› 4gp6

X-ray diffraction
2.1Å resolution

Polynucleotide kinase

Released:
DOI: 10.2210/pdb4gp6/pdb
PDB entry 4gp6 coloured by chain, front view.
PDB entry 4gp6 coloured by chain, side view.
PDB entry 4gp6 coloured by chain, top view.
Source organism: Acetivibrio thermocellus ATCC 27405
Primary publication:
Structure and mechanism of the polynucleotide kinase component of the bacterial Pnkp-Hen1 RNA repair system.
Wang LK, Das U, Smith P, Shuman S
RNA 18 2277-86 (2012)
PMID: 23118415

Function and Biology Details

Reaction catalysed: 
ATP + 5'-dephospho-DNA = ADP + 5'-phospho-DNA
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-107082 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Metallophosphoesterase Chains: A, B
Molecule details ›
Chains: A, B
Length: 171 amino acids
Theoretical weight: 19.47 KDa
Source organism: Acetivibrio thermocellus ATCC 27405
Expression system: Escherichia coli
UniProt:
  • Canonical: A3DJ38 (Residues: 1-170; Coverage: 20%)
Gene name: Cthe_2768
Sequence domains: AAA domain
Structure domains: P-loop containing nucleotide triphosphate hydrolases

Ligands and Environments

2 bound ligands:
Ligand ADP 2 x ADP
Ligand MG 2 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25
Spacegroup: P212121
Unit cell:
a: 43.69Å b: 71.56Å c: 118.61Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.181 0.177 0.228
Expression system: Escherichia coli

Quick links

Citations

2 review citations

RNA damage in biological conflicts and the diversity of responding RNA repair systems.
Burroughs et al. (2016)
1 more

2 mentions without citation

Structure and mechanism of the polynucleotide kinase component of the bacterial Pnkp-Hen1 RNA repair system.
Wang et al. (2012)
1 more