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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)DescriptionActionsGraphical viewLength
Metal bindingi12Divalent metal cation 1; catalytic1
Metal bindingi12Divalent metal cation 2; catalytic1
Binding sitei12Substrate1
Metal bindingi14Divalent metal cation 1; catalytic1
Binding sitei14Substrate1
Binding sitei61Substrate1
Binding sitei66Substrate1
Active sitei162Proton acceptor1
Metal bindingi167Divalent metal cation 1; catalytic1
Binding sitei167Substrate1

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
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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 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...

Pathology & Biotechi

Chemistry databases

ChEMBLiCHEMBL1075047.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001054831 – 243DNA polymerase III subunit epsilonAdd BLAST243

Proteomic databases

PaxDbiP03007.
PRIDEiP03007.

2D gel databases

SWISS-2DPAGEP03007.

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

BioGridi4262121. 63 interactors.
DIPiDIP-9462N.
IntActiP03007. 28 interactors.
MINTiMINT-1222832.
STRINGi511145.b0215.

Structurei

Secondary structure

1243
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi7 – 16Combined sources10
Beta strandi20 – 23Combined sources4
Turni24 – 27Combined sources4
Beta strandi30 – 39Combined sources10
Beta strandi48 – 51Combined sources4
Helixi60 – 66Combined sources7
Helixi70 – 73Combined sources4
Helixi79 – 90Combined sources12
Beta strandi93 – 97Combined sources5
Helixi100 – 113Combined sources14
Helixi121 – 123Combined sources3
Beta strandi125 – 129Combined sources5
Helixi130 – 137Combined sources8
Helixi145 – 151Combined sources7
Beta strandi156 – 158Combined sources3
Helixi164 – 178Combined sources15

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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[»]
5FKUelectron microscopy8.34D1-243[»]
5FKVelectron microscopy8.00D1-243[»]
5FKWelectron microscopy7.30D1-243[»]
ProteinModelPortaliP03007.
SMRiP03007.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP03007.

Family & Domainsi

Phylogenomic databases

eggNOGiENOG4107RZZ. Bacteria.
COG0847. LUCA.
HOGENOMiHOG000258616.
InParanoidiP03007.
KOiK02342.
OMAiFHVYLNP.
PhylomeDBiP03007.

Family and domain databases

CDDicd06131. DNA_pol_III_epsilon_Ecoli_like. 1 hit.
Gene3Di3.30.420.10. 1 hit.
InterProiIPR006054. DnaQ.
IPR006309. DnaQ_proteo.
IPR013520. Exonuclease_RNaseT/DNA_pol3.
IPR012337. RNaseH-like_dom.
[Graphical view]
PANTHERiPTHR30231:SF0. PTHR30231:SF0. 1 hit.
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 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:JW0205.
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
PDB 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[»]
5FKUelectron microscopy8.34D1-243[»]
5FKVelectron microscopy8.00D1-243[»]
5FKWelectron microscopy7.30D1-243[»]
ProteinModelPortaliP03007.
SMRiP03007.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4262121. 63 interactors.
DIPiDIP-9462N.
IntActiP03007. 28 interactors.
MINTiMINT-1222832.
STRINGi511145.b0215.

Chemistry databases

ChEMBLiCHEMBL1075047.

2D gel databases

SWISS-2DPAGEP03007.

Proteomic databases

PaxDbiP03007.
PRIDEiP03007.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC73320; AAC73320; b0215.
BAA77886; BAA77886; BAA77886.
GeneIDi946441.
KEGGiecj:JW0205.
eco:b0215.
PATRICi32115543. VBIEscCol129921_0217.

Organism-specific databases

EchoBASEiEB0239.
EcoGeneiEG10243. dnaQ.

Phylogenomic databases

eggNOGiENOG4107RZZ. Bacteria.
COG0847. LUCA.
HOGENOMiHOG000258616.
InParanoidiP03007.
KOiK02342.
OMAiFHVYLNP.
PhylomeDBiP03007.

Enzyme and pathway databases

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

Miscellaneous databases

EvolutionaryTraceiP03007.
PROiP03007.

Family and domain databases

CDDicd06131. DNA_pol_III_epsilon_Ecoli_like. 1 hit.
Gene3Di3.30.420.10. 1 hit.
InterProiIPR006054. DnaQ.
IPR006309. DnaQ_proteo.
IPR013520. Exonuclease_RNaseT/DNA_pol3.
IPR012337. RNaseH-like_dom.
[Graphical view]
PANTHERiPTHR30231:SF0. PTHR30231:SF0. 1 hit.
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...

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: November 2, 2016
This is version 161 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

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 one 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.