› 1rc8

X-ray diffraction
2.75Å resolution

T4 Polynucleotide Kinase bound to 5'-GTCAC-3' ssDNA

Released:
DOI: 10.2210/pdb1rc8/pdb
PDB entry 1rc8 coloured by chain, front view.
PDB entry 1rc8 coloured by chain, side view.
PDB entry 1rc8 coloured by chain, top view.
Source organism: Tequatrovirus T4
Primary publication:
Recognition of DNA substrates by T4 bacteriophage polynucleotide kinase.
Eastberg JH, Pelletier J, Stoddard BL
Nucleic Acids Res 32 653-60 (2004)
PMID: 14754987

Function and Biology Details

Reactions catalysed: 
ATP + 5'-dephospho-DNA = ADP + 5'-phospho-DNA
A deoxyribonucleoside 3'-phosphate + H(2)O = a deoxyribonucleoside + phosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
hetero octamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-114510 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
Polynucleotide kinase Chain: A
Molecule details ›
Chain: A
Length: 301 amino acids
Theoretical weight: 35.23 KDa
Source organism: Escherichia virus T4
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P06855 (Residues: 1-301; Coverage: 100%)
Gene name: pseT
Sequence domains: AAA domain
Structure domains:
5'-D(*GP*TP*CP*AP*C)-3' Chain: B
Molecule details ›
Chain: B
Length: 5 nucleotides
Theoretical weight: 1.48 KDa
Source organism: Tequatrovirus T4
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand CA 1 x CA
Ligand DMS 1 x DMS
Ligand ADP 1 x ADP
1 modified residue:
Ligand MSE 12 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.1
Spacegroup: I222
Unit cell:
a: 82.17Å b: 92.061Å c: 123.385Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.23 0.23 0.294
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

3 review citations

Tidying up loose ends: the role of polynucleotide kinase/phosphatase in DNA strand break repair.
Weinfeld et al. (2011)
2 more

3 mentions without citation

Recognition of DNA substrates by T4 bacteriophage polynucleotide kinase.
Eastberg et al. (2004)
2 more