› 2opf

X-ray diffraction
1.85Å resolution

Crystal structure of the DNA repair enzyme endonuclease-VIII (Nei) from E. coli (R252A) in complex with AP-site containing DNA substrate

Released:
DOI: 10.2210/pdb2opf/pdb
PDB entry 2opf coloured by chain, front view.
PDB entry 2opf coloured by chain, side view.
PDB entry 2opf coloured by chain, top view.
Source organism: Escherichia coli
Entry authors: Golan G, Zharov DO, Grollman AP, Shoham G

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:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-115735 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
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:
5'-D(*GP*GP*CP*TP*TP*CP*AP*TP*CP*CP*TP*G)-3' Chain: B
Molecule details ›
Chain: B
Length: 12 nucleotides
Theoretical weight: 3.63 KDa
Source organism: Escherichia coli
Expression system: Not provided
5'-D(P*CP*AP*GP*GP*AP*(PED)P*GP*AP*AP*GP*CP*C)-3' Chain: C
Molecule details ›
Chain: C
Length: 12 nucleotides
Theoretical weight: 3.57 KDa
Source organism: Escherichia coli
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand GOL 5 x GOL
Ligand ZN 1 x ZN
Ligand SO4 1 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 5ID-B
Spacegroup: P4322
Unit cell:
a: 73.556Å b: 73.556Å c: 170.113Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.24 0.24 0.267
Expression systems:
  • Escherichia coli
  • Not provided

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