PDBsum entry 6g0a

DNA binding protein

PDB id: 6g0a

Contents

Protein chain

1104 a.a.

DNA/RNA

Ligands

DTP

Metals

_FE

_CA ×2

Waters ×15

PDB id:

6g0a

Name:

DNA binding protein

Title:

The crystal structure of the pol2 catalytic domain of DNA polymerase epsilon carrying a p301r substitution.

Structure:

DNA polymerase epsilon catalytic subunit a. Chain: a. Synonym: DNA polymerase ii subunit a. Engineered: yes. Mutation: yes. DNA (5'-d(p Tp Ap Ap Cp Cp Gp Cp Gp Tp Tp Dc)-3'). Chain: p. Engineered: yes. DNA (5'-d(p Tp Cp Tp Tp Gp Ap Ap Cp Gp Cp Gp Gp Tp Tp A)-

Source:

Saccharomyces cerevisiae (strain atcc 204508 / s288c). Organism_taxid: 559292. Gene: pol2, dun2, ynl262w, n0825. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Synthetic: yes. Synthetic construct. Organism_taxid: 32630.

Resolution:

2.62Å R-factor: 0.226 R-free: 0.265

Authors:

V.Parkash,E.Johansson

Key ref:

V.Parkash et al. (2019). Structural consequence of the most frequently recurring cancer-associated substitution in DNA polymerase ε. Nat Commun, 10, 373. PubMed id: 30670696 DOI: 10.1038/s41467-018-08114-9

Date:

16-Mar-18 Release date: 30-Jan-19

Protein chain

P21951  (DPOE_YEAST) -  DNA polymerase epsilon catalytic subunit A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 2222 a.a.

Struc: 1104 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DNA/RNA chains

T-A-A-C-C-G-C-G-T-T-DOC 11 bases

T-C-T-T-G-A-A-C-G-C-G-G-T-T-A 15 bases

Enzyme reactions

• Enzyme class 2: E.C.2.7.7.7 - DNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
• Enzyme class 3: E.C.3.1.11.- - ?????

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1038/s41467-018-08114-9

Nat Commun 10:373 (2019)

PubMed id: 30670696

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

V.Parkash, Y.Kulkarni, J.Ter Beek, P.V.Shcherbakova, S.C.L.Kamerlin, E.Johansson.

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.