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› 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
Model geometry
Fit model/data
PDB entry 4ub1 coloured by chain, front view.
PDB entry 4ub1 coloured by chain, side view.
PDB entry 4ub1 coloured by chain, top view.
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
OpenAccess logo Nature 517 635-9 (2015)
PMID: 25409153

Function and Biology Details

Reactions catalysed: 
DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) +diphosphate.
2'-deoxyribonucleotide-(2'-deoxyribose 5'-phosphate)-2'-deoxyribonucleotide-DNA = a 3'-end 2'-deoxyribonucleotide-(2,3-dehydro-2,3-deoxyribose 5'-phosphate)-DNA + a 5'-end 5'-phospho-2'-deoxyribonucleoside-DNA + H(+).
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-118192 (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
5'-D(P*GP*TP*CP*GP*G)-3' Chain: D

Ligands and Environments

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

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
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

26 review citations

Oxidative Stress.
Sies et al. (2017)
25 more

2 mentions without citation

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