› 6dsy

X-ray diffraction
1.98Å resolution

Bst DNA polymerase I post-chemistry (n+1) structure

Released:
DOI: 10.2210/pdb6dsy/pdb
PDB entry 6dsy coloured by chain, front view.
PDB entry 6dsy coloured by chain, side view.
PDB entry 6dsy coloured by chain, top view.
Source organisms:
Primary publication:
Crystal structures of DNA polymerase I capture novel intermediates in the DNA synthesis pathway.
Chim N, Jackson LN, Trinh AM, Chaput JC
Elife 7 (2018)
PMID: 30338759

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-119806 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase I Chain: A
Molecule details ›
Chain: A
Length: 580 amino acids
Theoretical weight: 66.23 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Escherichia coli
UniProt:
  • Canonical: E1C9K5 (Residues: 1-580; Coverage: 100%)
Gene name: polA
Sequence domains: DNA polymerase family A
Structure domains:
DNA (5'-D(*GP*CP*GP*AP*TP*CP*AP*CP*GP*T)-3') Chain: P
Molecule details ›
Chain: P
Length: 11 nucleotides
Theoretical weight: 3.36 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(P*GP*TP*AP*CP*GP*TP*GP*AP*TP*CP*GP*CP*A)-3') Chain: T
Molecule details ›
Chain: T
Length: 13 nucleotides
Theoretical weight: 3.99 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand MG 1 x MG
Ligand SO4 1 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.2.2
Spacegroup: P212121
Unit cell:
a: 88.199Å b: 93.751Å c: 105.846Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.204 0.203 0.255
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

7 citation in other articles

Rolling circle RNA synthesis catalyzed by RNA.
Kristoffersen et al. (2022)
6 more

3 mentions without citation

Crystal structures of a natural DNA polymerase that functions as an XNA reverse transcriptase.
Jackson et al. (2019)
2 more