dnaB: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

dnaB

Gene Synonym(s)

ECK4044, b4052, JW4012, groP, grpA, grpD[1], grpD

Product Desc.

DnaB[2][3];

Component of replicative DNA helicase[3]; primosome[3]

Replicative DNA helicase; DNA-dependent ATPase involved in DNA synthesis; binds DNA contrahelicase termination protein Tus at Ter sites; possibly involved in DNA recombination[4]

Product Synonyms(s)

replicative DNA helicase[1], B4052[2][1], GrpD[2][1], GrpA[2][1], GroP[2][1], DnaB[2][1] , ECK4044, groP, grpA, grpD, JW4012, b4052

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): dnaB[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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The dnaB gene is essential.[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

dnaB

Mnemonic

DNA

Synonyms

ECK4044, b4052, JW4012, groP, grpA, grpD[1], grpD

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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

91.87 minutes 

MG1655: 4262337..4263752
<gbrowseImage> name=NC_000913:4262337..4263752 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 4243246..4244661
<gbrowseImage> name=NC_012967:4243246..4244661 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 4201182..4202597
<gbrowseImage> name=NC_012759:4201182..4202597 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 4267904..4269319
<gbrowseImage> name=NC_007779:4267904..4269319 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 4362033..4363448
<gbrowseImage> name=NC_010473:4362033..4363448 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

4262340

Edman degradation

PMID:6323420


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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

dnaB252(ts)

temperature sensitive

PMID:7012124 PMID:321430 PMID:7532169

CGSC:7240

dnaB107(ts)

temperature sensitive

CGSC:6400

dnaB6(ts)(Am)

Growth Phenotype

lowered rate of DNA synthesis at 40C; when growing in rich broth medium at 30C there is a loss of viability

PMID:4925091

CGSC:7327

experiments suggest that the strain's lethality can be uncoupled phenotypically from DNA synthesis cessation by treating cells after high temperature exposure

dnaB8(ts)

temperature sensitive

PMID:7532169

CGSC:7330

dnaB21

Growth Phenotype

DNA synthesis is slowed at higher temperatures

PMID:4884589

CGSC:8277

previously called 'FA21'

dnaB22(ts)

temperature sensitive

PMID:4884589

CGSC:8285

previously called 'FA22'

dnaB70(ts)

temperature sensitive

PMID:7532169

CGSC:8290

dnaB500(ts)

temperature sensitive

PMID:16559102

CGSC:8294

dnaB454(ts)

temperature sensitive

PMID:7532169

CGSC:8297

dnaB43(ts)

temperature sensitive

PMID:4861724 PMID:7532169

CGSC:9404

dnaB313(ts)

temperature sensitive

CGSC:13923

dnaB125(Am)

PMID:6263858

CGSC:19640

amber (UAG) mutation

dnaB1029

CGSC:73012

dnaB1035

CGSC:73013

dnaB1037

CGSC:73014

dnaB1041

CGSC:73017

dnaB1047

CGSC:73018

dnaB1071

CGSC:73022

dnaB1077

CGSC:73024

dnaB1080

CGSC:73025

dnaB1201

CGSC:73027

dnaB1203

CGSC:73032

dnaB1205

CGSC:73034

dnaB1208

CGSC:73067

dnaB1211

CGSC:73069

dnaB1301

CGSC:73071

dnaB1304

CGSC:73073

dnaB306

CGSC:73490

dnaB266

Growth Phenotype

at 40C DNA synthesis stops but synthesis can be re-initiated by shifting back to permissive temperature

PMID:4922218

previously called 'T266'

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Notes

Genetic Interactions

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<protect>

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

JW4012

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCGCAGGAAATAAACCCTTCAA

Primer 2:CCTTCGTCGTCGTACTGCGGCCC

1E4

Kohara Phage

Genobase

PMID:3038334

12D1

Kohara Phage

Genobase

PMID:3038334

malF3089::Tn10

Linked marker

CAG12164 = CGSC7476[5]

est. P1 cotransduction: 45% [6]

zje-2241::Tn10

Linked marker

CAG18427 = CGSC7481[5]

est. P1 cotransduction: 15% [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:EG10236

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10236

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000230

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948555

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0232

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013269

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

DnaB

Synonyms

replicative DNA helicase[1], B4052[2][1], GrpD[2][1], GrpA[2][1], GroP[2][1], DnaB[2][1] , ECK4044, groP, grpA, grpD, JW4012, b4052

Product description

DnaB[2][3];

Component of replicative DNA helicase[3]; primosome[3]

Replicative DNA helicase; DNA-dependent ATPase involved in DNA synthesis; binds DNA contrahelicase termination protein Tus at Ter sites; possibly involved in DNA recombination[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:0000166

nucleotide binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003593

F

Seeded from EcoCyc (v14.0)

complete

GO:0000166

nucleotide binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0547

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR007692

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0238

F

Seeded from EcoCyc (v14.0)

complete

GO:0003678

DNA helicase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR007692

F

Seeded from EcoCyc (v14.0)

complete

GO:0003678

DNA helicase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR007693

F

Seeded from EcoCyc (v14.0)

complete

GO:0003678

DNA helicase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR007694

F

Seeded from EcoCyc (v14.0)

complete

GO:0004386

helicase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0347

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR007692

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR007693

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR007694

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0067

F

Seeded from EcoCyc (v14.0)

complete

GO:0005658

alpha DNA polymerase:primase complex

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0639

C

Seeded from EcoCyc (v14.0)

complete

GO:0006260

DNA replication

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR007692

P

Seeded from EcoCyc (v14.0)

complete

GO:0006260

DNA replication

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR007693

P

Seeded from EcoCyc (v14.0)

complete

GO:0006260

DNA replication

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR007694

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:0006269

DNA replication, synthesis of RNA primer

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0639

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:0017111

nucleoside-triphosphatase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003593

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 replicative DNA helicase

could be indirect

Protein

aceE

PMID:15690043

Experiment(s):EBI-885640

Protein

yfaX

PMID:15690043

Experiment(s):EBI-885640

Protein

dnaC

PMID:15690043

Experiment(s):EBI-885640

Protein

rplA

PMID:15690043

Experiment(s):EBI-885640

Protein

rpsB

PMID:15690043

Experiment(s):EBI-885640, EBI-890751

Protein

tufA

PMID:15690043

Experiment(s):EBI-885640, EBI-890751

Protein

rhsA

PMID:16606699

Experiment(s):EBI-1147342

Protein

ynfL

PMID:16606699

Experiment(s):EBI-1147342

Protein

rplA

PMID:16606699

Experiment(s):EBI-1147342

Protein

thrS

PMID:16606699

Experiment(s):EBI-1147342

Protein

rhsC

PMID:16606699

Experiment(s):EBI-1147342

Protein

astA

PMID:16606699

Experiment(s):EBI-1147342

Protein

fimI

PMID:15690043

Experiment(s):EBI-890751

Protein

ftsY

PMID:15690043

Experiment(s):EBI-890751

Protein

rplD

PMID:15690043

Experiment(s):EBI-890751

Protein

rplL

PMID:15690043

Experiment(s):EBI-890751

Protein

rplO

PMID:15690043

Experiment(s):EBI-890751

Protein

rplW

PMID:15690043

Experiment(s):EBI-890751

Protein

rpmC

PMID:15690043

Experiment(s):EBI-890751

Protein

rpsE

PMID:15690043

Experiment(s):EBI-890751

Protein

thrA

PMID:15690043

Experiment(s):EBI-890751

Protein

fumA

PMID:15690043

Experiment(s):EBI-890751

Protein

rplO

PMID:19402753

LCMS(ID Probability):99.6

Protein

tufB

PMID:19402753

MALDI(Z-score):22.490996

Protein

ftsY

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplD

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplW

PMID:19402753

LCMS(ID Probability):99.6

Protein

fumA

PMID:19402753

LCMS(ID Probability):99.6

Protein

thrA

PMID:19402753

LCMS(ID Probability):99.0

Protein

priC

PMID:19402753

LCMS(ID Probability):98.5

Protein

rhmR

PMID:19402753

MALDI(Z-score):17.053160

Protein

fimI

PMID:19402753

LCMS(ID Probability):99.6

Protein

dnaC

PMID:19402753

MALDI(Z-score):38.529538

Protein

Subunits of primosome

could be indirect

Protein

DnaG

PMID:8917517

ELISA

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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 

MAGNKPFNKQ QAEPRERDPQ VAGLKVPPHS IEAEQSVLGG LMLDNERWDD VAERVVADDF
YTRPHRHIFT EMARLQESGS PIDLITLAES LERQGQLDSV GGFAYLAELS KNTPSAANIS
AYADIVRERA VVREMISVAN EIAEAGFDPQ GRTSEDLLDL AESRVFKIAE SRANKDEGPK
NIADVLDATV ARIEQLFQQP HDGVTGVNTG YDDLNKKTAG LQPSDLIIVA ARPSMGKTTF
AMNLVENAAM LQDKPVLIFS LEMPSEQIMM RSLASLSRVD QTKIRTGQLD DEDWARISGT
MGILLEKRNI YIDDSSGLTP TEVRSRARRI AREHGGIGLI MIDYLQLMRV PALSDNRTLE
IAEISRSLKA LAKELNVPVV ALSQLNRSLE QRADKRPVNS DLRESGSIEQ DADLIMFIYR
DEVYHENSDL KGIAEIIIGK QRNGPIGTVR LTFNGQWSRF DNYAGPQYDD E
Length

471

Mol. Wt

52.391 kDa

pI

4.8 (calculated)

Extinction coefficient

31,400 (calc based on 10 Y, 3 W, and 0 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

26..128

PF00772 DnaB-like helicase N terminal domain

PMID:19920124

Domain

206..391

PF03796 DnaB-like helicase C terminal domain

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=dnaB taxon=562,83333 </beststructure>

Models

View models at:

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</protect>

Structure figures

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</protect>

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:16131878

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:948555

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013269

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0ACB0

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10236

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10236

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:948555

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000230

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0232

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

34.033+/-0.195

Molecules/cell

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

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.073498233

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

694

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

210

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

364

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)

dnaB

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Figure courtesy of RegulonDB

</protect>

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_000913:4262317..4262357 source=MG1655 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

</protect>

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:b4052 (EcoliWiki Page)

NCBI GEO profiles for dnaB

microarray

GenExpDB:b4052 (EcoliWiki Page)

Summary of data for dnaB 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 dnaB Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG10236

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0232

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b4052

EcoGene

EcoGene:EG10236

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000230

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013269

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

Xenopus tropicalis

  • ENSXETP00000028799 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

DNAB

From SHIGELLACYC

E. coli O157

DNAB

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)

PF03796 DnaB-like helicase C terminal domain

Pfam (EcoliWiki Page)

PF00772 DnaB-like helicase N terminal domain

Superfamily (EcoliWiki Page)

SUPERFAMILY:48024

Superfamily (EcoliWiki Page)

SUPERFAMILY:52540

EcoCyc

EcoCyc:EG10236

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10236

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000230

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0232

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013269

Escherichia coli str. K-12 substr. MG1655

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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 1.12 1.13 1.14 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.00 2.01 2.02 2.03 2.04 2.05 2.06 2.07 2.08 2.09 2.10 2.11 2.12 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 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 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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