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Protein

DNA polymerase III subunit epsilon

Gene

dnaQ

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: -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 (PubMed:6340117). Contacts both the beta sliding clamp (dnaN) and the polymerase subunit (dnaE), stabilizing their interaction (PubMed:26499492).2 Publications

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

  • 3'-5' exonuclease activity Source: GO_Central
  • 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

Keywordsi

Molecular functionDNA-directed DNA polymerase, Exonuclease, Hydrolase, Nuclease, Nucleotidyltransferase, Transferase
Biological processDNA replication
LigandMagnesium, Manganese, Metal-binding

Enzyme and pathway databases

BioCyciEcoCyc:EG10243-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

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi183 – 187TSMAF → LSLPL: Increases binding to beta sliding clamp (dnaN), increases stability of enzyme complex. 1 Publication5

Chemistry databases

ChEMBLiCHEMBL1075047
DrugBankiDB01643 Thymidine-5'-Phosphate

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-2DPAGEiP03007

Interactioni

Subunit structurei

In a ternary complex this subunit contacts both the beta sliding clamp (dnaN) and the polymerase subunit (dnaE) (PubMed:26499492). The DNA polymerase III holoenzyme complex contains at least 10 different subunits 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 (PubMed:6340117). The polymerase is tethered to the template via the dimeric beta sliding clamp processivity factor. The clamp loader (also called gamma complex) assembles the beta sliding clamp onto the primed template and plays a central role in the organization and communication at the replication fork. The clamp-loading complex contains delta, delta', psi and chi, and 3 copies of either or both of two different DnaX proteins, gamma and tau. The DNA replisome complex has a single clamp loader (3 tau and 1 each of delta, delta', psi and chi subunits) which binds 3 Pol III cores (1 core on the leading strand and 2 on the lagging strand) each with a beta sliding clamp dimer. Additional proteins in the replisome are other copies of gamma, psi and chi, Ssb, DNA helicase and RNA primase (PubMed:20413500, PubMed:22157955).5 Publications

Binary interactionsi

Protein-protein interaction databases

BioGridi4262121, 73 interactors
ComplexPortaliCPX-1925 DNA polymerase III proofreading complex
DIPiDIP-9462N
IntActiP03007, 30 interactors
MINTiP03007
STRINGi316385.ECDH10B_0196

Structurei

Secondary structure

1243
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliP03007
SMRiP03007
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP03007

Family & Domainsi

Phylogenomic databases

eggNOGiENOG4107RZZ Bacteria
COG0847 LUCA
HOGENOMiHOG000258616
InParanoidiP03007
KOiK02342
PhylomeDBiP03007

Family and domain databases

CDDicd06131 DNA_pol_III_epsilon_Ecoli_like, 1 hit
Gene3Di3.30.420.10, 1 hit
InterProiView protein in InterPro
IPR006054 DnaQ
IPR006309 DnaQ_proteo
IPR013520 Exonuclease_RNaseT/DNA_pol3
IPR012337 RNaseH-like_sf
IPR036397 RNaseH_sf
PfamiView protein in Pfam
PF00929 RNase_T, 1 hit
SMARTiView protein in SMART
SM00479 EXOIII, 1 hit
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. Translation N-terminally shortened.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
WP_001340895.1, NZ_LN832404.1

Genome annotation databases

EnsemblBacteriaiAAC73320; AAC73320; b0215
BAA77886; BAA77886; BAA77886
GeneIDi946441
KEGGiecj:JW0205
eco:b0215
PATRICifig|511145.12.peg.217

Similar proteinsi

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
WP_001340895.1, NZ_LN832404.1

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[»]
5M1Selectron microscopy6.70D1-243[»]
ProteinModelPortaliP03007
SMRiP03007
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4262121, 73 interactors
ComplexPortaliCPX-1925 DNA polymerase III proofreading complex
DIPiDIP-9462N
IntActiP03007, 30 interactors
MINTiP03007
STRINGi316385.ECDH10B_0196

Chemistry databases

ChEMBLiCHEMBL1075047
DrugBankiDB01643 Thymidine-5'-Phosphate

2D gel databases

SWISS-2DPAGEiP03007

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
PATRICifig|511145.12.peg.217

Organism-specific databases

EchoBASEiEB0239
EcoGeneiEG10243 dnaQ

Phylogenomic databases

eggNOGiENOG4107RZZ Bacteria
COG0847 LUCA
HOGENOMiHOG000258616
InParanoidiP03007
KOiK02342
PhylomeDBiP03007

Enzyme and pathway databases

BioCyciEcoCyc:EG10243-MONOMER
MetaCyc:EG10243-MONOMER

Miscellaneous databases

EvolutionaryTraceiP03007
PROiPR:P03007

Family and domain databases

CDDicd06131 DNA_pol_III_epsilon_Ecoli_like, 1 hit
Gene3Di3.30.420.10, 1 hit
InterProiView protein in InterPro
IPR006054 DnaQ
IPR006309 DnaQ_proteo
IPR013520 Exonuclease_RNaseT/DNA_pol3
IPR012337 RNaseH-like_sf
IPR036397 RNaseH_sf
PfamiView protein in Pfam
PF00929 RNase_T, 1 hit
SMARTiView protein in SMART
SM00479 EXOIII, 1 hit
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 historyiIntegrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: April 1, 1988
Last modified: November 7, 2018
This is version 173 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
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Main funding by: National Institutes of Health

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