polA:Gene Product(s)

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Nomenclature Function Interactions Localization Sequence Domains Structure Resources Accessions Links References Suggestions

Nomenclature

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

Standard name

PolA

Synonyms

fused DNA polymerase I 5'->3' exonuclease[1], 3'->5' polymerase[1], 3'->5' exonuclease[1], B3863[2][1], ResA[2][1], PolA[2][1] , ECK3855, JW3835, resA, b3863

Product description

DNA polymerase I, 3' --> 5' polymerase, 5' --> 3' and 3' --> 5' exonuclease[2][3]

DNA polymerase I; required for plasmid replication; synthetic lethal with ygdG[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:IPR002562

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:IPR001098

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002298

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002421

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003583

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR008918

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020045

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020046

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020047

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:0003824

catalytic activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR008918

F

Seeded from EcoCyc (v14.0)

complete

GO:0003824

catalytic activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020045

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:IPR001098

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:IPR002298

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

PMID:4902142[5]

IMP: Inferred from Mutant Phenotype

F

W3110 thy- mutagenized with NNG. Ts mutant isolated based on lack of enzymatic activity.

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:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0269

F

Seeded from EcoCyc (v14.0)

complete

GO:0006139

nucleobase, nucleoside, nucleotide and nucleic acid metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002562

P

Seeded from EcoCyc (v14.0)

complete

GO:0006260

DNA replication

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001098

P

Seeded from EcoCyc (v14.0)

complete

GO:0006260

DNA replication

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002298

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:0006281

DNA repair

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003583

P

Seeded from EcoCyc (v14.0)

complete

GO:0006281

DNA repair

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0234

P

Seeded from EcoCyc (v14.0)

complete

GO:0006974

response to DNA damage stimulus

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0227

P

Seeded from EcoCyc (v14.0)

complete

GO:0008408

3'-5' exonuclease activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002562

F

Seeded from EcoCyc (v14.0)

complete

GO:0008409

5'-3' exonuclease activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002421

F

Seeded from EcoCyc (v14.0)

complete

GO:0008409

5'-3' exonuclease activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020046

F

Seeded from EcoCyc (v14.0)

complete

GO:0008409

5'-3' exonuclease activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020047

F

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:0003887

DNA-directed DNA polymerase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001098

F

Seeded from EcoCyc (v14.0)

complete

GO:0003887

DNA-directed DNA polymerase activity

PMID:381283[6]

IDA: Inferred from Direct Assay

F

Paper describes a simple purification from W3110. Assayed on poly dA:dT. Not the first paper.

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

hsdS

PMID:15690043[7]

Experiment(s):EBI-892889

Protein

aceF

PMID:15690043[7]

Experiment(s):EBI-886509, EBI-892889

Protein

lpdA

PMID:15690043[7]

Experiment(s):EBI-886509, EBI-892889

Protein

malP

PMID:15690043[7]

Experiment(s):EBI-886509, EBI-892889

Protein

metK

PMID:15690043[7]

Experiment(s):EBI-886509

Protein

rpoA

PMID:15690043[7]

Experiment(s):EBI-886509, EBI-892889

Protein

rpoB

PMID:15690043[7]

Experiment(s):EBI-886509

Protein

rpoC

PMID:15690043[7]

Experiment(s):EBI-886509

Protein

tufA

PMID:15690043[7]

Experiment(s):EBI-886509

Protein

mnmC

PMID:15690043[7]

Experiment(s):EBI-892889

Protein

fis

PMID:15690043[7]

Experiment(s):EBI-892889

Protein

hns

PMID:15690043[7]

Experiment(s):EBI-892889

Protein

hrpA

PMID:15690043[7]

Experiment(s):EBI-892889

Protein

hupA

PMID:15690043[7]

Experiment(s):EBI-892889

Protein

murF

PMID:15690043[7]

Experiment(s):EBI-892889

Protein

rplD

PMID:15690043[7]

Experiment(s):EBI-892889

Protein

rplL

PMID:15690043[7]

Experiment(s):EBI-892889

Protein

rplM

PMID:15690043[7]

Experiment(s):EBI-892889

Protein

rpmB

PMID:15690043[7]

Experiment(s):EBI-892889

Protein

rpsB

PMID:15690043[7]

Experiment(s):EBI-892889

Protein

slyD

PMID:15690043[7]

Experiment(s):EBI-892889

Protein

yidX

PMID:15690043[7]

Experiment(s):EBI-892889

Protein

hrpA

PMID:19402753[8]

LCMS(ID Probability):99.0

Protein

metK

PMID:19402753[8]

MALDI(Z-score):36.964539

Protein

tufB

PMID:19402753[8]

MALDI(Z-score):23.864151

Protein

kdsA

PMID:19402753[8]

MALDI(Z-score):39.157008

Protein

malP

PMID:19402753[8]

LCMS(ID Probability):99.0 MALDI(Z-score):15.660450

Protein

fis

PMID:19402753[8]

LCMS(ID Probability):99.0

Protein

rpoA

PMID:19402753[8]

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

Protein

yidX

PMID:19402753[8]

LCMS(ID Probability):99.0

Protein

hupA

PMID:19402753[8]

LCMS(ID Probability):99.0 MALDI(Z-score):5.741142

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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 

MVQIPQNPLI LVDGSSYLYR AYHAFPPLTN SAGEPTGAMY GVLNMLRSLI MQYKPTHAAV
VFDAKGKTFR DELFEHYKSH RPPMPDDLRA QIEPLHAMVK AMGLPLLAVS GVEADDVIGT
LAREAEKAGR PVLISTGDKD MAQLVTPNIT LINTMTNTIL GPEEVVNKYG VPPELIIDFL
ALMGDSSDNI PGVPGVGEKT AQALLQGLGG LDTLYAEPEK IAGLSFRGAK TMAAKLEQNK
EVAYLSYQLA TIKTDVELEL TCEQLEVQQP AAEELLGLFK KYEFKRWTAD VEAGKWLQAK
GAKPAAKPQE TSVADEAPEV TATVISYDNY VTILDEETLK AWIAKLEKAP VFAFDTETDS
LDNISANLVG LSFAIEPGVA AYIPVAHDYL DAPDQISRER ALELLKPLLE DEKALKVGQN
LKYDRGILAN YGIELRGIAF DTMLESYILN SVAGRHDMDS LAERWLKHKT ITFEEIAGKG
KNQLTFNQIA LEEAGRYAAE DADVTLQLHL KMWPDLQKHK GPLNVFENIE MPLVPVLSRI
ERNGVKIDPK VLHNHSEELT LRLAELEKKA HEIAGEEFNL SSTKQLQTIL FEKQGIKPLK
KTPGGAPSTS EEVLEELALD YPLPKVILEY RGLAKLKSTY TDKLPLMINP KTGRVHTSYH
QAVTATGRLS STDPNLQNIP VRNEEGRRIR QAFIAPEDYV IVSADYSQIE LRIMAHLSRD
KGLLTAFAEG KDIHRATAAE VFGLPLETVT SEQRRSAKAI NFGLIYGMSA FGLARQLNIP
RKEAQKYMDL YFERYPGVLE YMERTRAQAK EQGYVETLDG RRLYLPDIKS SNGARRAAAE
RAAINAPMQG TAADIIKRAM IAVDAWLQAE QPRVRMIMQV HDELVFEVHK DDVDAVAKQI
HQLMENCTRL DVPLLVEVGS GENWDQAH
Length

928

Mol. Wt

103.121 kDa

pI

5.4 (calculated)

Extinction coefficient

86,180 - 86,430 (calc based on 32 Y, 7 W, and 2 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

330..517

PF01612 3'-5' exonuclease

PMID:19920124[9]

Domain

7..169

PF02739 5'-3' exonuclease, N-terminal resolvase-like domain

PMID:19920124[9]

Domain

171..277

PF01367 5'-3' exonuclease, C-terminal SAM fold

PMID:19920124[9]

Domain

547..927

PF00476 DNA polymerase family A

PMID:19920124[9]

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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=polA taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

See Help:Jmol in EcoliWiki

DNA polymerase I Klenow fragment
<jmol> <jmolApplet> <color>white</color> <uploadedFileContents >1DPI.pdb</uploadedFileContents> <name></name> <script> wireframe off; spacefill off; trace off; rotate ON; cartoon; color chain; </script> </jmolApplet> </jmol>
<jmol> <jmolCheckbox > <scriptWhenChecked > rotate on; </scriptWhenChecked > <scriptWhenUnchecked > rotate off; </scriptWhenUnchecked > <checked>true</checked> <text>rotate</text> </jmolCheckbox > <jmolButton><script>reset; </script><text>reset</text></jmolButton> </jmol>









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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:16131704

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:948356

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012618

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P00582

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10746

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10746

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:948356

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000737

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0739

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. ↑ 1.0 1.1 1.2 1.3 1.4 1.5 1.6 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 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  5. ↑ De Lucia, P & Cairns, J (1969) Isolation of an E. coli strain with a mutation affecting DNA polymerase. Nature 224 1164-6 PubMed
  6. ↑ Rhodes, G et al. (1979) A simple and rapid purification method for Escherichia coli DNA polymerase I. J. Biol. Chem. 254 7465-7 PubMed
  7. ↑ 7.00 7.01 7.02 7.03 7.04 7.05 7.06 7.07 7.08 7.09 7.10 7.11 7.12 7.13 7.14 7.15 7.16 7.17 7.18 7.19 7.20 7.21 Butland, G et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 531-7 PubMed
  8. ↑ 8.0 8.1 8.2 8.3 8.4 8.5 8.6 8.7 8.8 Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed
  9. ↑ 9.0 9.1 9.2 9.3 Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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