› 1bsu

X-ray diffraction
2Å resolution

STRUCTURAL AND ENERGETIC ORIGINS OF INDIRECT READOUT IN SITE-SPECIFIC DNA CLEAVAGE BY A RESTRICTION ENDONUCLEASE

Released:
DOI: 10.2210/pdb1bsu/pdb
PDB entry 1bsu coloured by chain, front view.
PDB entry 1bsu coloured by chain, side view.
PDB entry 1bsu coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Structural and energetic origins of indirect readout in site-specific DNA cleavage by a restriction endonuclease.
Martin AM, Sam MD, Reich NO, Perona JJ
Nat Struct Biol 6 269-77 (1999)
PMID: 10074946

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:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-113509 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Type II restriction enzyme EcoRV Chains: A, B
Molecule details ›
Chains: A, B
Length: 244 amino acids
Theoretical weight: 28.56 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P04390 (Residues: 2-245; Coverage: 100%)
Gene name: ecoRVR
Sequence domains: Restriction endonuclease EcoRV
Structure domains: DNA mismatch repair MutH/Restriction endonuclease, type II
DNA (5'-D(P*AP*AP*GP*AP*(5CM)P*IP*TP*CP*TP*T)-3') Chain: C
Molecule details ›
Chain: C
Length: 10 nucleotides
Theoretical weight: 3.04 KDa
Source organism: Escherichia coli
Expression system: Not provided
DNA (5'-D(*AP*AP*AP*GP*AP*(5CM)P*IP*TP*CP*TP*T)-3') Chain: D
Molecule details ›
Chain: D
Length: 11 nucleotides
Theoretical weight: 3.36 KDa
Source organism: Escherichia coli
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand CA 2 x CA
1 modified residue:
Ligand 5CM 2 x 5CM

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU200
Spacegroup: P1
Unit cell:
a: 50.3Å b: 64Å c: 49.1Å
α: 109.1° β: 108.1° γ: 96.5°
R-values:
R R work R free
0.183 0.183 0.258
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

3 review citations

Structure and function of type II restriction endonucleases.
Pingoud et al. (2001)
2 more

3 mentions without citation

Homology modelling of protein-protein complexes: a simple method and its possibilities and limitations.
Launay et al. (2008)
2 more