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Standard Name

polB

Gene Synonym(s)

ECK0061, b0060, JW0059, dinA[1]

Product Desc.

DNA polymerase II[2][3]

DNA polymerase II, capable of translesion synthesis; role in the resumption of DNA synthesis after UV irradiation[4]

Product Synonyms(s)

DNA polymerase II[1], B0060[2][1], DinA[2][1], PolB[2][1]

Function from GO

Molecular Function

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): polB[2], dinA

Regulation/Activity
Quick Links

DNA display    Protein display    Pubmed(polB)    Textpresso(polB)

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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

polB

Mnemonic

Polymerase

Synonyms

ECK0061, b0060, JW0059, dinA[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

1.37 minutes 

MG1655: 65780..63429
gbrowse_img.php?coord=63429..65780&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 68584..66233
gbrowse_img.php?coord=66233..68584&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 65780..63429
gbrowse_img.php?coord=63429..65780&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

BW2952

NC_012759: 63429..65780
gbrowse_img.php?coord=63429..65780&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

ΔpolB (Keio:JW0059)

deletion

deletion

PMID:16738554

Shigen

polBG401D

G401D

(in allele POLB100)

Strain variation; seeded from UniProt:P21189

polB100

CGSC:6869


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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

JW0059

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCGCGCAGGCAGGTTTTATCTT

Primer 2:CCAAATAGCCCAAGTTGCCCGGT

carB96::Tn10

Linked marker

CAG12093 = CGSC7322[5]

est. P1 cotransduction: 30% [6]
Synonyms:car-96::Tn10

leuO3051::Tn10

Linked marker

CAG12095 = CGSC7324[5]

est. P1 cotransduction: 48% [6]
Synonyms:zab-3051::Tn10 nnnThe start of leuO was reannotated by Riley et al. (2006).

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Notes

Accessions in Other Databases

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DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG10747

EchoBASE (EcoliWiki Page)

EchoBASE:EB0740

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0060

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C0071

EcoGene (EcoliWiki Page)

EcoGene:EG10747

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:POLB

CGSC (EcoliWiki Page)

CGSC:374

ASAP (EcoliWikiPage)

ASAP:ABE-0000202


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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

PolB

Synonyms

DNA polymerase II[1], B0060[2][1], DinA[2][1], PolB[2][1]

Product description

DNA polymerase II[2][3]

DNA polymerase II, capable of translesion synthesis; role in the resumption of DNA synthesis after UV irradiation[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:0009432

SOS response

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0742

P

Seeded from EcoCyc [7]

complete

GO:0006974

response to DNA damage stimulus

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0227

P

Seeded from EcoCyc [7]

complete

GO:0006281

DNA repair

GO_REF:0000004
GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0234
SP_KW:KW-0742

P

Seeded from EcoCyc [7]

complete

GO:0006260

DNA replication

GO_REF:0000002
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006133
InterPro:IPR006134

P

Seeded from EcoCyc [7]

complete

GO:0006139

nucleobase, nucleoside, nucleotide and nucleic acid metabolic process

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006172

P

Seeded from EcoCyc 12.5 [8]

complete

GO:0003676

nucleic acid binding

GO_REF:0000002
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006172
InterPro:IPR012337

F

Seeded from EcoCyc 12.5 [8]

complete

GO:0000166

nucleotide binding

GO_REF:0000002
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006134
InterPro:IPR006172

F

Seeded from EcoCyc 12.5 [8]

complete

GO:0005515

protein binding

PMID:16606699

IPI: Inferred from Physical Interaction

UniProtKB:P0AC41

F

Seeded from EcoCyc [7]

complete

GO:0003887

DNA-directed DNA polymerase activity

GO_REF:0000002
GO_REF:0000002
GO_REF:0000002
GO_REF:0000003
GO_REF:0000004

IEA: Inferred from Electronic Annotation

InterPro:IPR006133
InterPro:IPR006134
InterPro:IPR006172
EC:2.7.7.7
SP_KW:KW-0239

F

Seeded from EcoCyc 12.5 [8]

complete

GO:0005737

cytoplasm

C

Seeded from EcoCyc 11.1[3].

required fields missing

GO:0003677

DNA binding

GO_REF:0000002
GO_REF:0000004

IEA: Inferred from Electronic Annotation

InterPro:IPR006134
SP_KW:KW-0238

F

Seeded from EcoCyc [7]

complete

GO:0006261

DNA-dependent DNA replication

P

Seeded from EcoCyc 11.1[3].

required fields missing

GO:0009314

response to radiation

P

Seeded from Riley et al 2006 [1].

required fields missing

GO:0008296

3'-5'-exodeoxyribonuclease activity

F

Seeded from EcoCyc 11.1[3].

required fields missing

GO:0045004

DNA replication proofreading

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

sdhA

PMID:16606699

Experiment(s):EBI-1135463

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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 

MAQAGFILTR HWRDTPQGTE VSFWLATDNG PLQVTLAPQE SVAFIPADQV PRAQHILQGE
QGFRLTPLAL KDFHRQPVYG LYCRAHRQLM NYEKRLREGG VTVYEADVRP PERYLMERFI
TSPVWVEGDM HNGTIVNARL KPHPDYRPPL KWVSIDIETT RHGELYCIGL EGCGQRIVYM
LGPENGDASS LDFELEYVAS RPQLLEKLNA WFANYDPDVI IGWNVVQFDL RMLQKHAERY
RLPLRLGRDN SELEWREHGF KNGVFFAQAK GRLIIDGIEA LKSAFWNFSS FSLETVAQEL
LGEGKSIDNP WDRMDEIDRR FAEDKPALAT YNLKDCELVT QIFHKTEIMP FLLERATVNG
LPVDRHGGSV AAFGHLYFPR MHRAGYVAPN LGEVPPHASP GGYVMDSRPG LYDSVLVLDY
KSLYPSIIRT FLIDPVGLVE GMAQPDPEHS TEGFLDAWFS REKHCLPEIV TNIWHGRDEA
KRQGNKPLSQ ALKIIMNAFY GVLGTTACRF FDPRLASSIT MRGHQIMRQT KALIEAQGYD
VIYGDTDSTF VWLKGAHSEE EAAKIGRALV QHVNAWWAET LQKQRLTSAL ELEYETHFCR
FLMPTIRGAD TGSKKRYAGL IQEGDKQRMV FKGLETVRTD WTPLAQQFQQ ELYLRIFRNE
PYQEYVRETI DKLMAGELDA RLVYRKRLRR PLSEYQRNVP PHVRAARLAD EENQKRGRPL
QYQNRGTIKY VWTTNGPEPL DYQRSPLDYE HYLTRQLQPV AEGILPFIED NFATLMTGQL GLF
Length

783

Mol. Wt

90.054 kDa

pI

6.9 (calculated)

Extinction coefficient

137,170 - 138,045 (calc based on 33 Y, 16 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.

TypeResiduesDescriptionNotesReferences

Initiator Methionine

1

Removed

UniProt:P21189


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

Structures
  • Representative Escherichia coli structure:
    1Q8I|A
    1-783 of 783 residues (E-value: 0e0) (Percent Identity: 99.87)
  • Representative homolog:
    3K5L|A ()
    4-786 of 783 residues (E-value: 0e0) (Percent Identity: 99.87)
  • View the PDB Table for polB
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:EG10747-MONOMER

UniProt (EcoliWiki Page)

UniProt:P21189

PFAM (EcoliWiki Page)

PFAM:PF03104

RefSeq (EcoliWiki Page)

RefSeq:NP_414602


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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)

polB

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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=65760..65800&genome=ecoli&name=MG1655&trackset=Gene+DNA_+Protein+flip&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:b0060 (EcoliWiki Page)

NCBI GEO profiles for polB

microarray

GenExpDB:b0060 (EcoliWiki Page)

Summary of data for polB 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

GFP Fusion

Intergenic region (65704..65932) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ20; Well:E6[9]

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Notes

Accessions Related to polB Expression

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

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG10747

EchoBASE (EcoliWiki Page)

EchoBASE:EB0740

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0060

EcoGene (EcoliWiki Page)

EcoGene:EG10747


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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

Anopheles gambiae

  • ENSANGP00000018383 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Apis mellifera

  • ENSAPMP00000022139 (score: 1.000; bootstrap: 76%)

From Inparanoid:20070104

Arabidopsis thaliana

  • AT5G63960 (score: 1.000; bootstrap: 89%)
  • AT1G67500 (score: 0.090)

From Inparanoid:20070104

Bos taurus

  • ENSBTAP00000010742 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Caenorhabditis briggsae

  • WBGene00041727 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Caenorhabditis elegans

  • WBGene00012936 (score: 1.000; bootstrap: 78%)

From Inparanoid:20070104

Canis familiaris

  • ENSCAFP00000019936 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Ciona intestinalis

  • ENSCINP00000005791 (score: 1.000; bootstrap: 100%)
  • ENSCINP00000015719 (score: 0.108)

From Inparanoid:20070104

Danio rerio

  • ZDB-GENE-030114-9 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Dictyostelium discoideum

  • DDB0232274 (score: 1.000; bootstrap: 100%)
  • DDB0232268 (score: 1.000; bootstrap: 100%)
  • DDB0232271 (score: 0.096)

From Inparanoid:20070104

Drosophila melanogaster

  • FBgn0004493 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Drosophila pseudoobscura

  • GA19530-PA (score: 1.000; bootstrap: 85%)

From Inparanoid:20070104

Gallus gallus

  • ENSGALP00000026266 (score: 1.000; bootstrap: 88%)

From Inparanoid:20070104

Homo sapiens

  • ENSP00000314415 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Macaca mulatta

  • ENSMMUP00000028348 (score: 1.000; bootstrap: 53%)
  • ENSMMUP00000028356 (score: 0.109)

From Inparanoid:20070104

Monodelphis domestica

  • ENSMODP00000009125 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Mus musculus

  • MGI:97741 (score: 1.000; bootstrap: 100%)
  • MGI:1337131 (score: 0.125)

From Inparanoid:20070104

Oryza gramene

  • Q9LRE6 (score: 1.000; bootstrap: 82%)
  • Q53P50 (score: 1.000; bootstrap: 84%)
  • Q53NH0 (score: 0.518)

From Inparanoid:20070104

Pan troglodytes

  • ENSPTRP00000019473 (score: 1.000; bootstrap: 62%)
  • ENSPTRP00000031607 (score: 0.062)

From Inparanoid:20070104

Rattus norvegicus

  • ENSRNOP00000026797 (score: 1.000; bootstrap: 100%)
  • ENSRNOP00000000725 (score: 0.119)

From Inparanoid:20070104

Saccharomyces cerevisiae

  • YDL102W (score: 1.000; bootstrap: 100%)
  • YPL167C (score: 0.085)

From Inparanoid:20070104

Schizosaccharomyces pombe

  • SPBC3364 (score: 1.000; bootstrap: 100%)
  • SPAC6880 (score: 0.077)

From Inparanoid:20070104

Takifugu rubripes

  • NEWSINFRUP00000160398 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Tetraodon nigroviridis

  • GSTENP00021892001 (score: 1.000; bootstrap: 97%)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000047196 (score: 1.000; bootstrap: 77%)

From Inparanoid:20070104

Shigella flexneri

POLB

From SHIGELLACYC

E. coli O157

POLB

From ECOO157CYC

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Do-It-Yourself Web Tools

Notes

Families

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DatabaseAccessionNotes

PFAM (EcoliWiki Page)

PFAM:PF03104


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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 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 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
  9. ↑ Zaslaver A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat Methods 3: 623-8 PubMed EcoliWiki page

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