› 6fwk

X-ray diffraction
2.5Å resolution

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

Released:
DOI: 10.2210/pdb6fwk/pdb
PDB entry 6fwk coloured by chain, front view.
PDB entry 6fwk coloured by chain, side view.
PDB entry 6fwk coloured by chain, top view.
Source organisms:
Primary publication:
Structural consequence of the most frequently recurring cancer-associated substitution in DNA polymerase ε.
Parkash V, Kulkarni Y, Ter Beek J, Shcherbakova PV, Kamerlin SCL, Johansson E
Nat Commun 10 373 (2019)
PMID: 30670696

Function and Biology Details

Reaction catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-119926 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase epsilon catalytic subunit A Chains: A, B
Molecule details ›
Chains: A, B
Length: 1191 amino acids
Theoretical weight: 137.1 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P21951 (Residues: 1-1186; Coverage: 53%)
Gene names: DUN2, N0825, POL2, YNL262W
Sequence domains:
DNA (5'-D(P*TP*AP*AP*CP*CP*GP*CP*GP*TP*TP*(DOC))-3') Chains: C, P
Molecule details ›
Chains: C, P
Length: 11 nucleotides
Theoretical weight: 3.29 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(P*TP*CP*TP*TP*GP*AP*AP*CP*GP*CP*GP*GP*TP*TP*A)-3') Chains: D, T
Molecule details ›
Chains: D, T
Length: 15 nucleotides
Theoretical weight: 4.6 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand DTP 2 x DTP
Ligand CA 5 x CA
Ligand FE 2 x FE
1 modified residue:
Ligand DOC 2 x DOC

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-1
Spacegroup: P2
Unit cell:
a: 153.961Å b: 70.342Å c: 158.965Å
α: 90° β: 112.82° γ: 90°
R-values:
R R work R free
0.225 0.223 0.263
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

6 review citations

DNA Polymerases at the Eukaryotic Replication Fork Thirty Years after: Connection to Cancer.
Pavlov et al. (2020)
5 more

3 mentions without citation

Structural consequence of the most frequently recurring cancer-associated substitution in DNA polymerase ε.
Parkash et al. (2019)
2 more