› 8b79

X-ray diffraction
2.65Å resolution

The crystal structure of M644G variant of DNA Pol Epsilon containing UTP in the polymerase active site

Released:
DOI: 10.2210/pdb8b79/pdb
PDB entry 8b79 coloured by chain, front view.
PDB entry 8b79 coloured by chain, side view.
PDB entry 8b79 coloured by chain, top view.
Source organisms:
Primary publication:
A sensor complements the steric gate when DNA polymerase ϵ discriminates ribonucleotides.
Parkash V, Kulkarni Y, Bylund GO, Osterman P, Kamerlin SCL, Johansson E
OpenAccess logo Nucleic Acids Res (2023)
PMID: 37819038

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-270314 (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
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P21951 (Residues: 1-1186; Coverage: 53%)
Gene names: DUN2, N0825, POL2, YNL262W
Sequence domains:
Primer DNA sequence Chains: C, P
Molecule details ›
Chains: C, P
Length: 11 nucleotides
Theoretical weight: 3.29 KDa
Source organism: synthetic construct
Expression system: Not provided
Template DNA Sequence Chains: D, T
Molecule details ›
Chains: D, T
Length: 16 nucleotides
Theoretical weight: 4.9 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand UTP 2 x UTP
Ligand CA 6 x CA
Ligand ACT 2 x ACT
1 modified residue:
Ligand DOC 2 x DOC

Experiments and Validation Details

Entry percentile scores
X-ray source: MAX IV BEAMLINE BioMAX
Spacegroup: P2
Unit cell:
a: 154.4Å b: 70.7Å c: 159.4Å
α: 90° β: 112.8° γ: 90°
R-values:
R R work R free
0.217 0.215 0.248
Expression systems:
  • Escherichia coli BL21
  • Not provided

Quick links

Citations

1 mention without citation

A sensor complements the steric gate when DNA polymerase ϵ discriminates ribonucleotides.
Parkash et al. (2023)