6G0A

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 

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This is version 1.2 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: https://doi.org/10.1038/s41467-018-08114-9
  • Primary Citation of Related Structures:  
    6FWK, 6G0A, 6I8A

  • 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 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.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase epsilon catalytic subunit A1,191Saccharomyces cerevisiae S288CMutation(s): 1 
Gene Names: POL2DUN2YNL262WN0825
EC: 2.7.7.7
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
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(P*TP*AP*AP*CP*CP*GP*CP*GP*TP*TP*DC)-3')B [auth P]11synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(P*TP*CP*TP*TP*GP*AP*AP*CP*GP*CP*GP*GP*TP*TP*A)-3')C [auth T]15synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 159.895α = 90
b = 67.252β = 111.5
c = 151.639γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-30
    Type: Initial release
  • Version 1.1: 2019-02-06
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-17
    Changes: Advisory, Author supporting evidence, Data collection, Database references, Derived calculations, Refinement description