› 2wsh

X-ray diffraction
1.9Å resolution

Structure of bacteriophage T4 EndoII E118A mutant

Released:
DOI: 10.2210/pdb2wsh/pdb
PDB entry 2wsh coloured by chain, front view.
PDB entry 2wsh coloured by chain, side view.
PDB entry 2wsh coloured by chain, top view.
Source organism: Escherichia virus T4
Primary publication:
Structure of bacteriophage T4 endonuclease II mutant E118A, a tetrameric GIY-YIG enzyme.
Andersson CE, Lagerbäck P, Carlson K
J Mol Biol 397 1003-16 (2010)
PMID: 20156453

Function and Biology Details

Reaction catalysed: 
Endonucleolytic nicking and cleavage of cytosine-containing double-stranded DNA.
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-139358 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Endonuclease II Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 143 amino acids
Theoretical weight: 16.91 KDa
Source organism: Escherichia virus T4
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P07059 (Residues: 1-136; Coverage: 100%)
Gene name: denA
Sequence domains: GIY-YIG catalytic domain
Structure domains: GIY-YIG endonuclease

Ligands and Environments

2 bound ligands:
Ligand PO4 1 x PO4
Ligand PEG 2 x PEG
1 modified residue:
Ligand MSE 16 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-1
Spacegroup: P21
Unit cell:
a: 57.417Å b: 104.974Å c: 57.865Å
α: 90° β: 113.56° γ: 90°
R-values:
R R work R free
0.202 0.2 0.247
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

3 citation in other articles

Hpy188I-DNA pre- and post-cleavage complexes--snapshots of the GIY-YIG nuclease mediated catalysis.
Sokolowska et al. (2011)
2 more

1 mention without citation

Folding, DNA recognition, and function of GIY-YIG endonucleases: crystal structures of R.Eco29kI.
Mak et al. (2010)