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

Parkash, Vimal ; Kulkarni, Yashraj ; Ter Beek, Josy ; Shcherbakova, Polina V ; Kamerlin, Shina Caroline Lynn LU orcid and Johansson, Erik (2019) In Nature Communications 10(1).
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... (More)

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.

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author
; ; ; ; and
publishing date
type
Contribution to journal
publication status
published
keywords
Amino Acid Sequence, Carcinogenesis, DNA, DNA Mismatch Repair, DNA Polymerase II/genetics, DNA-Binding Proteins/genetics, Exonucleases/genetics, Humans, Molecular Dynamics Simulation, Mutagenesis, Mutation, Neoplasm Recurrence, Local/genetics, Neoplasms/genetics, Protein Conformation, Protein Domains/genetics, Saccharomyces cerevisiae/genetics, Sequence Alignment
in
Nature Communications
volume
10
issue
1
article number
373
publisher
Nature Publishing Group
external identifiers
  • pmid:30670696
  • scopus:85060366876
ISSN
2041-1723
DOI
10.1038/s41467-018-08114-9
language
English
LU publication?
no
id
1883efc6-4c31-4399-9252-7167c94b7f6d
date added to LUP
2025-01-11 20:28:47
date last changed
2025-04-20 11:47:34
@article{1883efc6-4c31-4399-9252-7167c94b7f6d,
  abstract     = {{<p>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.</p>}},
  author       = {{Parkash, Vimal and Kulkarni, Yashraj and Ter Beek, Josy and Shcherbakova, Polina V and Kamerlin, Shina Caroline Lynn and Johansson, Erik}},
  issn         = {{2041-1723}},
  keywords     = {{Amino Acid Sequence; Carcinogenesis; DNA; DNA Mismatch Repair; DNA Polymerase II/genetics; DNA-Binding Proteins/genetics; Exonucleases/genetics; Humans; Molecular Dynamics Simulation; Mutagenesis; Mutation; Neoplasm Recurrence, Local/genetics; Neoplasms/genetics; Protein Conformation; Protein Domains/genetics; Saccharomyces cerevisiae/genetics; Sequence Alignment}},
  language     = {{eng}},
  month        = {{01}},
  number       = {{1}},
  publisher    = {{Nature Publishing Group}},
  series       = {{Nature Communications}},
  title        = {{Structural consequence of the most frequently recurring cancer-associated substitution in DNA polymerase ε}},
  url          = {{http://dx.doi.org/10.1038/s41467-018-08114-9}},
  doi          = {{10.1038/s41467-018-08114-9}},
  volume       = {{10}},
  year         = {{2019}},
}