› 6us5

X-ray diffraction
2.25Å resolution

DNA polymerase I Large Fragment from Bacillus stearothermophilus with DNA template, 3'-amino primer, dGpNHpp analog, and Mn2+

Released:
DOI: 10.2210/pdb6us5/pdb
PDB entry 6us5 coloured by chain, front view.
PDB entry 6us5 coloured by chain, side view.
PDB entry 6us5 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-113001 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase I Chains: A, D
Molecule details ›
Chains: A, D
Length: 579 amino acids
Theoretical weight: 66.07 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))-3') Chains: B, E
Molecule details ›
Chains: B, E
Length: 9 nucleotides
Theoretical weight: 2.74 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*CP*AP*CP*GP*CP*TP*GP*AP*TP*CP*GP*CP*A)-3') Chains: C, F
Molecule details ›
Chains: C, F
Length: 13 nucleotides
Theoretical weight: 3.94 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand XG4 2 x XG4
Ligand MN 2 x MN
Ligand SO4 7 x SO4
1 modified residue:
Ligand C42 2 x C42

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.2.2
Spacegroup: P212121
Unit cell:
a: 93.761Å b: 108.805Å c: 149.969Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.227 0.224 0.278
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)