› 1h56

X-ray diffraction
3Å resolution

Structural and biochemical characterization of a new magnesium ion binding site near Tyr94 in the restriction endonuclease PvuII

Released:
DOI: 10.2210/pdb1h56/pdb
PDB entry 1h56 coloured by chain, front view.
PDB entry 1h56 coloured by chain, side view.
PDB entry 1h56 coloured by chain, top view.
Source organism: Proteus vulgaris
Primary publication:
Structural and biochemical characterization of a new Mg(2+) binding site near Tyr94 in the restriction endonuclease PvuII.
Spyridaki A, Matzen C, Lanio T, Jeltsch A, Simoncsits A, Athanasiadis A, Scheuring-Vanamee E, Kokkinidis M, Pingoud A
J Mol Biol 331 395-406 (2003)
PMID: 12888347

Function and Biology Details

Reaction catalysed: 
Endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-150034 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Type II restriction enzyme PvuII Chains: A, B
Molecule details ›
Chains: A, B
Length: 156 amino acids
Theoretical weight: 18.24 KDa
Source organism: Proteus vulgaris
Expression system: Escherichia coli HB101
UniProt:
  • Canonical: P23657 (Residues: 2-157; Coverage: 99%)
Gene name: pvuIIR
Sequence domains: Restriction endonuclease PvuII
Structure domains: PVUII Endonuclease, subunit A

Ligands and Environments

1 bound ligand:
Ligand MG 2 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: EMBL/DESY, HAMBURG BEAMLINE X11
Spacegroup: P21212
Unit cell:
a: 84.18Å b: 105.28Å c: 46.67Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.15 0.15 not available
Expression system: Escherichia coli HB101

Quick links

Citations

8 citation in other articles

Controlling the enzymatic activity of a restriction enzyme by light.
Schierling et al. (2010)
7 more

2 mentions without citation

Structural characterization of MepB from Staphylococcus aureus reveals homology to endonucleases.
Agah et al. (2014)
1 more