› 2w35

X-ray diffraction
2.15Å resolution

Structures of endonuclease V with DNA reveal initiation of deaminated adenine repair

Released:
DOI: 10.2210/pdb2w35/pdb
PDB entry 2w35 coloured by chain, front view.
PDB entry 2w35 coloured by chain, side view.
PDB entry 2w35 coloured by chain, top view.
Source organisms:
Primary publication:
Structures of endonuclease V with DNA reveal initiation of deaminated adenine repair.
Dalhus B, Arvai AS, Rosnes I, Olsen ØE, Backe PH, Alseth I, Gao H, Cao W, Tainer JA, Bjørås M
Nat Struct Mol Biol 16 138-43 (2009)
PMID: 19136958

Function and Biology Details

Reaction catalysed: 
Endonucleolytic cleavage at apurinic or apyrimidinic sites to products with a 5'-phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domain:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-115893 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Endonuclease V Chains: A, B
Molecule details ›
Chains: A, B
Length: 225 amino acids
Theoretical weight: 25.64 KDa
Source organism: Thermotoga maritima
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9X2H9 (Residues: 1-225; Coverage: 100%)
Gene names: TM_1865, nfi
Sequence domains: Endonuclease V
Structure domains: archaeoglobus fulgidus dsm 4304 superfamily
5'-D(*AP*TP*GP*CP*GP*AP*CP*IP*GP)-3' Chains: C, F
Molecule details ›
Chains: C, F
Length: 9 nucleotides
Theoretical weight: 2.77 KDa
Source organism: synthetic construct
Expression system: Not provided
5'-D(*AP*GP*CP*CP*GP*TP)-3' Chains: D, G
Molecule details ›
Chains: D, G
Length: 6 nucleotides
Theoretical weight: 1.81 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand MG 2 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-4
Spacegroup: I222
Unit cell:
a: 55.064Å b: 134.292Å c: 194.45Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.259 0.259 0.288
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

15 review citations

DNA damage by reactive species: Mechanisms, mutation and repair.
Jena NR. (2012)
14 more

12 mentions without citation

The cutting edges in DNA repair, licensing, and fidelity: DNA and RNA repair nucleases sculpt DNA to measure twice, cut once.
Tsutakawa et al. (2014)
11 more