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Protein

DNA polymerase III subunit epsilon

Gene

dnaQ

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. The epsilon subunit contain the editing function and is a proofreading 3'-5' exonuclease.

Catalytic activityi

Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).

Cofactori

Mg2+, Mn2+Note: Binds 2 divalent metal cations. Magnesium or manganese.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi12 – 121Divalent metal cation 1; catalytic
Metal bindingi12 – 121Divalent metal cation 2; catalytic
Binding sitei12 – 121Substrate
Metal bindingi14 – 141Divalent metal cation 1; catalytic
Binding sitei14 – 141Substrate
Binding sitei61 – 611Substrate
Binding sitei66 – 661Substrate
Active sitei162 – 1621Proton acceptor
Metal bindingi167 – 1671Divalent metal cation 1; catalytic
Binding sitei167 – 1671Substrate

GO - Molecular functioni

  • DNA binding Source: InterPro
  • DNA-directed DNA polymerase activity Source: UniProtKB-KW
  • exonuclease activity Source: EcoCyc
  • metal ion binding Source: UniProtKB-KW

GO - Biological processi

  • DNA replication proofreading Source: EcoCyc
  • nucleic acid phosphodiester bond hydrolysis Source: GOC
Complete GO annotation...

Keywords - Molecular functioni

DNA-directed DNA polymerase, Exonuclease, Hydrolase, Nuclease, Nucleotidyltransferase, Transferase

Keywords - Biological processi

DNA replication

Keywords - Ligandi

Magnesium, Manganese, Metal-binding

Enzyme and pathway databases

BioCyciEcoCyc:EG10243-MONOMER.
ECOL316407:JW0205-MONOMER.
MetaCyc:EG10243-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA polymerase III subunit epsilon (EC:2.7.7.7)
Gene namesi
Name:dnaQ
Synonyms:mutD
Ordered Locus Names:b0215, JW0205
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318 Componenti: Chromosome UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10243. dnaQ.

Subcellular locationi

GO - Cellular componenti

  • DNA polymerase III, core complex Source: EcoCyc
Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 243243DNA polymerase III subunit epsilonPRO_0000105483Add
BLAST

2D gel databases

SWISS-2DPAGEP03007.

Expressioni

Gene expression databases

GenevestigatoriP03007.

Interactioni

Subunit structurei

The DNA polymerase holoenzyme is a complex that contains 10 different types of subunits. These subunits are organized into 3 functionally essential subassemblies: the pol III core, the beta sliding clamp processivity factor and the clamp-loading complex. The pol III core (subunits alpha,epsilon and theta) contains the polymerase and the 3'-5' exonuclease proofreading activities. The polymerase is tethered to the template via the sliding clamp processivity factor. The clamp-loading complex assembles the beta processivity factor onto the primer template and plays a central role in the organization and communication at the replication fork. This complex contains delta, delta', psi and chi, and copies of either or both of two different DnaX proteins, gamma and tau. The composition of the holoenzyme is, therefore: (alpha,epsilon,theta)[2]-(gamma/tau)[3]-delta,delta', psi,chi-beta[4].1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
dnaEP1044320EBI-549131,EBI-549111
dnaNP0A9886EBI-549131,EBI-542385
dnaXP067104EBI-549131,EBI-549140
holEP0ABS811EBI-549131,EBI-549182

Protein-protein interaction databases

DIPiDIP-9462N.
IntActiP03007. 28 interactions.
MINTiMINT-1222832.
STRINGi511145.b0215.

Structurei

Secondary structure

1
243
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi7 – 1610Combined sources
Beta strandi20 – 234Combined sources
Turni24 – 274Combined sources
Beta strandi30 – 3910Combined sources
Beta strandi48 – 514Combined sources
Helixi60 – 667Combined sources
Helixi70 – 734Combined sources
Helixi79 – 9012Combined sources
Beta strandi93 – 975Combined sources
Helixi100 – 11314Combined sources
Helixi121 – 1233Combined sources
Beta strandi125 – 1295Combined sources
Helixi130 – 1378Combined sources
Helixi145 – 1517Combined sources
Beta strandi156 – 1583Combined sources
Helixi164 – 17815Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1J53X-ray1.80A1-186[»]
1J54X-ray1.70A1-186[»]
1MGZmodel-A1-186[»]
2GUIX-ray1.60A2-186[»]
2IDOX-ray2.10A/C1-186[»]
2XY8NMR-A1-186[»]
4GX8X-ray1.70A/B/C/D209-243[»]
4GX9X-ray2.15A/B/C/D200-243[»]
ProteinModelPortaliP03007.
SMRiP03007. Positions 5-180, 210-243.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP03007.

Family & Domainsi

Phylogenomic databases

eggNOGiCOG0847.
HOGENOMiHOG000258616.
InParanoidiP03007.
KOiK02342.
OMAiFHVYLNP.
OrthoDBiEOG696BTR.
PhylomeDBiP03007.

Family and domain databases

Gene3Di3.30.420.10. 1 hit.
InterProiIPR006054. DnaQ.
IPR006309. DnaQ_proteo.
IPR006055. Exonuclease.
IPR013520. Exonuclease_RNaseT/DNA_pol3.
IPR012337. RNaseH-like_dom.
[Graphical view]
PfamiPF00929. RNase_T. 1 hit.
[Graphical view]
SMARTiSM00479. EXOIII. 1 hit.
[Graphical view]
SUPFAMiSSF53098. SSF53098. 1 hit.
TIGRFAMsiTIGR00573. dnaq. 1 hit.
TIGR01406. dnaQ_proteo. 1 hit.

Sequencei

Sequence statusi: Complete.

P03007-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSTAITRQIV LDTETTGMNQ IGAHYEGHKI IEIGAVEVVN RRLTGNNFHV
60 70 80 90 100
YLKPDRLVDP EAFGVHGIAD EFLLDKPTFA EVADEFMDYI RGAELVIHNA
110 120 130 140 150
AFDIGFMDYE FSLLKRDIPK TNTFCKVTDS LAVARKMFPG KRNSLDALCA
160 170 180 190 200
RYEIDNSKRT LHGALLDAQI LAEVYLAMTG GQTSMAFAME GETQQQQGEA
210 220 230 240
TIQRIVRQAS KLRVVFATDE EIAAHEARLD LVQKKGGSCL WRA
Length:243
Mass (Da):27,099
Last modified:April 1, 1988 - v1
Checksum:i4211C9A00744964F
GO

Sequence cautioni

The sequence AAB08637.1 differs from that shown. Reason: Erroneous initiation. Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X04027 Genomic DNA. Translation: CAA27661.1.
K00985 Genomic DNA. Translation: AAA24564.1.
U70214 Genomic DNA. Translation: AAB08637.1. Different initiation.
U00096 Genomic DNA. Translation: AAC73320.1.
AP009048 Genomic DNA. Translation: BAA77886.1.
PIRiA64746. IQECQ.
RefSeqiNP_414751.1. NC_000913.3.

Genome annotation databases

EnsemblBacteriaiAAC73320; AAC73320; b0215.
BAA77886; BAA77886; BAA77886.
GeneIDi946441.
KEGGiecj:Y75_p0206.
eco:b0215.
PATRICi32115543. VBIEscCol129921_0217.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X04027 Genomic DNA. Translation: CAA27661.1.
K00985 Genomic DNA. Translation: AAA24564.1.
U70214 Genomic DNA. Translation: AAB08637.1. Different initiation.
U00096 Genomic DNA. Translation: AAC73320.1.
AP009048 Genomic DNA. Translation: BAA77886.1.
PIRiA64746. IQECQ.
RefSeqiNP_414751.1. NC_000913.3.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1J53X-ray1.80A1-186[»]
1J54X-ray1.70A1-186[»]
1MGZmodel-A1-186[»]
2GUIX-ray1.60A2-186[»]
2IDOX-ray2.10A/C1-186[»]
2XY8NMR-A1-186[»]
4GX8X-ray1.70A/B/C/D209-243[»]
4GX9X-ray2.15A/B/C/D200-243[»]
ProteinModelPortaliP03007.
SMRiP03007. Positions 5-180, 210-243.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-9462N.
IntActiP03007. 28 interactions.
MINTiMINT-1222832.
STRINGi511145.b0215.

Chemistry

ChEMBLiCHEMBL1075047.

2D gel databases

SWISS-2DPAGEP03007.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC73320; AAC73320; b0215.
BAA77886; BAA77886; BAA77886.
GeneIDi946441.
KEGGiecj:Y75_p0206.
eco:b0215.
PATRICi32115543. VBIEscCol129921_0217.

Organism-specific databases

EchoBASEiEB0239.
EcoGeneiEG10243. dnaQ.

Phylogenomic databases

eggNOGiCOG0847.
HOGENOMiHOG000258616.
InParanoidiP03007.
KOiK02342.
OMAiFHVYLNP.
OrthoDBiEOG696BTR.
PhylomeDBiP03007.

Enzyme and pathway databases

BioCyciEcoCyc:EG10243-MONOMER.
ECOL316407:JW0205-MONOMER.
MetaCyc:EG10243-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP03007.
PROiP03007.

Gene expression databases

GenevestigatoriP03007.

Family and domain databases

Gene3Di3.30.420.10. 1 hit.
InterProiIPR006054. DnaQ.
IPR006309. DnaQ_proteo.
IPR006055. Exonuclease.
IPR013520. Exonuclease_RNaseT/DNA_pol3.
IPR012337. RNaseH-like_dom.
[Graphical view]
PfamiPF00929. RNase_T. 1 hit.
[Graphical view]
SMARTiSM00479. EXOIII. 1 hit.
[Graphical view]
SUPFAMiSSF53098. SSF53098. 1 hit.
TIGRFAMsiTIGR00573. dnaq. 1 hit.
TIGR01406. dnaQ_proteo. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "DNA sequence and coding properties of mutD(dnaQ) a dominant Escherichia coli mutator gene."
    Cox E.C., Horner D.L.
    J. Mol. Biol. 190:113-117(1986) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "Structure and expression of the dnaQ mutator and the RNase H genes of Escherichia coli: overlap of the promoter regions."
    Maki H., Horiuchi T., Sekiguchi M.
    Proc. Natl. Acad. Sci. U.S.A. 80:7137-7141(1983) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  3. "Structure and function of dnaQ and mutD mutators of Escherichia coli."
    Takano K., Nakabeppu Y., Maki H., Horiuchi T., Sekiguchi M.
    Mol. Gen. Genet. 205:9-13(1986) [PubMed] [Europe PMC] [Abstract]
    Cited for: SEQUENCE REVISION.
  4. "Systematic sequencing of the Escherichia coli genome: analysis of the 4.0 - 6.0 min (189,987 - 281,416bp) region."
    Takemoto K., Mori H., Murayama N., Kataoka K., Yano M., Itoh T., Yamamoto Y., Inokuchi H., Miki T., Hatada E., Fukuda R., Ichihara S., Mizuno T., Makino K., Nakata A., Yura T., Sampei G., Mizobuchi K.
    Submitted (FEB-1996) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  5. "Sequence of minutes 4-25 of Escherichia coli."
    Chung E., Allen E., Araujo R., Aparicio A.M., Davis K., Duncan M., Federspiel N., Hyman R., Kalman S., Komp C., Kurdi O., Lew H., Lin D., Namath A., Oefner P., Roberts D., Schramm S., Davis R.W.
    Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  6. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  7. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  8. "Accessory protein function in the DNA polymerase III holoenzyme from E. coli."
    O'Donnell M.
    Bioessays 14:105-111(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: REVIEW.
  9. "Escherichia coli proteome analysis using the gene-protein database."
    VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.
    Electrophoresis 18:1243-1251(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY 2D-GEL.
  10. "Structural basis for proofreading during replication of the Escherichia coli chromosome."
    Hamdan S., Carr P.D., Brown S.E., Ollis D.L., Dixon N.E.
    Structure 10:535-546(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF 1-186 IN COMPLEX WITH METAL IONS AND SUBSTRATE ANALOG.

Entry informationi

Entry nameiDPO3E_ECOLI
AccessioniPrimary (citable) accession number: P03007
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: April 1, 1988
Last modified: May 27, 2015
This is version 150 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.