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P03007

- DPO3E_ECOLI

UniProt

P03007 - DPO3E_ECOLI

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
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    • History
      Entry version 146 (01 Oct 2014)
      Sequence version 1 (01 Apr 1988)
      Previous versions | rss
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    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
    5. protein binding Source: IntAct

    GO - Biological processi

    1. DNA replication proofreading Source: EcoCyc
    2. nucleic acid phosphodiester bond hydrolysis Source: GOC

    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

    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.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP03007.

    Family & Domainsi

    Phylogenomic databases

    eggNOGiCOG0847.
    HOGENOMiHOG000258616.
    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.

    P03007-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSTAITRQIV LDTETTGMNQ IGAHYEGHKI IEIGAVEVVN RRLTGNNFHV    50
    YLKPDRLVDP EAFGVHGIAD EFLLDKPTFA EVADEFMDYI RGAELVIHNA 100
    AFDIGFMDYE FSLLKRDIPK TNTFCKVTDS LAVARKMFPG KRNSLDALCA 150
    RYEIDNSKRT LHGALLDAQI LAEVYLAMTG GQTSMAFAME GETQQQQGEA 200
    TIQRIVRQAS KLRVVFATDE EIAAHEARLD LVQKKGGSCL WRA 243
    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.
    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.
    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

    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 1, 2014
    This is version 146 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