› 4b9l

X-ray diffraction
2.05Å resolution

Structure of the high fidelity DNA polymerase I with the oxidative formamidopyrimidine-dA DNA lesion in the pre-insertion site.

Released:
DOI: 10.2210/pdb4b9l/pdb
PDB entry 4b9l coloured by chain, front view.
PDB entry 4b9l coloured by chain, side view.
PDB entry 4b9l coloured by chain, top view.
Source organism: Geobacillus stearothermophilus
Primary publication:
Unexpected non-Hoogsteen-based mutagenicity mechanism of FaPy-DNA lesions.
Gehrke TH, Lischke U, Gasteiger KL, Schneider S, Arnold S, Müller HC, Stephenson DS, Zipse H, Carell T
Nat Chem Biol 9 455-61 (2013)
PMID: 23685671

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-117242 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (4 distinct):
DNA polymerase I Chain: A
Molecule details ›
Chain: A
Length: 619 amino acids
Theoretical weight: 70.45 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: E1C9K5 (Residues: 1-580; Coverage: 100%)
Gene name: polA
Sequence domains: DNA polymerase family A
Structure domains:
5'-D(*GP*CP*CP*TP*GP*AP*CP*TP*CP*TP)-3' Chain: B
Molecule details ›
Chain: B
Length: 10 nucleotides
Theoretical weight: 3 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Not provided
5'-D(*CP*AP*GP*FAX*AP*GP*AP*GP*TP*CP*AP*GP*GP*CP*TP)-3' Chain: C
Molecule details ›
Chain: C
Length: 15 nucleotides
Theoretical weight: 4.66 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Not provided

Ligands and Environments

Carbohydrate polymer : NEW Components: GLC, FRU
Carbohydrate polymer
2 bound ligands:
Ligand MG 1 x MG
Ligand SO4 4 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P212121
Unit cell:
a: 87.528Å b: 93.265Å c: 106.107Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.19 0.189 0.226
Expression systems:
  • Escherichia coli BL21
  • Not provided

Quick links

Citations

3 review citations

Role of oxidative stress in carbon nanotube-generated health effects.
Møller et al. (2014)
2 more