dnaG: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

dnaG

Gene Synonym(s)

ECK3056, b3066, JW3038, dnaP, parB, sdgA[1], sdgA

Product Desc.

DNA primase[2][3];

Component of primosome[3]

Primase for DNA replication; primer synthesis for leading- and lagging-strand synthesis; binds Zn(II)[4]

Product Synonyms(s)

DNA primase[1], B3066[2][1], SdgA[2][1], ParB[2][1], DnaP[2][1], DnaG[2][1] , dnaP, ECK3056, JW3038, parB, sdgA, b3066

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): rpsU-dnaG-rpoD[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

dnaG

Mnemonic

DNA

Synonyms

ECK3056, b3066, JW3038, dnaP, parB, sdgA[1], sdgA

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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

69.17 minutes 

MG1655: 3209129..3210874
<gbrowseImage> name=NC_000913:3209129..3210874 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3143924..3145669
<gbrowseImage> name=NC_012967:3143924..3145669 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3096277..3098022
<gbrowseImage> name=NC_012759:3096277..3098022 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3209763..3211508
<gbrowseImage> name=NC_007779:3209763..3211508 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3306874..3308619
<gbrowseImage> name=NC_010473:3306874..3308619 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

3209132

Edman degradation

PMID:6750604


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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

ΔdnaG (Keio:JW3038)

deletion

deletion

PMID:16738554

Shigen

dnaG::Tn5KAN-I-SceI (FB21017)

Insertion at nt 798 in Plus orientation

PMID:15262929

E. coli Genome Project:FB21017

does not contain pKD46

dnaG18

CGSC:5755

dnaG3(ts)

temperature sensitive

PMID:3536848 PMID:3886637

CGSC:7015

dnaG308(ts)

temperature sensitive

CGSC:9400

dnaG399(ts)

temperature sensitive

CGSC:9406

dnaG2903

Growth Phenotype

phage gamma could not multiply at 42C; TS revertants were spontaneously produced at high frequency; at high temperatures, cell growth and DNA replication is halted

PMID:3886637

previously named dnaP18

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Notes

The Keio collection[5] lists a deletion of dnaG. The insertion in this strain is a duplication of the dnaG region.[6]


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

JW3038

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCGCTGGACGAATCCCACGCGT

Primer 2:CCtTTTTTCGCCAGCTCCTGGTT

19F2

Kohara Phage

Genobase

PMID:3038334

tolC210::Tn10

Linked marker

CAG12184 = CGSC7437[7]

est. P1 cotransduction: 30% [8]

aer-3075::Tn10

Linked marker

CAG12152 = CGSC7438[7]

est. P1 cotransduction: 81% [8]
Synonyms:zgh-3075::Tn10, zgj-3075::Tn10

pGNG1

Plasmid Clone

PMID:2055480

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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:EG10239

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10239

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000233

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947570

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0235

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010065

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

DnaG

Synonyms

DNA primase[1], B3066[2][1], SdgA[2][1], ParB[2][1], DnaP[2][1], DnaG[2][1] , dnaP, ECK3056, JW3038, parB, sdgA, b3066

Product description

DNA primase[2][3];

Component of primosome[3]

Primase for DNA replication; primer synthesis for leading- and lagging-strand synthesis; binds Zn(II)[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:0003676

nucleic acid binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006154

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002694

F

Seeded from EcoCyc (v14.0)

complete

GO:0003896

DNA primase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002694

F

Seeded from EcoCyc (v14.0)

complete

GO:0003896

DNA primase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006295

F

Seeded from EcoCyc (v14.0)

complete

GO:0003896

DNA primase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013173

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:0006259

DNA metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006154

P

Seeded from EcoCyc (v14.0)

complete

GO:0006260

DNA replication

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002694

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:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006295

P

Seeded from EcoCyc (v14.0)

complete

GO:0006269

DNA replication, synthesis of RNA primer

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013173

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:0006350

transcription

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0804

P

Seeded from EcoCyc (v14.0)

complete

GO:0008270

zinc ion binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002694

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:0008270

zinc ion binding

PMID:1511009

IDA: Inferred from Direct Assay

F

complete

GO:0006269

DNA replication, synthesis of RNA primer

PMID:340457

IDA: Inferred from Direct Assay

P

complete

GO:0005737

cytoplasm

PMID:340457

IDA: Inferred from Direct Assay

C

complete

GO:0003896

DNA primase activity

PMID:340457

IDA: Inferred from Direct Assay

F

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 primosome

could be indirect

Protein

rplA

PMID:15690043

Experiment(s):EBI-885817

Protein

nusG

PMID:15690043

Experiment(s):EBI-890837

Protein

rplL

PMID:15690043

Experiment(s):EBI-890837

Protein

rpsG

PMID:15690043

Experiment(s):EBI-890837

Protein

yfiF

PMID:15690043

Experiment(s):EBI-890837

Protein

ygdH

PMID:15690043

Experiment(s):EBI-890837

Protein

rho

PMID:16606699

Experiment(s):EBI-1144696

Protein

flu

PMID:16606699

Experiment(s):EBI-1144696

Protein

aspS

PMID:16606699

Experiment(s):EBI-1144696

Protein

ybcW

PMID:16606699

Experiment(s):EBI-1144696

Protein

ygdH

PMID:19402753

LCMS(ID Probability):99.0

Protein

DnaB

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 

MAGRIPRVFI NDLLARTDIV DLIDARVKLK KQGKNFHACC PFHNEKTPSF TVNGEKQFYH
CFGCGAHGNA IDFLMNYDKL EFVETVEELA AMHNLEVPFE AGSGPSQIER HQRQTLYQLM
DGLNTFYQQS LQQPVATSAR QYLEKRGLSH EVIARFAIGF APPGWDNVLK RFGGNPENRQ
SLIDAGMLVT NDQGRSYDRF RERVMFPIRD KRGRVIGFGG RVLGNDTPKY LNSPETDIFH
KGRQLYGLYE AQQDNAEPNR LLVVEGYMDV VALAQYGINY AVASLGTSTT ADHIQLLFRA
TNNVICCYDG DRAGRDAAWR ALETALPYMT DGRQLRFMFL PDGEDPDTLV RKEGKEAFEA
RMEQAMPLSA FLFNSLMPQV DLSTPDGRAR LSTLALPLIS QVPGETLRIY LRQELGNKLG
ILDDSQLERL MPKAAESGVS RPVPQLKRTT MRILIGLLVQ NPELATLVPP LENLDENKLP
GLGLFRELVN TCLSQPGLTT GQLLEHYRGT NNAATLEKLS MWDDIADKNI AEQTFTDSLN
HMFDSLLELR QEELIARERT HGLSNEERLE LWTLNQELAK K
Length

581

Mol. Wt

65.566 kDa

pI

5.9 (calculated)

Extinction coefficient

45,840 - 46,715 (calc based on 16 Y, 4 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

259..341

PF01751 Toprim domain

PMID:19920124

Domain

5..102

PF01807 CHC2 zinc finger

PMID:19920124

Domain

126..252

PF08275 DNA primase catalytic core, N-terminal domain

PMID:19920124

Domain

450..575

PF08278 DNA primase DnaG DnaB-binding

PMID:19920124

Domain

368..426

PF10410 DnaB-helicase binding domain of primase

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=dnaG taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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Notes

  • Purification of DnaG is described in reference[9]
  • Km data

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:16130962

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947570

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010065

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0ABS5

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10239

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10239

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947570

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000233

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0235

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

356

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

98

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

181

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)

rpsU-dnaG-rpoD

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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_000913:3209109..3209149 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:b3066 (EcoliWiki Page)

NCBI GEO profiles for dnaG

microarray

GenExpDB:b3066 (EcoliWiki Page)

Summary of data for dnaG 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 dnaG Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG10239

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0235

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3066

EcoGene

EcoGene:EG10239

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000233

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010065

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

Shigella flexneri

DNAG

From SHIGELLACYC

E. coli O157

DNAG

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

Superfamily (EcoliWiki Page)

SUPERFAMILY:56731

Superfamily (EcoliWiki Page)

SUPERFAMILY:57783

Superfamily (EcoliWiki Page)

SUPERFAMILY:117023

Pfam (EcoliWiki Page)

PF01751 Toprim domain

Pfam (EcoliWiki Page)

PF01807 CHC2 zinc finger

Pfam (EcoliWiki Page)

PF08275 DNA primase catalytic core, N-terminal domain

Pfam (EcoliWiki Page)

PF08278 DNA primase DnaG DnaB-binding

Pfam (EcoliWiki Page)

PF10410 DnaB-helicase binding domain of primase

EcoCyc

EcoCyc:EG10239

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10239

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000233

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0235

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010065

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 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 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. ↑ Baba, T et al. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol. 2 2006.0008 PubMed
  6. ↑ Yamamoto, N et al. (2009) Update on the Keio collection of Escherichia coli single-gene deletion mutants. Mol. Syst. Biol. 5 335 PubMed
  7. ↑ 7.0 7.1 CGSC: The Coli Genetics Stock Center
  8. ↑ 8.0 8.1 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).
  9. ↑ Rowen, L & Kornberg, A (1978) Primase, the dnaG protein of Escherichia coli. An enzyme which starts DNA chains. J. Biol. Chem. 253 758-64 PubMed

Categories

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