› 4ub1

X-ray diffraction
2.34Å resolution

DNA polymerase beta product complex with a templating adenine and 8-oxodGMP, 90 s

Released:
DOI: 10.2210/pdb4ub1/pdb
PDB 4ub1 coloured by chain and viewed from the front.
PDB 4ub1 coloured by chain and viewed from the side.
PDB 4ub1 coloured by chain and viewed from the top.
Source organisms:
Primary publication:
Uncovering the polymerase-induced cytotoxicity of an oxidized nucleotide.
Freudenthal BD, Beard WA, Perera L, Shock DD, Kim T, Schlick T, Wilson SH
Nature (2014)
PMID: 25409153

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 tetramer (preferred)
Entry contents:
1 distinct polypeptide molecule
3 distinct DNA molecules
Macromolecules (4 distinct):
DNA polymerase beta Chain: A
Molecule details ›
Chain: A
Length: 335 amino acids
Theoretical weight: 38.24 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P06746 (Residues: 1-335; Coverage: 100%)
Gene name: POLB
Sequence domains:
Structure domains:
5'-D(*CP*CP*GP*AP*CP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3' Chain: T
Molecule details ›
Chain: T
Length: 16 nucleotides
Theoretical weight: 4.85 KDa
Source organism: synthetic construct
Expression system: Not provided
5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*CP*(8OG))-3' Chain: P
Molecule details ›
Chain: P
Length: 11 nucleotides
Theoretical weight: 3.41 KDa
Source organism: synthetic construct
Expression system: Not provided
5'-D(P*GP*TP*CP*GP*G)-3' Chain: D
Molecule details ›
Chain: D
Length: 5 nucleotides
Theoretical weight: 1.54 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand NA 2 x NA
1 modified residue:
Ligand 8OG 1 x 8OG

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-BM
Spacegroup: P21
Unit cell:
a: 55.131Å b: 80.8Å c: 55.462Å
α: 90° β: 109.58° γ: 90°
R-values:
R R work R free
0.228 0.222 0.277
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

23 review citations

8-Oxoguanine: from oxidative damage to epigenetic and epitranscriptional modification.
Hahm et al. (2022)
22 more

2 mentions without citation

Uncovering the polymerase-induced cytotoxicity of an oxidized nucleotide.
Freudenthal et al. (2015)
1 more