› 6h1v

X-ray diffraction
2.7Å resolution

The crystal structure of Pol2CORE in complex with DNA and an incoming nucleotide, carrying an Fe-S cluster

Released:
DOI: 10.2210/pdb6h1v/pdb
PDB entry 6h1v coloured by chain, front view.
PDB entry 6h1v coloured by chain, side view.
PDB entry 6h1v coloured by chain, top view.
Source organisms:
Primary publication:
Structural evidence for an essential Fe-S cluster in the catalytic core domain of DNA polymerase ϵ.
Ter Beek J, Parkash V, Bylund GO, Osterman P, Sauer-Eriksson AE, Johansson E
Nucleic Acids Res 47 5712-5722 (2019)
PMID: 30968138

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-119984 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase epsilon catalytic subunit A Chain: A
Molecule details ›
Chain: A
Length: 1187 amino acids
Theoretical weight: 136.74 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P21951 (Residues: 1-1187; 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') Chain: P
Molecule details ›
Chain: P
Length: 11 nucleotides
Theoretical weight: 3.29 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(P*AP*AP*TP*TP*GP*AP*AP*CP*GP*CP*GP*GP*TP*TP*A)-3') Chain: T
Molecule details ›
Chain: T
Length: 16 nucleotides
Theoretical weight: 4.89 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand SF4 1 x SF4
Ligand DTP 1 x DTP
Ligand MG 1 x MG
1 modified residue:
Ligand DOC 1 x DOC

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-1
Spacegroup: C2
Unit cell:
a: 148.21Å b: 70.04Å c: 149.93Å
α: 90° β: 109.43° γ: 90°
R-values:
R R work R free
0.24 0.239 0.266
Expression systems:
  • Saccharomyces cerevisiae
  • Not provided

Quick links

Citations

8 review citations

Diversity and evolution of B-family DNA polymerases.
Kazlauskas et al. (2020)
7 more

3 mentions without citation

Structural evidence for an essential Fe-S cluster in the catalytic core domain of DNA polymerase ϵ.
Ter Beek et al. (2019)
2 more