› 1yjm

X-ray diffraction
2.2Å resolution

Crystal structure of the FHA domain of mouse polynucleotide kinase in complex with an XRCC4-derived phosphopeptide.

Released:
DOI: 10.2210/pdb1yjm/pdb
PDB entry 1yjm coloured by chain, front view.
PDB entry 1yjm coloured by chain, side view.
PDB entry 1yjm coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
The molecular architecture of the mammalian DNA repair enzyme, polynucleotide kinase.
Bernstein NK, Williams RS, Rakovszky ML, Cui D, Green R, Karimi-Busheri F, Mani RS, Galicia S, Koch CA, Cass CE, Durocher D, Weinfeld M, Glover JN
Mol Cell 17 657-70 (2005)
PMID: 15749016

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:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-162567 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Bifunctional polynucleotide phosphatase/kinase Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 110 amino acids
Theoretical weight: 11.8 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9JLV6 (Residues: 1-110; Coverage: 21%)
Gene name: Pnkp
Sequence domains: FHA domain
Structure domains: Tumour Suppressor Smad4
12-mer peptide from DNA-repair protein XRCC4 Chains: E, F, G
Molecule details ›
Chains: E, F, G
Length: 13 amino acids
Theoretical weight: 1.57 KDa
Source organism: Mus musculus
Expression system: Not provided

Ligands and Environments

No bound ligands
1 modified residue:
Ligand TPO 3 x TPO

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.3.1
Spacegroup: C2221
Unit cell:
a: 51.155Å b: 122.999Å c: 136.71Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.213 0.211 0.243
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

33 review citations

The mechanism of double-strand DNA break repair by the nonhomologous DNA end-joining pathway.
Lieber MR. (2010)
32 more

7 mentions without citation

Nonhomologous end joining: a good solution for bad ends.
Waters et al. (2014)
6 more