7R3X

The crystal structure of the L439V variant of Pol2CORE in complex with DNA and an incoming nucleotide

7R3X の概要

• エントリーDOI: 10.2210/pdb7r3x/pdb
• 分子名称: DNA polymerase epsilon catalytic subunit A, DNA Primer, DNA Template, ... (7 entities in total)
• 機能のキーワード: protein-dna complex, dna binding protein
• 由来する生物種: Saccharomyces cerevisiae (baker's yeast); 詳細
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 145408.75

構造登録者

Barbari, S.R.,Beach, A.K.,Markgren, J.G.,Parkash, V.,Johansson, E.,Shcherbakova, P.V. (登録日: 2022-02-08, 公開日: 2022-07-27, 最終更新日: 2024-11-13)

主引用文献

Barbari, S.R.,Beach, A.K.,Markgren, J.G.,Parkash, V.,Moore, E.A.,Johansson, E.,Shcherbakova, P.V.
Enhanced polymerase activity permits efficient synthesis by cancer-associated DNA polymerase ε variants at low dNTP levels.
Nucleic Acids Res., 50:8023-8040, 2022

PubMed Abstract: Amino acid substitutions in the exonuclease domain of DNA polymerase ϵ (Polϵ) cause ultramutated tumors. Studies in model organisms suggested pathogenic mechanisms distinct from a simple loss of exonuclease. These mechanisms remain unclear for most recurrent Polϵ mutations. Particularly, the highly prevalent V411L variant remained a long-standing puzzle with no detectable mutator effect in yeast despite the unequivocal association with ultramutation in cancers. Using purified four-subunit yeast Polϵ, we assessed the consequences of substitutions mimicking human V411L, S459F, F367S, L424V and D275V. While the effects on exonuclease activity vary widely, all common cancer-associated variants have increased DNA polymerase activity. Notably, the analog of Polϵ-V411L is among the strongest polymerases, and structural analysis suggests defective polymerase-to-exonuclease site switching. We further show that the V411L analog produces a robust mutator phenotype in strains that lack mismatch repair, indicating a high rate of replication errors. Lastly, unlike wild-type and exonuclease-dead Polϵ, hyperactive variants efficiently synthesize DNA at low dNTP concentrations. We propose that this characteristic could promote cancer cell survival and preferential participation of mutator polymerases in replication during metabolic stress. Our results support the notion that polymerase fitness, rather than low fidelity alone, is an important determinant of variant pathogenicity.

PubMed: 35822874
DOI: 10.1093/nar/gkac602

実験手法

X-RAY DIFFRACTION (2.46 Å)