› 6ur2

X-ray diffraction
2.27Å resolution

DNA polymerase I Large Fragment from Bacillus stearothermophilus with DNA template and primer containing an N3'-> P5' linkage

Released:
DOI: 10.2210/pdb6ur2/pdb
PDB entry 6ur2 coloured by chain, front view.
PDB entry 6ur2 coloured by chain, side view.
PDB entry 6ur2 coloured by chain, top view.
Source organisms:
Primary publication:
Synthesis of phosphoramidate-linked DNA by a modified DNA polymerase.
Lelyveld VS, Zhang W, Szostak JW
Proc Natl Acad Sci U S A 117 7276-7283 (2020)
PMID: 32188786

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-112998 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase I Chain: A
Molecule details ›
Chain: A
Length: 579 amino acids
Theoretical weight: 66.1 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Escherichia coli
UniProt:
  • Canonical: D9N168 (Residues: 1-579; Coverage: 100%)
Gene names: DPO1, polA
Sequence domains: DNA polymerase family A
DNA (5'-D(*GP*CP*GP*AP*TP*CP*AP*GP*(C42)P*G)-3') Chain: B
Molecule details ›
Chain: B
Length: 10 nucleotides
Theoretical weight: 3.07 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(P*AP*CP*GP*CP*TP*GP*AP*TP*CP*GP*CP*A)-3') Chain: C
Molecule details ›
Chain: C
Length: 12 nucleotides
Theoretical weight: 3.65 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

No bound ligands
1 modified residue:
Ligand C42 1 x C42

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.2.2
Spacegroup: P212121
Unit cell:
a: 85.197Å b: 93.679Å c: 107.14Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.231 0.229 0.277
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

2 review citations

Synthetic Life with Alternative Nucleic Acids as Genetic Materials.
Nie et al. (2020)
1 more

1 mention without citation

Synthesis of phosphoramidate-linked DNA by a modified DNA polymerase.
Lelyveld et al. (2020)