› 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 entry 3zvn coloured by chain, front view.
PDB entry 3zvn coloured by chain, side view.
PDB entry 3zvn coloured by chain, top view.
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: 
ATP + 5'-dephospho-DNA = ADP + 5'-phospho-DNA
A 3'-phosphopolynucleotide + H(2)O = a polynucleotide + phosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-117125 (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

Repair of double-strand breaks by end joining.
Chiruvella et al. (2013)
2 more

3 mentions without citation

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