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 

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Ligand Structure Quality Assessment 


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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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase epsilon catalytic subunit AA1228Saccharomyces cerevisiae S288CMutation(s): 2 
Gene Names: POL2DUN2YNL262WN0825
EC: 2.7.7.7 (PDB Primary Data), 3.1.11 (UniProt)
UniProt
Find proteins for P21951 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P21951 
Go to UniProtKB:  P21951
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21951
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
PRIMER DNAB [auth P]11N/A
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
TEMPLATE DNAC [auth T]16N/A
Protein Feature View
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  • Reference Sequence
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

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G [auth A],
H [auth A]
2-AMINOETHANESULFONIC ACID
C2 H7 N O3 S
XOAAWQZATWQOTB-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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F [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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I [auth P],
J [auth P]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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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

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Ligand Structure Quality Assessment 



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