Evidence map›Paper›PMID 30670696›Full record

ArticleNature communications2019

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

Abstract read
In one paragraph

Article in Nature communications, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.

0numbers the graph read from it
0cells of the map it votes in
38citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

38 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. The proofreading mechanism of the human leading-strand DNA polymerase ε holoenzyme.Proceedings of the National Academy of Sciences of the United States of America · 2025
    Article
  5. Functions, interactions and prognostic role ofJournal of gynecologic oncology · 2025
    Article
  6. Article
  7. Review
  8. Article
  9. Clamping Pol ε to the leading strand.Nature structural & molecular biology · 2024
    Article
  10. Article
  11. Article
  12. Article
  13. Review
  14. Article
  15. Article
  16. Article
  17. Article
  18. The mismatch recognition protein MutSα promotes nascent strand degradation at stalled replication forks.Proceedings of the National Academy of Sciences of the United States of America · 2022
    Article
  19. Extrinsic proofreading.DNA repair · 2022
    Review
  20. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

6 authors.

Vimal ParkashDepartment of Medical Biochemistry and Biophysics, Umeå University, Umeå, SE-90187, Sweden.ORCID http://orcid.org/0000-0003-4365-6213
Yashraj KulkarniDepartment of Chemistry - BMC, Uppsala University, Box 576, Uppsala, S-751 23, Sweden.ORCID http://orcid.org/0000-0002-7643-9867
Josy Ter BeekDepartment of Medical Biochemistry and Biophysics, Umeå University, Umeå, SE-90187, Sweden.ORCID http://orcid.org/0000-0003-4165-9277
Polina V ShcherbakovaEppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198, USA.
Shina Caroline Lynn KamerlinDepartment of Chemistry - BMC, Uppsala University, Box 576, Uppsala, S-751 23, Sweden. lynn.kamerlin@kemi.uu.se.ORCID http://orcid.org/0000-0002-3190-1173
Erik JohanssonDepartment of Medical Biochemistry and Biophysics, Umeå University, Umeå, SE-90187, Sweden. erik.tm.johansson@umu.se.ORCID http://orcid.org/0000-0002-8526-6224

Funding

Translesion Synthesis DNA Polymerases and Genome InstabilityR01ES015869 · NIEHS · UNIVERSITY OF NEBRASKA MEDICAL CENTER · PI SHCHERBAKOVA, POLINA V · 2009 to 2023
$4.7M
NIEHS NIH HHS R01 ES015869
6 · The paper itself

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.

Indexed as

Amino Acid SequenceCarcinogenesisDNADNA-Binding ProteinsDNA Mismatch RepairDNA Polymerase IIExonucleasesHumansMolecular Dynamics SimulationMutagenesisMutationNeoplasm Recurrence, LocalNeoplasmsProtein ConformationProtein DomainsSaccharomyces cerevisiaeDNADNA-Binding ProteinsDNA Polymerase IIExonucleases

Identifiers

PMID30670696
PMCPMC6342957

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.