6I8A

The crystal structure of the Pol2 catalytic domain of DNA polymerase epsilon carrying a P301R substitution.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.652 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.229 

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
  • Primary Citation of Related Structures:  

  • 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 Chemistry - BMC, Uppsala University, Box 576, Uppsala, S-751 23, Sweden. lynn.kamerlin@kemi.uu.se.,Department of Chemistry - BMC, Uppsala University, Box 576, Uppsala, S-751 23, Sweden.,Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198, USA.,Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, SE-90187, Sweden.,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
1190Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 1 
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 DNAP,C11synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
Template DNAT,D16synthetic construct
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DTP
Query on DTP

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

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Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

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Download CCD File 
A, B
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
DOC
Query on DOC
C, P
DNA LINKINGC9 H14 N3 O6 PDC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.652 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.229 
  • Space Group: P 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 154.466α = 90.00
b = 70.257β = 112.85
c = 159.335γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden--
Knut and Alice Wallenberg FoundationSweden2011.0042

Revision History 

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