› 3rmd

X-ray diffraction
2.98Å resolution

Crystal Structure of a replicative DNA polymerase bound to DNA containing Thymine Glycol

Released:
DOI: 10.2210/pdb3rmd/pdb
PDB entry 3rmd coloured by chain, front view.
PDB entry 3rmd coloured by chain, side view.
PDB entry 3rmd coloured by chain, top view.
Source organism: Escherichia phage RB69
Primary publication:
A crystallographic study of the role of sequence context in thymine glycol bypass by a replicative DNA polymerase serendipitously sheds light on the exonuclease complex.
Aller P, Duclos S, Wallace SS, Doublié S
J Mol Biol 412 22-34 (2011)
PMID: 21781974

Function and Biology Details

Reaction catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116831 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA-directed DNA polymerase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 906 amino acids
Theoretical weight: 105.07 KDa
Source organism: Escherichia phage RB69
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q38087 (Residues: 1-903; Coverage: 100%)
Gene name: 43
Sequence domains:
Structure domains:
DNA (5'-D(*CP*GP*TP*(CTG)P*G*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3') Chains: E, G, I, K
Molecule details ›
Chains: E, G, I, K
Length: 18 nucleotides
Theoretical weight: 5.58 KDa
Source organism: Escherichia phage RB69
Expression system: Not provided
DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*CP*AP*A)-3') Chains: F, H, J, L
Molecule details ›
Chains: F, H, J, L
Length: 15 nucleotides
Theoretical weight: 4.58 KDa
Source organism: Escherichia phage RB69
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand DTP 2 x DTP
1 modified residue:
Ligand CTG 4 x CTG

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-17A
Spacegroup: P21
Unit cell:
a: 132.837Å b: 123.025Å c: 168.775Å
α: 90° β: 95.87° γ: 90°
R-values:
R R work R free
0.22 0.22 0.275
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

3 review citations

DNA polymerase ε and its roles in genome stability.
Henninger et al. (2014)
2 more

2 mentions without citation

A crystallographic study of the role of sequence context in thymine glycol bypass by a replicative DNA polymerase serendipitously sheds light on the exonuclease complex.
Aller et al. (2011)
1 more