› 3zvn

X-ray diffraction
2.15Å resolution

The structural basis for substrate recognition by mammalian polynucleotide kinase 3' phosphatase

Released:
DOI: 10.2210/pdb3zvn/pdb
PDB 3zvn coloured by chain and viewed from the front.
PDB 3zvn coloured by chain and viewed from the side.
PDB 3zvn coloured by chain and viewed from the top.
Source organisms:
Primary publication:
The structural basis for substrate recognition by mammalian polynucleotide kinase 3' phosphatase.
Garces F, Pearl LH, Oliver AW
Mol. Cell 44 385-96 (2011)
PMID: 22055185

Function and Biology Details

Reactions catalysed: 
A 3'-phosphopolynucleotide + H(2)O = a polynucleotide + phosphate
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:
hetero hexamer (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
Bifunctional polynucleotide phosphatase/kinase Chain: A
Molecule details ›
Chain: A
Length: 416 amino acids
Theoretical weight: 45.95 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9JLV6 (Residues: 111-522; Coverage: 79%)
Gene name: Pnkp
Sequence domains:
Structure domains:
5'-D(*GP*TP*CP*AP*CP)-3' Chains: E, F, G, H, I
Molecule details ›
Chains: E, F, G, H, I
Length: 5 nucleotides
Theoretical weight: 1.48 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand MN 1 x MN
Ligand GOL 2 x GOL
Ligand ADP 1 x ADP
1 modified residue:
Ligand CSX 1 x CSX

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I02
Spacegroup: P212121
Unit cell:
a: 69.27Å b: 72.99Å c: 114.44Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.208 0.205 0.269
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

3 review citations

Non-homologous end joining: Common interaction sites and exchange of multiple factors in the DNA repair process.
Rulten et al. (2017)
2 more

3 mentions without citation

Recognition and repair of chemically heterogeneous structures at DNA ends.
Andres et al. (2015)
2 more