dnaQ: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

dnaQ

Gene Synonym(s)

ECK0215, b0215, JW0205, mutD[1], mutD

Product Desc.

DNA polymerase III, ε subunit[2][3];

Component of DNA polymerase III, core enzyme[3]; DNA polymerase III, holoenzyme[3]

DNA polymerase III epsilon subunit; streptomycin, azaserine resistant; 3' to 5' proofreading, lexA regulon[4]

Product Synonyms(s)

DNA polymerase III epsilon subunit[1], B0215[2][1], MutD[2][1], DnaQ[2][1] , ECK0215, JW0205, mutD, b0215

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): dnaQ[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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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

dnaQ

Mnemonic

DNA

Synonyms

ECK0215, b0215, JW0205, mutD[1], mutD

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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

5.09 minutes 

MG1655: 236067..236798
<gbrowseImage> name=NC_000913:236067..236798 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 238991..239722
<gbrowseImage> name=NC_012967:238991..239722 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 236066..236797
<gbrowseImage> name=NC_012759:236066..236797 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 236067..236798
<gbrowseImage> name=NC_007779:236067..236798 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 210171..210902
<gbrowseImage> name=NC_010473:210171..210902 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

dnaQ(del) (Keio:JW0205)

deletion

deletion

PMID:16738554

Shigen

CGSC8445[5]

dnaQ::Tn5KAN-2 (FB20052)

Insertion at nt 486 in Minus orientation

PMID:15262929

E. coli Genome Project:FB20052

does not contain pKD46

dnaQ49(ts)

temperature sensitive

PMID:7012548 PMID:3515128

CGSC:10707

dnaQ905

CGSC:12916

dnaQ744(del)::kan

PMID:16738554

CGSC:100630

mutD5

73Leu (TTG)----Trp (TGG) and 164Ala (GCA)----Val (GTA),

L73W A164V

mutator

mutator, conditional on media conditions

PMID:3540531

mutD51

73Leu (TTG)----Trp (TGG)

L73W

PMID:3540531

one of two mutations in mutD5

mutD52

164Ala (GCA)----Val (GTA),

A164V

PMID:3540531

one of two mutations in mutD5

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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

JW0205

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCAGCACTGCAATTACACGCCA

Primer 2:CCTGCTCGCCAGAGGCAACTTCC

7D5

Kohara Phage

Genobase

PMID:3038334

4A11

Kohara Phage

Genobase

PMID:3038334

yafC502::Tn10

Linked marker

CAG18436 = CGSC7328[5]

est. P1 cotransduction: 87% [6]
Synonyms:zae-502::Tn10

proA81::Tn10

Linked marker

CAG18447 = CGSC7330[5]

est. P1 cotransduction: 41% [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:EG10243

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10243

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946441

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000237

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0239

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000722

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

DnaQ

Synonyms

DNA polymerase III epsilon subunit[1], B0215[2][1], MutD[2][1], DnaQ[2][1] , ECK0215, JW0205, mutD, b0215

Product description

DNA polymerase III, ε subunit[2][3];

Component of DNA polymerase III, core enzyme[3]; DNA polymerase III, holoenzyme[3]

DNA polymerase III epsilon subunit; streptomycin, azaserine resistant; 3' to 5' proofreading, lexA regulon[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:0000287

magnesium ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0460

F

Seeded from EcoCyc (v14.0)

complete

GO:0003676

nucleic acid binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012337

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006054

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006309

F

Seeded from EcoCyc (v14.0)

complete

GO:0003887

DNA-directed DNA polymerase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006054

F

Seeded from EcoCyc (v14.0)

complete

GO:0003887

DNA-directed DNA polymerase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006309

F

Seeded from EcoCyc (v14.0)

complete

GO:0003887

DNA-directed DNA polymerase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:2.7.7.7

F

Seeded from EcoCyc (v14.0)

complete

GO:0003887

DNA-directed DNA polymerase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0239

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:0004527

exonuclease activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006055

F

Seeded from EcoCyc (v14.0)

complete

GO:0004527

exonuclease activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0269

F

Seeded from EcoCyc (v14.0)

complete

GO:0005622

intracellular

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006055

C

Seeded from EcoCyc (v14.0)

complete

GO:0006260

DNA replication

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006054

P

Seeded from EcoCyc (v14.0)

complete

GO:0006260

DNA replication

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006309

P

Seeded from EcoCyc (v14.0)

complete

GO:0006260

DNA replication

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0235

P

Seeded from EcoCyc (v14.0)

complete

GO:0016740

transferase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0808

F

Seeded from EcoCyc (v14.0)

complete

GO:0016779

nucleotidyltransferase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0548

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

Subunits of DNA polymerase III, core enzyme

could be indirect

Protein

ssb

PMID:15690043

Experiment(s):EBI-883264

Protein

dnaE

PMID:15690043

Experiment(s):EBI-883264, EBI-883487, EBI-890575, EBI-890781

Protein

dnaX

PMID:15690043

Experiment(s):EBI-883264, EBI-890575, EBI-890677

Protein

holA

PMID:15690043

Experiment(s):EBI-883264

Protein

holB

PMID:15690043

Experiment(s):EBI-883264, EBI-890575

Protein

holC

PMID:15690043

Experiment(s):EBI-883264, EBI-880166, EBI-885330, EBI-890575

Protein

holD

PMID:15690043

Experiment(s):EBI-883264, EBI-880133, EBI-890575

Protein

rplA

PMID:15690043

Experiment(s):EBI-883264, EBI-890575

Protein

tufA

PMID:15690043

Experiment(s):EBI-883264

Protein

yciK

PMID:16606699

Experiment(s):EBI-1135945

Protein

napC

PMID:16606699

Experiment(s):EBI-1135945

Protein

slyD

PMID:16606699

Experiment(s):EBI-1135945

Protein

atpB

PMID:15690043

Experiment(s):EBI-890575

Protein

cspC

PMID:15690043

Experiment(s):EBI-890575

Protein

fecB

PMID:15690043

Experiment(s):EBI-890575

Protein

lon

PMID:15690043

Experiment(s):EBI-890575

Protein

nusG

PMID:15690043

Experiment(s):EBI-890575

Protein

rplL

PMID:15690043

Experiment(s):EBI-890575

Protein

rplM

PMID:15690043

Experiment(s):EBI-890575

Protein

rplS

PMID:15690043

Experiment(s):EBI-890575

Protein

rpmC

PMID:15690043

Experiment(s):EBI-890575

Protein

rpmG

PMID:15690043

Experiment(s):EBI-890575

Protein

slyD

PMID:15690043

Experiment(s):EBI-890575

Protein

yfiF

PMID:15690043

Experiment(s):EBI-890575

Protein

ydiH

PMID:15690043

Experiment(s):EBI-890575

Protein

rpmG

PMID:19402753

LCMS(ID Probability):99.6

Protein

tufB

PMID:19402753

MALDI(Z-score):21.928144

Protein

rplA

PMID:19402753

LCMS(ID Probability):99.0 MALDI(Z-score):17.053160

Protein

holA

PMID:19402753

MALDI(Z-score):38.028436

Protein

ssb

PMID:19402753

MALDI(Z-score):33.961415

Protein

holB

PMID:19402753

LCMS(ID Probability):99.0 MALDI(Z-score):36.837342

Protein

holE

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):38.098428

Protein

holD

PMID:19402753

LCMS(ID Probability):99.0 MALDI(Z-score):27.315717

Protein

dnaX

PMID:19402753

LCMS(ID Probability):99.0 MALDI(Z-score):28.496617

Protein

atpB

PMID:19402753

LCMS(ID Probability):99.0

Protein

fecB

PMID:19402753

LCMS(ID Probability):99.0

Protein

rplL

PMID:19402753

LCMS(ID Probability):99.6

Protein

Subunits of DNA polymerase III, holoenzyme

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 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 

MSTAITRQIV LDTETTGMNQ IGAHYEGHKI IEIGAVEVVN RRLTGNNFHV YLKPDRLVDP
EAFGVHGIAD EFLLDKPTFA EVADEFMDYI RGAELVIHNA AFDIGFMDYE FSLLKRDIPK
TNTFCKVTDS LAVARKMFPG KRNSLDALCA RYEIDNSKRT LHGALLDAQI LAEVYLAMTG
GQTSMAFAME GETQQQQGEA TIQRIVRQAS KLRVVFATDE EIAAHEARLD LVQKKGGSCL WRA
Length

243

Mol. Wt

27.098 kDa

pI

5.9 (calculated)

Extinction coefficient

14,440 - 14,815 (calc based on 6 Y, 1 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 Notes References

Domain

8..175

PF00929 Exonuclease

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=dnaQ 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:16128202

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:946441

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000722

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P03007

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10243

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10243

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:946441

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000237

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0239

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

E. coli K-12 MG1655

988

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

516

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

642

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)

dnaQ

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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_000913:236047..236087 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

</protect>

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:b0215 (EcoliWiki Page)

NCBI GEO profiles for dnaQ

microarray

GenExpDB:b0215 (EcoliWiki Page)

Summary of data for dnaQ 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 (235927..236085) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ12; Well:C11[7]

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Notes

Accessions Related to dnaQ Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG10243

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0239

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0215

EcoGene

EcoGene:EG10243

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000237

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000722

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

  • ENSANGP00000001979 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Dictyostelium discoideum

  • DDB0219227 (score: 1.000; bootstrap: 100%)
  • DDB0204513 (score: 0.070)
  • DDB0202221 (score: 0.070)
  • DDB0220685 (score: 0.066)
  • DDB0231411 (score: 0.062)
  • DDB0191683 (score: 0.060)
  • DDB0189303 (score: 0.051)

From Inparanoid:20070104

Shigella flexneri

DNAQ

From SHIGELLACYC

E. coli O157

DNAQ

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)

PF00929 Exonuclease

Superfamily (EcoliWiki Page)

SUPERFAMILY:53098

PFAM (EcoliWiki Page)

PFAM:PF00929

EcoCyc

EcoCyc:EG10243

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10243

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000237

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0239

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000722

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 2.7 2.8 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 3.2 3.3 3.4 3.5 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

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