESI NIALDKTQGV TAVIENTAGQ GSNLGFKFEH LAAIIDGVED KSRVGVCIDT
CHAFAAGYDL RTPAECEKTF ADFARTVGFK YLRGMHLNDA KSTFGSRVDR HHSLGEGNIG
HDAFRWIMQD DRFDGIPLIL ETINPDIWAE EIAWLKAQQT EKAVA
Length

285

Mol. Wt

31.479 kDa

pI

5.6 (calculated)

Extinction coefficient

30,940 - 31,690 (calc based on 6 Y, 4 W, and 6 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

19..239

PF01261 Xylose isomerase-like TIM barrel

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=nfo 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:16130097

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:946669

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0007146

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0A6C1

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10651

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10651

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:946669

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000644

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0645

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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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

15.691+/-0.068

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.037922987

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

1041

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

436

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

695

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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<protect>

See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)

nfo

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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_000913:2248842..2248882 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:b2159 (EcoliWiki Page)

NCBI GEO profiles for nfo

microarray

GenExpDB:b2159 (EcoliWiki Page)

Summary of data for nfo 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 (2248701..2248881) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ12; Well:G12[7]

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Notes

Accessions Related to nfo Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG10651

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0645

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2159

EcoGene

EcoGene:EG10651

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000644

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0007146

Escherichia coli str. K-12 substr. MG1655

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Notes

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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

Caenorhabditis briggsae

  • WBGene00034190 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Caenorhabditis elegans

  • WBGene00000151 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Dictyostelium discoideum

  • DDB0206584 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Saccharomyces cerevisiae

  • YKL114C (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Schizosaccharomyces pombe

  • SPCC6227 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Takifugu rubripes

  • NEWSINFRUP00000160071 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Tetraodon nigroviridis

  • GSTENP00024229001 (score: 1.000; bootstrap: 100%)
  • GSTENP00007576001 (score: 0.119)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000034840 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

NFO

From SHIGELLACYC

E. coli O157

NFO

From ECOO157CYC

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Do-It-Yourself Web Tools

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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)

PF01261 Xylose isomerase-like TIM barrel

Superfamily (EcoliWiki Page)

SUPERFAMILY:51658

Panther (EcoliWiki Page)

PTHR21445:SF0

EcoCyc

EcoCyc:EG10651

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10651

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000644

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0645

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0007146

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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See Help:References for how to manage references in EcoliWiki.

  1. ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 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. ↑ 3.0 3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 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. ↑ 5.0 5.1 5.2 CGSC: The Coli Genetics Stock Center
  6. ↑ 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).
  7. ↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

Categories

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