4M8O

TERNARY COMPLEX OF DNA POLYMERASE EPSILON WITH AN INCOMING dATP

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.183 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Structural basis for processive DNA synthesis by yeast DNA polymerase epsilon.

Hogg, M., Osterman, P., Bylund, G.O., Ganai, R.A., Lundstrom, E.B., Sauer-Eriksson, A.E., Johansson, E.

(2014) Nat Struct Mol Biol 21: 49-55

  • DOI: 10.1038/nsmb.2712
  • Primary Citation of Related Structures:  
    4M8O

  • PubMed Abstract: 

    • DNA polymerase ɛ (Pol ɛ) is a high-fidelity polymerase that has been shown to participate in leading-strand synthesis during DNA replication in eukaryotic cells. We present here a ternary structure of the catalytic core of Pol ɛ (142 kDa) from Saccharomyces cerevisiae in complex with DNA and an incoming nucleotide ...

    DNA polymerase ɛ (Pol ɛ) is a high-fidelity polymerase that has been shown to participate in leading-strand synthesis during DNA replication in eukaryotic cells. We present here a ternary structure of the catalytic core of Pol ɛ (142 kDa) from Saccharomyces cerevisiae in complex with DNA and an incoming nucleotide. This structure provides information about the selection of the correct nucleotide and the positions of amino acids that might be critical for proofreading activity. Pol ɛ has the highest fidelity among B-family polymerases despite the absence of an extended β-hairpin loop that is required for high-fidelity replication by other B-family polymerases. Moreover, the catalytic core has a new domain that allows Pol ɛ to encircle the nascent double-stranded DNA. Altogether, the structure provides an explanation for the high processivity and high fidelity of leading-strand DNA synthesis in eukaryotes.

    Organizational Affiliation: 

    Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden.



Macromolecules

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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase epsilon catalytic subunit AA1228Saccharomyces cerevisiae S288CMutation(s): 2 
Gene Names: POL2, DUN2, YNL262W, N0825
EC: 2.7.7.7 (PDB Primary Data), 3.1.11 (UniProt)
Find proteins for P21951 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P21951 
Go to UniProtKB:  P21951
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    PRIMER DNAB [auth P]11N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      TEMPLATE DNAC [auth T]16N/A
      Small Molecules
      Ligands 5 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      DTP
      Query on DTP
      Download Ideal Coordinates CCD File 
      		 D [auth A]2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
      C10 H16 N5 O12 P3
      SUYVUBYJARFZHO-RRKCRQDMSA-N      		 Ligand Interaction
      TAU
      Query on TAU
      Download Ideal Coordinates CCD File 
      		 G [auth A], H [auth A]2-AMINOETHANESULFONIC ACID
      C2 H7 N O3 S
      XOAAWQZATWQOTB-UHFFFAOYSA-N      		 Ligand Interaction
      ZN
      Query on ZN
      Download Ideal Coordinates CCD File 
      		 F [auth A]ZINC ION
      Zn
      PTFCDOFLOPIGGS-UHFFFAOYSA-N      		 Ligand Interaction
      CL
      Query on CL
      Download Ideal Coordinates CCD File 
      		 I [auth P], J [auth P]CHLORIDE ION
      Cl
      VEXZGXHMUGYJMC-UHFFFAOYSA-M      		 Ligand Interaction
      MG
      Query on MG
      Download Ideal Coordinates CCD File 
      		 E [auth A]MAGNESIUM ION
      Mg
      JLVVSXFLKOJNIY-UHFFFAOYSA-N      		 Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.20 Å
      • R-Value Free: 0.237 
      • R-Value Work: 0.180 
      • R-Value Observed: 0.183 
      • Space Group: C 1 2 1
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 148.495α = 90
      b = 68.919β = 109.5
      c = 149.852γ = 90
      Software Package:
      Software NamePurpose
      DNAdata collection
      PHASERphasing
      REFMACrefinement
      XDSdata reduction
      SCALAdata scaling

      Structure Validation

      View Full Validation Report


      View more in-depth experimental data

      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2013-11-27
        Type: Initial release
      • Version 1.1: 2013-12-11
        Changes: Database references
      • Version 1.2: 2014-03-19
        Changes: Database references
      • Version 1.3: 2017-01-11
        Changes: Other