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

Vimal Parkash, Yashraj Kulkarni, Josy ter Beek, Polina V. Shcherbakova, Shina Caroline Lynn Kamerlin, Erik Johansson

Research output: Contribution to journalArticle

3 Citations (Scopus)

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.

Original languageEnglish (US)
Article number373
JournalNature communications
Volume10
Issue number1
DOIs
StatePublished - Dec 1 2019

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Exonucleases
DNA-Directed DNA Polymerase
Substitution reactions
deoxyribonucleic acid
cancer
substitutes
disrupting
Neoplasms
genome
yeast
mutations
deactivation
molecular dynamics
proteins
crystal structure
Genomic Instability
DNA
Molecular Dynamics Simulation
Yeast
Molecular dynamics

ASJC Scopus subject areas

  • Chemistry(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Physics and Astronomy(all)

Cite this

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; Johansson, Erik.

In: Nature communications, Vol. 10, No. 1, 373, 01.12.2019.

Research output: Contribution to journalArticle

Parkash, Vimal ; Kulkarni, Yashraj ; ter Beek, Josy ; Shcherbakova, Polina V. ; Kamerlin, Shina Caroline Lynn ; Johansson, Erik. / Structural consequence of the most frequently recurring cancer-associated substitution in DNA polymerase ε. In: Nature communications. 2019 ; Vol. 10, No. 1.
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