› 3b39

X-ray diffraction
2.35Å resolution

Structure of the DnaG primase catalytic domain bound to ssDNA

Released:
DOI: 10.2210/pdb3b39/pdb
PDB entry 3b39 coloured by chain, front view.
PDB entry 3b39 coloured by chain, side view.
PDB entry 3b39 coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Identification of a DNA primase template tracking site redefines the geometry of primer synthesis.
Corn JE, Pelton JG, Berger JM
Nat Struct Mol Biol 15 163-9 (2008)
PMID: 18193061

Function and Biology Details

Reaction catalysed: 
SsDNA + n NTP = ssDNA/pppN(pN)(n-1) hybrid + (n-1) diphosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116085 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
DNA primase Chains: A, B
Molecule details ›
Chains: A, B
Length: 322 amino acids
Theoretical weight: 36.29 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P0ABS5 (Residues: 111-429; Coverage: 55%)
Gene names: JW3038, b3066, dnaG, dnaP, parB
Sequence domains:
Structure domains:
DNA (5'-D(*DCP*DAP*DAP*DAP*DGP*DCP*DCP*DAP*DAP*DAP*DAP*DGP*DGP*DAP*DC)-3') Chains: C, D
Molecule details ›
Chains: C, D
Length: 15 nucleotides
Theoretical weight: 4.61 KDa
Source organism: Escherichia coli K-12
Expression system: Not provided

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.3.1
Spacegroup: P62
Unit cell:
a: 136.829Å b: 136.829Å c: 71.071Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.214 0.212 0.254
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

6 review citations

Mechanism and evolution of DNA primases.
Kuchta et al. (2010)
5 more

7 mentions without citation

Architecture and conservation of the bacterial DNA replication machinery, an underexploited drug target.
Robinson et al. (2012)
6 more