› 1q3b

X-ray diffraction
2.05Å resolution

Crystal structure of the DNA repair enzyme endonuclease-VIII (Nei) from E. coli: The R252A mutant at 2.05 resolution.

Released:
DOI: 10.2210/pdb1q3b/pdb
PDB entry 1q3b coloured by chain, front view.
PDB entry 1q3b coloured by chain, side view.
PDB entry 1q3b coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Structure of the uncomplexed DNA repair enzyme endonuclease VIII indicates significant interdomain flexibility.
Golan G, Zharkov DO, Feinberg H, Fernandes AS, Zaika EI, Kycia JH, Grollman AP, Shoham G
Nucleic Acids Res 33 5006-16 (2005)
PMID: 16145054

Function and Biology Details

Reaction catalysed: 
The C-O-P bond 3' to the apurinic or apyrimidinic site in DNA is broken by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-156189 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Endonuclease 8 Chain: A
Molecule details ›
Chain: A
Length: 262 amino acids
Theoretical weight: 29.73 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P50465 (Residues: 2-263; Coverage: 100%)
Gene names: JW0704, b0714, nei
Sequence domains:
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand ZN 1 x ZN
Ligand MG 2 x MG
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 5ID-B
Spacegroup: I222
Unit cell:
a: 57.722Å b: 80.051Å c: 169.311Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.228 0.228 0.26
Expression system: Escherichia coli

Quick links

Citations

4 review citations

DNA base repair--recognition and initiation of catalysis.
Dalhus et al. (2009)
3 more

7 mentions without citation

Recent advances in the structural mechanisms of DNA glycosylases.
Brooks et al. (2013)
6 more