› 2nqj

X-ray diffraction
2.45Å resolution

Crystal structure of Escherichia coli endonuclease IV (Endo IV) E261Q mutant bound to damaged DNA

Released:
DOI: 10.2210/pdb2nqj/pdb
PDB entry 2nqj coloured by chain, front view.
PDB entry 2nqj coloured by chain, side view.
PDB entry 2nqj 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

Assemblies composition:
hetero trimer (preferred)
monomeric
Assembly name:
PDBe Complex ID:
PDB-CPX-115684 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Endonuclease 4 Chains: A, B
Molecule details ›
Chains: A, B
Length: 285 amino acids
Theoretical weight: 31.52 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21(DE3)
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(*GP*CP*GP*TP*CP*CP*(3DR)P*CP*GP*AP*CP*GP*AP*CP*G)-3' Chain: C
Molecule details ›
Chain: C
Length: 15 nucleotides
Theoretical weight: 4.45 KDa
Source organism: Escherichia coli
Expression system: Not provided
5'-D(*CP*GP*TP*CP*GP*TP*CP*GP*GP*GP*GP*AP*CP*GP*C)-3' Chain: D
Molecule details ›
Chain: D
Length: 15 nucleotides
Theoretical weight: 4.63 KDa
Source organism: Escherichia coli
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand ZN 4 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL9-1
Spacegroup: P212121
Unit cell:
a: 55.6Å b: 86.2Å c: 148.3Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.198 0.198 0.254
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

13 review citations

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

11 mentions without citation

Conserved structural chemistry for incision activity in structurally non-homologous apurinic/apyrimidinic endonuclease APE1 and endonuclease IV DNA repair enzymes.
Tsutakawa et al. (2013)
10 more