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P03007

- DPO3E_ECOLI

UniProt

P03007 - DPO3E_ECOLI

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Protein

DNA polymerase III subunit epsilon

Gene

dnaQ

Organism
Escherichia coli (strain K12)
Status
Reviewed - 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

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

  1. DNA binding Source: InterPro
  2. DNA-directed DNA polymerase activity Source: UniProtKB-KW
  3. exonuclease activity Source: EcoCyc
  4. metal ion binding Source: UniProtKB-KW

GO - Biological processi

  1. DNA replication proofreading Source: EcoCyc
  2. 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: Chromosome, UP000000625: Chromosome

Organism-specific databases

EcoGeneiEG10243. dnaQ.

Subcellular locationi

GO - Cellular componenti

  1. 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 – 1610
Beta strandi20 – 234
Turni24 – 274
Beta strandi30 – 3910
Beta strandi48 – 514
Helixi60 – 667
Helixi70 – 734
Helixi79 – 9012
Beta strandi93 – 975
Helixi100 – 11314
Helixi121 – 1233
Beta strandi125 – 1295
Helixi130 – 1378
Helixi145 – 1517
Beta strandi156 – 1583
Helixi164 – 17815

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
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.
OMAiGFMDHEF.
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 [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.

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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.
YP_488512.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC73320; AAC73320; b0215.
BAA77886; BAA77886; BAA77886.
GeneIDi12933127.
946441.
KEGGiecj:Y75_p0206.
eco:b0215.
PATRICi32115543. VBIEscCol129921_0217.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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 .
PIRi A64746. IQECQ.
RefSeqi NP_414751.1. NC_000913.3.
YP_488512.1. NC_007779.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1J53 X-ray 1.80 A 1-186 [» ]
1J54 X-ray 1.70 A 1-186 [» ]
1MGZ model - A 1-186 [» ]
2GUI X-ray 1.60 A 2-186 [» ]
2IDO X-ray 2.10 A/C 1-186 [» ]
2XY8 NMR - A 1-186 [» ]
4GX8 X-ray 1.70 A/B/C/D 209-243 [» ]
4GX9 X-ray 2.15 A/B/C/D 200-243 [» ]
ProteinModelPortali P03007.
SMRi P03007. Positions 5-180, 210-243.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

DIPi DIP-9462N.
IntActi P03007. 28 interactions.
MINTi MINT-1222832.
STRINGi 511145.b0215.

Chemistry

ChEMBLi CHEMBL1075047.

2D gel databases

SWISS-2DPAGE P03007.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAC73320 ; AAC73320 ; b0215 .
BAA77886 ; BAA77886 ; BAA77886 .
GeneIDi 12933127.
946441.
KEGGi ecj:Y75_p0206.
eco:b0215.
PATRICi 32115543. VBIEscCol129921_0217.

Organism-specific databases

EchoBASEi EB0239.
EcoGenei EG10243. dnaQ.

Phylogenomic databases

eggNOGi COG0847.
HOGENOMi HOG000258616.
InParanoidi P03007.
KOi K02342.
OMAi GFMDHEF.
OrthoDBi EOG696BTR.
PhylomeDBi P03007.

Enzyme and pathway databases

BioCyci EcoCyc:EG10243-MONOMER.
ECOL316407:JW0205-MONOMER.
MetaCyc:EG10243-MONOMER.

Miscellaneous databases

EvolutionaryTracei P03007.
PROi P03007.

Gene expression databases

Genevestigatori P03007.

Family and domain databases

Gene3Di 3.30.420.10. 1 hit.
InterProi IPR006054. DnaQ.
IPR006309. DnaQ_proteo.
IPR006055. Exonuclease.
IPR013520. Exonuclease_RNaseT/DNA_pol3.
IPR012337. RNaseH-like_dom.
[Graphical view ]
Pfami PF00929. RNase_T. 1 hit.
[Graphical view ]
SMARTi SM00479. EXOIII. 1 hit.
[Graphical view ]
SUPFAMi SSF53098. SSF53098. 1 hit.
TIGRFAMsi TIGR00573. dnaq. 1 hit.
TIGR01406. dnaQ_proteo. 1 hit.
ProtoNeti Search...

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: October 29, 2014
This is version 147 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