TY - JOUR
T1 - Structural consequence of the most frequently recurring cancer-associated substitution in DNA polymerase ε
AU - Parkash, Vimal
AU - Kulkarni, Yashraj
AU - ter Beek, Josy
AU - Shcherbakova, Polina V.
AU - Kamerlin, Shina Caroline Lynn
AU - Johansson, Erik
N1 - Funding Information:
The data were collected at beamline ID 23 of the European Synchrotron Radiation Facility. This research was supported by the Knut and Alice Wallenberg foundation (Wallenberg Academy fellowship to S.C.L.K. and project grant to E.J.), the Swedish Cancer Foundation (E.J.), the Swedish Research Council (E.J.), the Sven and Lilly Lawski Foundation (J.t.B. and Y.K.), and the National Institutes of Health (grant ES015869 to P. V.S.). Finally, all simulations were performed using computational resources provided by an allocation of computing time through the Swedish National Infrastructure for Computing.
Publisher Copyright:
© 2019, The Author(s).
PY - 2019/12/1
Y1 - 2019/12/1
N2 - 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.
AB - 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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U2 - 10.1038/s41467-018-08114-9
DO - 10.1038/s41467-018-08114-9
M3 - Article
C2 - 30670696
AN - SCOPUS:85060366876
SN - 2041-1723
VL - 10
JO - Nature communications
JF - Nature communications
IS - 1
M1 - 373
ER -