2oq4

X-ray diffraction
2.6Å resolution

Crystal structure of the DNA repair enzyme endonuclease-VIII (Nei) from E. coli (E2Q) in complex with AP-site containing DNA substrate

Released:
Source organism: Escherichia coli
Entry authors: Golan G, Zharkov DO, Grollman AP, Shoahm 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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Endonuclease 8 Chains: A, B
Molecule details ›
Chains: A, B
Length: 262 amino acids
Theoretical weight: 29.81 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(*G*GP*CP*TP*TP*CP*AP*TP*CP*CP*TP*GP*G)-3' Chains: C, E
Molecule details ›
Chains: C, E
Length: 13 nucleotides
Theoretical weight: 3.96 KDa
Source organism: Escherichia coli
Expression system: Not provided
5'-D(*C*CP*AP*GP*GP*AP*(PED)P*GP*AP*AP*GP*CP*C)-3' Chains: D, F
Molecule details ›
Chains: D, F
Length: 13 nucleotides
Theoretical weight: 3.86 KDa
Source organism: Escherichia coli
Expression system: Not provided

Ligands and Environments

3 bound ligands:
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 5ID-B
Spacegroup: P43212
Unit cell:
a: 107.13Å b: 107.13Å c: 164.86Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.374 0.374 0.432
Expression systems:
  • Escherichia coli
  • Not provided