› 4edk

X-ray diffraction
2Å resolution

The structure of the S. aureus DnaG RNA Polymerase Domain bound to GTP and Manganese

Released:
DOI: 10.2210/pdb4edk/pdb
PDB entry 4edk coloured by chain, front view.
PDB entry 4edk coloured by chain, side view.
PDB entry 4edk coloured by chain, top view.
Source organism: Staphylococcus aureus
Primary publication:
Binding mechanism of metalâ‹…NTP substrates and stringent-response alarmones to bacterial DnaG-type primases.
Rymer RU, Solorio FA, Tehranchi AK, Chu C, Corn JE, Keck JL, Wang JD, Berger JM
Structure 20 1478-89 (2012)
PMID: 22795082

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:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-126474 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
DNA primase Chain: A
Molecule details ›
Chain: A
Length: 329 amino acids
Theoretical weight: 37.68 KDa
Source organism: Staphylococcus aureus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O05338 (Residues: 111-436; Coverage: 54%)
Gene name: dnaG
Sequence domains:
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand BEN 3 x BEN
Ligand GTP 1 x GTP
Ligand MN 3 x MN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.3.1
Spacegroup: P61
Unit cell:
a: 151.742Å b: 151.742Å c: 38.72Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.163 0.161 0.2
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

16 review citations

The stringent response and physiological roles of (pp)pGpp in bacteria.
Irving et al. (2021)
15 more

1 mention without citation

Structural insight into the DNA-binding mode of the primosomal proteins PriA, PriB, and DnaT.
Huang et al. (2014)