4M8O

TERNARY COMPLEX OF DNA POLYMERASE EPSILON WITH AN INCOMING dATP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.180 

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

  • 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 Saccha ...

    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.,Department of Chemistry, Umeå University, Umeå, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase epsilon catalytic subunit A
A
1228Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 2 
Gene Names: POL2 (DUN2)
EC: 2.7.7.7
Find proteins for P21951 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P21951
Entity ID: 2
MoleculeChainsLengthOrganism
PRIMER DNAP11N/A
Entity ID: 3
MoleculeChainsLengthOrganism
TEMPLATE DNAT16N/A
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DTP
Query on DTP

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A
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
C10 H16 N5 O12 P3
SUYVUBYJARFZHO-RRKCRQDMSA-N
 Ligand Interaction
ZN
Query on ZN

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A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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P
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
TAU
Query on TAU

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A
2-AMINOETHANESULFONIC ACID
C2 H7 N O3 S
XOAAWQZATWQOTB-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
C38
Query on C38
P, T
DNA LINKINGC9 H13 I N3 O7 PDC
DOC
Query on DOC
P
DNA LINKINGC9 H14 N3 O6 PDC
5IU
Query on 5IU
P, T
DNA LINKINGC9 H12 I N2 O8 PDU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.180 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 148.495α = 90.00
b = 68.919β = 109.50
c = 149.852γ = 90.00
Software Package:
Software NamePurpose
DNAdata collection
REFMACrefinement
PHASERphasing
SCALAdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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