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dnaE:On One Page

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Quickview | Gene | Product(s) | Expression| Evolution | References |

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Standard Name

dnaE

Gene Synonym(s)

ECK0183, b0184, JW0179, polC, sdgC[1]

Product Desc.

DNA polymerase III, α subunit[2][3];

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

DNA polymerase III, alpha subunit; suppressor of dnaG-Ts[4]

Product Synonyms(s)

DNA polymerase III alpha subunit[1], B0184[2][1], SdgC[2][1], PolC[2][1], DnaE[2][1]

Function from GO

Molecular Function

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): yaeT-hlpA-lpxD-fabZ-lpxAB-rnhB-dnaE[2], ecfK-skp-lpxD-fabZ-lpxAB-rnhB-dnaE

Regulation/Activity
Quick Links

DNA display    Protein display    Pubmed(dnaE)    Textpresso(dnaE)

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Notes

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Has a PHP domin, like YcdX.[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

dnaE

Mnemonic

DNA

Synonyms

ECK0183, b0184, JW0179, polC, sdgC[1]

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Notes

Location(s) and DNA Sequence

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See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

StrainMap locationGenome coordinatesGenome browsersSequence links

MG1655

4.42 minutes 

MG1655: 205126..208608
gbrowse_img.php?coord=205126..208608&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 207968..211450
gbrowse_img.php?coord=207968..211450&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 205126..208608
gbrowse_img.php?coord=205126..208608&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 179230..182712
gbrowse_img.php?coord=179230..182712&genome=ecoli_DH10B&name=DH10B&trackset=0&width=300&.png

BW2952

NC_012759: 205125..208607
gbrowse_img.php?coord=205125..208607&genome=BW2952&name=NC_012759&trackset=0&width=300&.png

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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 typeLocationDescription
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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.

AlleleNt change(s)AA change(s)Phenotype: TypePhenotype: DescriptionReferenceAvailabilityComments

dnaE1026(ts)

temperature sensitive

CGSC:8012

dnaE486(ts)

temperature sensitive

CGSC:5641

dnaE1044

CGSC:73004

dnaE1061

CGSC:73007

dnaE1126

CGSC:73010

dnaE74(ts)

temperature sensitive

PMID:3158798 PMID:15028700

CGSC:85748


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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

ResourceResource TypeSourceNotes/Reference

JW0179

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCTCTGAACCACGTTTCGTACA

Primer 2:CCGTCAAACTCCAGTTCCACCTG

zad-220::Tn10

Linked marker

CAG12025 = CGSC7326[5]

est. P1 cotransduction: 6% [6]

yafC502::Tn10

Linked marker

CAG18436 = CGSC7328[5]

est. P1 cotransduction: 36% [6]
Synonyms:zae-502::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.

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG10238

EchoBASE (EcoliWiki Page)

EchoBASE:EB0234

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0184

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C0221

EcoGene (EcoliWiki Page)

EcoGene:EG10238

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:DNAE

CGSC (EcoliWiki Page)

CGSC:373

ASAP (EcoliWikiPage)

ASAP:ABE-0000624


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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

DnaE

Synonyms

DNA polymerase III alpha subunit[1], B0184[2][1], SdgC[2][1], PolC[2][1], DnaE[2][1]

Product description

DNA polymerase III, α subunit[2][3];

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

DNA polymerase III, alpha subunit; suppressor of dnaG-Ts[4]

EC number (for enzymes)
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Notes

Function

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Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

QualifierGO IDGO term nameReference(s)Evidence Codewith/fromAspectNotesStatus

GO:0016779

nucleotidyltransferase activity

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0548

F

Seeded from EcoCyc [7]

complete

GO:0016740

transferase activity

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0808

F

Seeded from EcoCyc [7]

complete

GO:0008408

3'-5' exonuclease activity

GO_REF:0000002
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004805
InterPro:IPR011708

F

Seeded from EcoCyc [7]

complete

GO:0006260

DNA replication

GO_REF:0000002
GO_REF:0000002
GO_REF:0000002
GO_REF:0000004

IEA: Inferred from Electronic Annotation

InterPro:IPR003141
InterPro:IPR004805
InterPro:IPR011708
SP_KW:KW-0235

P

Seeded from EcoCyc [7]

complete

GO:0005737

cytoplasm

GO_REF:0000002
GO_REF:0000002
GO_REF:0000004

IEA: Inferred from Electronic Annotation

InterPro:IPR004805
InterPro:IPR011708
SP_KW:KW-0963

C

Seeded from EcoCyc 12.5 [8]

complete

GO:0003887

DNA-directed DNA polymerase activity

GO_REF:0000002
GO_REF:0000003
GO_REF:0000004

IEA: Inferred from Electronic Annotation

InterPro:IPR003141
EC:2.7.7.7
SP_KW:KW-0239

F

Seeded from EcoCyc [7]

complete

GO:0003677

DNA binding

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003141

F

Seeded from EcoCyc [7]

complete

GO:0003676

nucleic acid binding

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004365

F

Seeded from EcoCyc [7]

complete

GO:0005515

protein binding

PMID:16606699

IPI: Inferred from Physical Interaction

UniProtKB:P30855

F

Seeded from EcoCyc 12.5 [8]

complete

GO:0005515

protein binding

PMID:16606699

IPI: Inferred from Physical Interaction

UniProtKB:P77374

F

Seeded from EcoCyc 12.5 [8]

complete

GO:0005515

protein binding

PMID:17109382

IPI: Inferred from Physical Interaction

UniProtKB:P03007

F

Seeded from EcoCyc 12.5 [8]

complete

GO:0003824

catalytic activity

GO_REF:0000002
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004013
InterPro:IPR016195

F

Seeded from EcoCyc [7]

complete

GO:0006261

DNA-dependent DNA replication

P

Seeded from EcoCyc 11.1[3].

required fields missing

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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 TypePartnerNotesReferencesEvidence

Protein

Subunits of DNA polymerase III, core enzyme

could be indirect

Protein

ssb

PMID:15690043

Experiment(s):EBI-883487

Protein

aceE

PMID:15690043

Experiment(s):EBI-883487

Protein

dnaX

PMID:15690043

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

Protein

holA

PMID:15690043

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

Protein

holB

PMID:15690043

Experiment(s):EBI-883487, EBI-880223

Protein

holC

PMID:15690043

Experiment(s):EBI-883487, EBI-880166, EBI-885330, EBI-890781

Protein

holD

PMID:15690043

Experiment(s):EBI-883487, EBI-880133, EBI-890781

Protein

rpsB

PMID:15690043

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

Protein

tufA

PMID:15690043

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

Protein

pta

PMID:16606699

Experiment(s):EBI-1135853

Protein

helD

PMID:16606699

Experiment(s):EBI-1135853

Protein

asnB

PMID:15690043

Experiment(s):EBI-890781

Protein

dnaK

PMID:15690043

Experiment(s):EBI-890781

Protein

hrpB

PMID:15690043

Experiment(s):EBI-890781

Protein

lpdA

PMID:15690043

Experiment(s):EBI-890781

Protein

nikD

PMID:15690043

Experiment(s):EBI-890781

Protein

rhsD

PMID:15690043

Experiment(s):EBI-890781

Protein

rplA

PMID:15690043

Experiment(s):EBI-890781

Protein

rplC

PMID:15690043

Experiment(s):EBI-890781

Protein

rplD

PMID:15690043

Experiment(s):EBI-890781

Protein

rplL

PMID:15690043

Experiment(s):EBI-890781

Protein

rplM

PMID:15690043

Experiment(s):EBI-890781

Protein

rplU

PMID:15690043

Experiment(s):EBI-890781

Protein

rpsA

PMID:15690043

Experiment(s):EBI-890781

Protein

rpsP

PMID:15690043

Experiment(s):EBI-890781

Protein

tpiA

PMID:15690043

Experiment(s):EBI-890781

Protein

ybdL

PMID:15690043

Experiment(s):EBI-890781

Protein

bcsA

PMID:15690043

Experiment(s):EBI-890781

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.

CompartmentDescriptionEvidenceSourceNotes
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Notes

Structure and Physical Properties

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Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Sequence

at EcoCyc 

MSEPRFVHLR VHSDYSMIDG LAKTAPLVKK AAALGMPALA ITDFTNLCGL VKFYGAGHGA
GIKPIVGADF NVQCDLLGDE LTHLTVLAAN NTGYQNLTLL ISKAYQRGYG AAGPIIDRDW
LIELNEGLIL LSGGRMGDVG RSLLRGNSAL VDECVAFYEE HFPDRYFLEL IRTGRPDEES
YLHAAVELAE ARGLPVVATN DVRFIDSSDF DAHEIRVAIH DGFTLDDPKR PRNYSPQQYM
RSEEEMCELF ADIPEALANT VEIAKRCNVT VRLGEYFLPQ FPTGDMSTED YLVKRAKEGL
EERLAFLFPD EEERLKRRPE YDERLETELQ VINQMGFPGY FLIVMEFIQW SKDNGVPVGP
GRGSGAGSLV AYALKITDLD PLEFDLLFER FLNPERVSMP DFDVDFCMEK RDQVIEHVAD
MYGRDAVSQI ITFGTMAAKA VIRDVGRVLG HPYGFVDRIS KLIPPDPGMT LAKAFEAEPQ
LPEIYEADEE VKALIDMARK LEGVTRNAGK HAGGVVIAPT KITDFAPLYC DEEGKHPVTQ
FDKSDVEYAG LVKFDFLGLR TLTIINWALE MINKRRAKNG EPPLDIAAIP LDDKKSFDML
QRSETTAVFQ LESRGMKDLI KRLQPDCFED MIALVALFRP GPLQSGMVDN FIDRKHGREE
ISYPDVQWQH ESLKPVLEPT YGIILYQEQV MQIAQVLSGY TLGGADMLRR AMGKKKPEEM
AKQRSVFAEG AEKNGINAEL AMKIFDLVEK FAGYGFNKSH SAAYALVSYQ TLWLKAHYPA
EFMAAVMTAD MDNTEKVVGL VDECWRMGLK ILPPDINSGL YHFHVNDDGE IVYGIGAIKG
VGEGPIEAII EARNKGGYFR ELFDLCARTD TKKLNRRVLE KLIMSGAFDR LGPHRAALMN
SLGDALKAAD QHAKAEAIGQ ADMFGVLAEE PEQIEQSYAS CQPWPEQVVL DGERETLGLY
LTGHPINQYL KEIERYVGGV RLKDMHPTER GKVITAAGLV VAARVMVTKR GNRIGICTLD
DRSGRLEVML FTDALDKYQQ LLEKDRILIV SGQVSFDDFS GGLKMTAREV MDIDEAREKY
ARGLAISLTD RQIDDQLLNR LRQSLEPHRS GTIPVHLYYQ RADARARLRF GATWRVSPSD
RLLNDLRGLI GSEQVELEFD
Length

1,160

Mol. Wt

129.908 kDa

pI

5.1 (calculated)

Extinction coefficient

102,110 - 103,610 (calc based on 39 Y, 8 W, and 12 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.

TypeResiduesDescriptionNotesReferences
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Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures
Models

View models at:

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Structure figures

Notes

Gene Product Resources

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Resource typeSourceNotes/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.

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG10238-MONOMER

UniProt (EcoliWiki Page)

UniProt:P10443

PFAM (EcoliWiki Page)

PFAM:PF02231

RefSeq (EcoliWiki Page)

RefSeq:NP_414726


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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

MoleculeOrganism or StrainCellular levelUnitsMediumTemperature °COther (e.g. anaerobic)Growth rateAssay usedNotesReference(s)
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Notes

Transcription and Transcriptional Regulation

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

Transcription unit(s)

yaeT-hlpA-lpxD-fabZ-lpxAB-rnhB-dnaE

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Figure courtesy of RegulonDB

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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gbrowse_img.php?coord=205106..205146&genome=ecoli&name=MG1655&trackset=Gene+DNA_+Protein&width=400&figure=Nterm&.png
This picture shows the sequence around the N-terminus.

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

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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Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele NameMutationPhenotypeReference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

TypeReferenceNotes

microarray

GEO Profiles:b0184 (EcoliWiki Page)

NCBI GEO profiles for dnaE

microarray

GenExpDB:b0184 (EcoliWiki Page)

Summary of data for dnaE 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 NameResource TypeDescriptionSourceNotes
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Notes

Accessions Related to dnaE Expression

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

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG10238

EchoBASE (EcoliWiki Page)

EchoBASE:EB0234

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0184

EcoGene (EcoliWiki Page)

EcoGene:EG10238


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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.

OrganismHomologs (Statistics)Comments

Shigella flexneri

DNAE

From SHIGELLACYC

E. coli O157

DNAE

From ECOO157CYC

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Do-It-Yourself Web Tools

Notes

Families

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

DatabaseAccessionNotes

PFAM (EcoliWiki Page)

PFAM:PF02231


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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 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 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 3.6 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).
  7. ↑ 7.0 7.1 7.2 7.3 7.4 7.5 7.6 7.7 EcoCyc (release 13.0; 2009) Keseler, IM et al. (2009) Nucleic Acids Res. 37(Database issue):D464-70
  8. ↑ 8.0 8.1 8.2 8.3 EcoCyc (release 12.5; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7

Categories

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