› 4b20

X-ray diffraction
2.75Å resolution

Structural basis of DNA loop recognition by Endonuclease V

Released:
DOI: 10.2210/pdb4b20/pdb
PDB entry 4b20 coloured by chain, front view.
PDB entry 4b20 coloured by chain, side view.
PDB entry 4b20 coloured by chain, top view.
Source organism: Thermotoga maritima
Primary publication:
Structural basis of DNA loop recognition by endonuclease V.
Rosnes I, Rowe AD, Vik ES, Forstrøm RJ, Alseth I, Bjørås M, Dalhus B
Structure 21 257-65 (2013)
PMID: 23313664

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

Assemblies composition:
hetero trimer (preferred)
hetero hexamer
Assembly name:
PDBe Complex ID:
PDB-CPX-117226 (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
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(*GP*CP*GP*AP*CP*AP*GP)-3' Chains: C, F
Molecule details ›
Chains: C, F
Length: 7 nucleotides
Theoretical weight: 2.15 KDa
Source organism: Thermotoga maritima
Expression system: Not provided
5'-D(*AP*TP*CP*TP*TP*GP*TP*CP*GP*CP)-3' Chains: D, G
Molecule details ›
Chains: D, G
Length: 10 nucleotides
Theoretical weight: 3.01 KDa
Source organism: Thermotoga maritima
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: BESSY BEAMLINE 14.1
Spacegroup: I222
Unit cell:
a: 55.231Å b: 135.37Å c: 194.993Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.227 0.227 0.291
Expression systems:
  • Escherichia coli BL21
  • Not provided

Quick links

Citations

3 review citations

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)
2 more

4 mentions without citation

Crystal structure of E. coli endonuclease V, an essential enzyme for deamination repair.
Zhang et al. (2015)
3 more