6FWK

The crystal structure of Pol2CORE-M644G in complex with DNA and an incoming nucleotide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural consequence of the most frequently recurring cancer-associated substitution in DNA polymerase epsilon.

Parkash, V.Kulkarni, Y.Ter Beek, J.Shcherbakova, P.V.Kamerlin, S.C.L.Johansson, E.

(2019) Nat Commun 10: 373-373

  • DOI: 10.1038/s41467-018-08114-9
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The most frequently recurring cancer-associated DNA polymerase ε (Pol ε) mutation is a P286R substitution in the exonuclease domain. While originally proposed to increase genome instability by disrupting exonucleolytic proofreading, the P286R variant ...

    The most frequently recurring cancer-associated DNA polymerase ε (Pol ε) mutation is a P286R substitution in the exonuclease domain. While originally proposed to increase genome instability by disrupting exonucleolytic proofreading, the P286R variant was later found to be significantly more pathogenic than Pol ε proofreading deficiency per se. The mechanisms underlying its stronger impact remained unclear. Here we report the crystal structure of the yeast orthologue, Pol ε-P301R, complexed with DNA and an incoming dNTP. Structural changes in the protein are confined to the exonuclease domain, with R301 pointing towards the exonuclease site. Molecular dynamics simulations suggest that R301 interferes with DNA binding to the exonuclease site, an outcome not observed with the exonuclease-inactive Pol ε-D290A,E292A variant lacking the catalytic residues. These results reveal a distinct mechanism of exonuclease inactivation by the P301R substitution and a likely basis for its dramatically higher mutagenic and tumorigenic effects.


    Organizational Affiliation

    Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, SE-90187, Sweden. erik.tm.johansson@umu.se.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase epsilon catalytic subunit A
A, B
1191Saccharomyces cerevisiae S288CMutation(s): 1 
Gene Names: POL2DUN2YNL262WN0825
EC: 2.7.7.7 (PDB Primary Data), 3.1.11 (UniProt)
Find proteins for P21951 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P21951
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(P*TP*AP*AP*CP*CP*GP*CP*GP*TP*TP*(DOC))-3')C, P11synthetic construct
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(P*TP*CP*TP*TP*GP*AP*AP*CP*GP*CP*GP*GP*TP*TP*A)-3')D, T15synthetic construct
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DTP
Query on DTP

Download CCD File 
A, B
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
C10 H16 N5 O12 P3
SUYVUBYJARFZHO-RRKCRQDMSA-N
 Ligand Interaction
FE
Query on FE

Download CCD File 
A, B
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 
  • Space Group: P 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 153.961α = 90
b = 70.342β = 112.82
c = 158.965γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden--
CancerfondenSweden--
Knut and Alice Wallenberg FoundationSweden--

Revision History 

  • Version 1.0: 2019-01-30
    Type: Initial release
  • Version 1.1: 2019-02-06
    Changes: Data collection, Database references