› 2nq9

X-ray diffraction
1.45Å resolution

High resolution crystal structure of Escherichia coli endonuclease IV (Endo IV) Y72A mutant bound to damaged DNA

Released:
DOI: 10.2210/pdb2nq9/pdb
PDB entry 2nq9 coloured by chain, front view.
PDB entry 2nq9 coloured by chain, side view.
PDB entry 2nq9 coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
DNA apurinic-apyrimidinic site binding and excision by endonuclease IV.
Garcin ED, Hosfield DJ, Desai SA, Haas BJ, Björas M, Cunningham RP, Tainer JA
Nat Struct Mol Biol 15 515-22 (2008)
PMID: 18408731

Function and Biology Details

Reaction catalysed: 
Endonucleolytic cleavage to 5'-phosphooligonucleotide end-products
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-115682 (preferred)
Entry contents:
1 distinct polypeptide molecule
3 distinct DNA molecules
Macromolecules (4 distinct):
Endonuclease 4 Chain: A
Molecule details ›
Chain: A
Length: 285 amino acids
Theoretical weight: 31.43 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A6C1 (Residues: 1-285; Coverage: 100%)
Gene names: JW2146, b2159, nfo
Sequence domains: Xylose isomerase-like TIM barrel
Structure domains: Divalent-metal-dependent TIM barrel enzymes
5'-D(*AP*TP*AP*TP*CP*T)-3' Chain: B
Molecule details ›
Chain: B
Length: 6 nucleotides
Theoretical weight: 1.78 KDa
Source organism: Escherichia coli
Expression system: Not provided
5'-D(P*(3DR)P*AP*GP*AP*T)-3' Chain: C
Molecule details ›
Chain: C
Length: 5 nucleotides
Theoretical weight: 1.39 KDa
Source organism: Escherichia coli
Expression system: Not provided
5'-D(*AP*TP*CP*TP*GP*AP*AP*GP*TP*AP*T)-3' Chain: D
Molecule details ›
Chain: D
Length: 11 nucleotides
Theoretical weight: 3.37 KDa
Source organism: Escherichia coli
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand ZN 3 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL9-1
Spacegroup: C2
Unit cell:
a: 138.5Å b: 59.1Å c: 51.2Å
α: 90° β: 94° γ: 90°
R-values:
R R work R free
0.22 0.22 0.234
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

12 review citations

Nucleases: diversity of structure, function and mechanism.
Yang W. (2011)
11 more

5 mentions without citation

Evolutionary Origins of DNA Repair Pathways: Role of Oxygen Catastrophe in the Emergence of DNA Glycosylases.
Prorok et al. (2021)
4 more