nth:On One Page

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

Quickview

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Standard Name

nth

Gene Synonym(s)

ECK1629, b1633, JW1625[1], JW1625

Product Desc.

endonuclease III; specific for apurinic and/or apyrimidinic sites[2][3]

Endonuclease III, DNA glycosylase/apyrimidinic (AP) lyase[4]

Product Synonyms(s)

DNA glycosylase and apyrimidinic (AP) lyase (endonuclease III)[1], B1633[2][1], Nth[2][1], Endo III[2][1] , ECK1629, JW1625, b1633

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): rsxABCDGE-nth[2], ydgK-rsxABCDGE-nth[2]

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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Nth is specific for damaged pyrimidine sites, particularly Thy.[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

nth

Mnemonic

eNdonuclease THree

Synonyms

ECK1629, b1633, JW1625[1], JW1625

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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

36.85 minutes 

MG1655: 1709547..1710182
<gbrowseImage> name=NC_000913:1709547..1710182 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1688717..1689352
<gbrowseImage> name=NC_012967:1688717..1689352 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1601606..1602241
<gbrowseImage> name=NC_012759:1601606..1602241 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1713237..1713872
<gbrowseImage> name=NC_007779:1713237..1713872 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1800118..1800753
<gbrowseImage> name=NC_010473:1800118..1800753 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

Coding Start (SO:0000323)

MG1655

1709547

Edman degradation

PMID:2669955


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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

Δnth (Keio:JW1625)

deletion

deletion

PMID:16738554

Shigen
CGSC9384[5]

nth::Tn5KAN-2 (FB20397)

Insertion at nt 339 in Minus orientation

PMID:15262929

E. coli Genome Project:FB20397

contains pKD46

nth::Tn5KAN-2 (FB20398)

Insertion at nt 339 in Minus orientation

PMID:15262929

E. coli Genome Project:FB20398

does not contain pKD46

nthK120Q

K120Q

10000-fold decrease in activity

seeded from UniProt:P0AB83

nth-1::kan,ble

CGSC:10918

Δnth-782::kan

PMID:16738554

CGSC:102130


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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

JW1625

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCAATAAAGCAAAACGCCTGGA

Primer 2:CCGATGTCAACTTTCTCTTTGTA

9A1

Kohara Phage

Genobase

PMID:3038334

20B5

Kohara Phage

Genobase

PMID:3038334

zdd-235::Tn10

Linked marker

CAG18461 = CGSC7378[5]

est. P1 cotransduction: % [6]
Synonyms:zdc-235::Tn10

zdi-925::Tn10

Linked marker

CAG12151 = CGSC7385[5]

est. P1 cotransduction: 2% [6]
Synonyms:zdh-925::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:EG10662

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10662

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000655

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947122

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0656

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0005463

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

Nth

Synonyms

DNA glycosylase and apyrimidinic (AP) lyase (endonuclease III)[1], B1633[2][1], Nth[2][1], Endo III[2][1] , ECK1629, JW1625, b1633

Product description

endonuclease III; specific for apurinic and/or apyrimidinic sites[2][3]

Endonuclease III, DNA glycosylase/apyrimidinic (AP) lyase[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:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000445

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003583

F

Seeded from EcoCyc (v14.0)

complete

GO:0009314

response to radiation

P

Seeded from Riley et al 2006 [1].

Missing: evidence, reference

GO:0003824

catalytic activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011257

F

Seeded from EcoCyc (v14.0)

complete

GO:0003906

DNA-(apurinic or apyrimidinic site) lyase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005759

F

Seeded from EcoCyc (v14.0)

complete

GO:0003906

DNA-(apurinic or apyrimidinic site) lyase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:4.2.99.18

F

Seeded from EcoCyc (v14.0)

complete

GO:0004519

endonuclease activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003651

F

Seeded from EcoCyc (v14.0)

complete

GO:0004519

endonuclease activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004035

F

Seeded from EcoCyc (v14.0)

complete

GO:0004519

endonuclease activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004036

F

Seeded from EcoCyc (v14.0)

complete

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:0005622

intracellular

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000445

C

Seeded from EcoCyc (v14.0)

complete

GO:0005622

intracellular

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005759

C

Seeded from EcoCyc (v14.0)

complete

GO:0006281

DNA repair

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003583

P

Seeded from EcoCyc (v14.0)

complete

GO:0006281

DNA repair

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004035

P

Seeded from EcoCyc (v14.0)

complete

GO:0006281

DNA repair

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004036

P

Seeded from EcoCyc (v14.0)

complete

GO:0006281

DNA repair

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011257

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:0006284

base-excision repair

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003265

P

Seeded from EcoCyc (v14.0)

complete

GO:0006284

base-excision repair

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005759

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:0008152

metabolic process

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0326

P

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:0016798

hydrolase activity, acting on glycosyl bonds

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0326

F

Seeded from EcoCyc (v14.0)

complete

GO:0016829

lyase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0456

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

GO:0051536

iron-sulfur cluster binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0411

F

Seeded from EcoCyc (v14.0)

complete

GO:0051539

4 iron, 4 sulfur cluster binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003651

F

Seeded from EcoCyc (v14.0)

complete

GO:0051539

4 iron, 4 sulfur cluster binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0004

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

aceE

PMID:15690043

Experiment(s):EBI-881855, EBI-889335

Protein

slyD

PMID:16606699

Experiment(s):EBI-1140328

Protein

dnaK

PMID:16606699

Experiment(s):EBI-1140328

Protein

lpdA

PMID:15690043

Experiment(s):EBI-889335

Protein

rplW

PMID:15690043

Experiment(s):EBI-889335

Protein

tufA

PMID:15690043

Experiment(s):EBI-889335

Protein

rplW

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 

MNKAKRLEIL TRLRENNPHP TTELNFSSPF ELLIAVLLSA QATDVSVNKA TAKLYPVANT
PAAMLELGVE GVKTYIKTIG LYNSKAENII KTCRILLEQH NGEVPEDRAA LEALPGVGRK
TANVVLNTAF GWPTIAVDTH IFRVCNRTQF APGKNVEQVE EKLLKVVPAE FKVDCHHWLI
LHGRYTCIAR KPRCGSCIIE DLCEYKEKVD I
Length

211

Mol. Wt

23.562 kDa

pI

8.3 (calculated)

Extinction coefficient

18,450 - 19,325 (calc based on 5 Y, 2 W, and 7 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

99..128

PF00633 Helix-hairpin-helix motif

PMID:19920124

Domain

34..169

PF00730 HhH-GPD superfamily base excision DNA repair protein

PMID:19920124

Domain

187..203

PF10576 Iron-sulfur binding domain of endonuclease III

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=nth 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:16129591

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947122

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0005463

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0AB83

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10662

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10662

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947122

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000655

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0656

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

6.104+/-0.051

Molecules/cell

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

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.018110236

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

542

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

188

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

327

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)

rsxABCDGE-nth

ydgK-rsxABCDGE-nth

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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_000913:1709527..1709567 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:b1633 (EcoliWiki Page)

NCBI GEO profiles for nth

microarray

GenExpDB:b1633 (EcoliWiki Page)

Summary of data for nth 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 nth Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG10662

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0656

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b1633

EcoGene

EcoGene:EG10662

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000655

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0005463

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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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

  • ENSANGP00000014971 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Arabidopsis thaliana

  • AT1G05900 (score: 1.000; bootstrap: 100%)
  • AT2G31450 (score: 0.606)

From Inparanoid:20070104

Bos taurus

  • ENSBTAP00000008229 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Caenorhabditis briggsae

  • WBGene00033270 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Caenorhabditis elegans

  • WBGene00011201 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Canis familiaris

  • ENSCAFP00000028745 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Dictyostelium discoideum

  • DDB0232975 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Drosophila melanogaster

  • FBgn0032907 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Gallus gallus

  • ENSGALP00000008999 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Homo sapiens

  • ENSP00000219066 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Macaca mulatta

  • ENSMMUP00000003755 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Monodelphis domestica

  • ENSMODP00000020016 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Mus musculus

  • MGI:1313275 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Oryza gramene

  • Q53LY1 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Rattus norvegicus

  • ENSRNOP00000016490 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Saccharomyces cerevisiae

  • YOL043C (score: 1.000; bootstrap: 100%)
  • YAL015C (score: 0.318)

From Inparanoid:20070104

Schizosaccharomyces pombe

  • SPAC30D117 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000034748 (score: 1.000; bootstrap: 100%)
  • ENSXETP00000034872 (score: 0.410)

From Inparanoid:20070104

Shigella flexneri

NTH

From SHIGELLACYC

E. coli O157

NTH

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)

PF00633 Helix-hairpin-helix motif

Pfam (EcoliWiki Page)

PF00730 HhH-GPD superfamily base excision DNA repair protein

Superfamily (EcoliWiki Page)

SUPERFAMILY:48150

Panther (EcoliWiki Page)

PTHR10359:SF16

Pfam (EcoliWiki Page)

PF10576 Iron-sulfur binding domain of endonuclease III

EcoCyc

EcoCyc:EG10662

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10662

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000655

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0656

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0005463

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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  1. ↑ 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. ↑ 2.0 2.1 2.2 2.3 2.4 2.5 2.6 2.7 2.8 2.9 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 4.2 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).

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