› 3nic

X-ray diffraction
2.8Å resolution

DNA binding and cleavage by the GIY-YIG endonuclease R.Eco29kI inactive variant Y49F

Released:
DOI: 10.2210/pdb3nic/pdb
PDB entry 3nic coloured by chain, front view.
PDB entry 3nic coloured by chain, side view.
PDB entry 3nic coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Folding, DNA recognition, and function of GIY-YIG endonucleases: crystal structures of R.Eco29kI.
Mak AN, Lambert AR, Stoddard BL
Structure 18 1321-31 (2010)
PMID: 20800503

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116624 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Eco29kIR Chains: A, B, C, D, E, F, G, H
Molecule details ›
Chains: A, B, C, D, E, F, G, H
Length: 235 amino acids
Theoretical weight: 26.79 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: Q46944 (Residues: 2-214; Coverage: 100%)
Gene name: eco29kIR
Sequence domains: Eco29kI restriction endonuclease
DNA (5'-D(P*CP*GP*GP*GP*AP*GP*GP*CP*CP*CP*GP*CP*GP*GP*GP*CP*CP*GP*CP*CP*GP*C)-3') Chains: I, K, M, O
Molecule details ›
Chains: I, K, M, O
Length: 22 nucleotides
Theoretical weight: 6.78 KDa
Source organism: Escherichia coli
Expression system: Not provided
DNA (5'-D(P*GP*CP*GP*GP*CP*GP*GP*CP*CP*CP*GP*CP*GP*GP*GP*CP*CP*TP*CP*CP*CP*G)-3') Chains: J, L, N, P
Molecule details ›
Chains: J, L, N, P
Length: 22 nucleotides
Theoretical weight: 6.73 KDa
Source organism: Escherichia coli
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand PO4 11 x PO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.1
Spacegroup: P21
Unit cell:
a: 99.87Å b: 101.346Å c: 142.346Å
α: 90° β: 109.59° γ: 90°
R-values:
R R work R free
0.21 0.206 0.279
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

6 review citations

Homing endonucleases: from microbial genetic invaders to reagents for targeted DNA modification.
Stoddard BL. (2011)
5 more

6 mentions without citation

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