6FWK

The crystal structure of Pol2CORE-M644G in complex with DNA and an incoming nucleotide

Summary for 6FWK

• Entry DOI: 10.2210/pdb6fwk/pdb
• Descriptor: DNA polymerase epsilon catalytic subunit A, DNA (5'-D(P*TP*AP*AP*CP*CP*GP*CP*GP*TP*TP*(DOC))-3'), DNA (5'-D(P*TP*CP*TP*TP*GP*AP*AP*CP*GP*CP*GP*GP*TP*TP*A)-3'), ... (7 entities in total)
• Functional Keywords: pol epsilon, m644g, dna, complex, dna binding protein
• Biological source: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast); More
• Total number of polymer chains: 6
• Total formula weight: 291283.69

Authors

Parkash, V.,Johansson, E. (deposition date: 2018-03-06, release date: 2019-01-30, Last modification date: 2024-05-08)

Primary citation

Parkash, V.,Kulkarni, Y.,Ter Beek, J.,Shcherbakova, P.V.,Kamerlin, S.C.L.,Johansson, E.
Structural consequence of the most frequently recurring cancer-associated substitution in DNA polymerase epsilon.
Nat Commun, 10:373-373, 2019

PubMed 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.

PubMed: 30670696
DOI: 10.1038/s41467-018-08114-9

Experimental method

X-RAY DIFFRACTION (2.503 Å)