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Structure of the high fidelity DNA polymerase I with an oxidative formamidopyrimidine-dG DNA lesion -dA basepair in the post-insertion site.

X-ray diffraction
2.1Å resolution
PDB entry 4b9u coloured by chain, front view.
PDB entry 4b9u coloured by chain, side view.
PDB entry 4b9u coloured by chain, top view.
Source organism: Geobacillus stearothermophilus
Assembly composition:
hetero trimer (preferred)
Entry contents: 1 distinct polypeptide molecule
2 distinct DNA molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: DNA polymerase I and DNA
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Multimeric state: hetero trimer
Accessible surface area: 28447.42 Å2
Buried surface area: 6147.82 Å2
Dissociation area: 1,522.15 Å2
Dissociation energy (ΔGdiss): 23.42 kcal/mol
Dissociation entropy (TΔSdiss): 10.79 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-117247

Macromolecules

DNA polymerase I
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
Pfam: DNA polymerase family A
InterPro:
CATH:
DNA polymerase I in PDB entry 4b9u, assembly 1, front view.
DNA polymerase I in PDB entry 4b9u, assembly 1, side view.
DNA polymerase I in PDB entry 4b9u, assembly 1, top view.
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DNA chain B
Name: 5'-D(*GP*CP*CP*TP*GP*AP*CP*TP*CP*GP*AP)-3'
Representative chains: B
Source organism: Geobacillus stearothermophilus [1422]
Expression system: Not provided
Length: 11 nucleotides
Theoretical weight: 3.33 KDa
5'-D(*GP*CP*CP*TP*GP*AP*CP*TP*CP*GP*AP)-3' in PDB entry 4b9u, assembly 1, front view.
5'-D(*GP*CP*CP*TP*GP*AP*CP*TP*CP*GP*AP)-3' in PDB entry 4b9u, assembly 1, side view.
5'-D(*GP*CP*CP*TP*GP*AP*CP*TP*CP*GP*AP)-3' in PDB entry 4b9u, assembly 1, top view.
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DNA chain C
Name: 5'-D(*CP*AP*AP*FOXP*CP*GP*AP*GP*TP*CP*AP*GP*GP*CP*TP)-3'
Representative chains: C
Source organism: Geobacillus stearothermophilus [1422]
Expression system: Not provided
Length: 15 nucleotides
Theoretical weight: 4.64 KDa
5'-D(*CP*AP*AP*FOXP*CP*GP*AP*GP*TP*CP*AP*GP*GP*CP*TP)-3' in PDB entry 4b9u, assembly 1, front view.
5'-D(*CP*AP*AP*FOXP*CP*GP*AP*GP*TP*CP*AP*GP*GP*CP*TP)-3' in PDB entry 4b9u, assembly 1, side view.
5'-D(*CP*AP*AP*FOXP*CP*GP*AP*GP*TP*CP*AP*GP*GP*CP*TP)-3' in PDB entry 4b9u, assembly 1, top view.
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