› 3hqg

X-ray diffraction
2.6Å resolution

Crystal structure of restriction endonuclease EcoRII catalytic C-terminal domain in complex with cognate DNA

Released:
DOI: 10.2210/pdb3hqg/pdb
PDB entry 3hqg coloured by chain, front view.
PDB entry 3hqg coloured by chain, side view.
PDB entry 3hqg coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Structural mechanisms for the 5'-CCWGG sequence recognition by the N- and C-terminal domains of EcoRII.
Golovenko D, Manakova E, Tamulaitiene G, Grazulis S, Siksnys V
Nucleic Acids Res 37 6613-24 (2009)
PMID: 19729506

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 analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116375 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Type II restriction enzyme EcoRII Chain: A
Molecule details ›
Chain: A
Length: 222 amino acids
Theoretical weight: 25.58 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P14633 (Residues: 183-404; Coverage: 55%)
Gene name: ecoRIIR
Sequence domains: EcoRII C terminal
Structure domains: Restriction Endonuclease
5'-D(*TP*CP*GP*AP*CP*CP*AP*GP*GP*CP*TP*A)-3' Chain: B
Molecule details ›
Chain: B
Length: 12 nucleotides
Theoretical weight: 3.65 KDa
Source organism: Escherichia coli
Expression system: Not provided
5'-D(*TP*AP*GP*CP*CP*TP*GP*GP*TP*CP*GP*A)-3' Chain: C
Molecule details ›
Chain: C
Length: 12 nucleotides
Theoretical weight: 3.68 KDa
Source organism: Escherichia coli
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: EMBL/DESY, HAMBURG BEAMLINE X13
Spacegroup: P21212
Unit cell:
a: 77.054Å b: 57.971Å c: 61.01Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.242 0.236 0.293
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

2 review citations

Type II restriction endonucleases--a historical perspective and more.
Pingoud et al. (2014)
1 more

5 mentions without citation

Structural mechanisms for the 5'-CCWGG sequence recognition by the N- and C-terminal domains of EcoRII.
Golovenko et al. (2009)
4 more