› 3u7h

X-ray diffraction
2Å resolution

Crystal structure of mPNKP catalytic fragment (D170A) bound to single-stranded DNA (TCCTTp)

Released:
DOI: 10.2210/pdb3u7h/pdb
PDB entry 3u7h coloured by chain, front view.
PDB entry 3u7h coloured by chain, side view.
PDB entry 3u7h coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
Structural basis for the phosphatase activity of polynucleotide kinase/phosphatase on single- and double-stranded DNA substrates.
Coquelle N, Havali-Shahriari Z, Bernstein N, Green R, Glover JN
Proc Natl Acad Sci U S A 108 21022-7 (2011)
PMID: 22171004

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 dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116975 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
Bifunctional polynucleotide phosphatase/kinase Chain: B
Molecule details ›
Chain: B
Length: 381 amino acids
Theoretical weight: 42.38 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9JLV6 (Residues: 142-522; Coverage: 73%)
Gene name: Pnkp
Sequence domains:
Structure domains:
DNA Chain: X
Molecule details ›
Chain: X
Length: 5 nucleotides
Theoretical weight: 1.45 KDa
Source organism: Mus musculus
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand GOL 5 x GOL
Ligand MG 1 x MG
Ligand PO4 1 x PO4
2 modified residues:
Ligand MSE 5 x MSE
Ligand CSO 1 x CSO

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL9-2
Spacegroup: P21
Unit cell:
a: 42.83Å b: 62.53Å c: 67.98Å
α: 90° β: 91.69° γ: 90°
R-values:
R R work R free
0.194 0.192 0.236
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

4 review citations

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

1 mention without citation

Structural basis for the phosphatase activity of polynucleotide kinase/phosphatase on single- and double-stranded DNA substrates.
Coquelle et al. (2011)