› 6ozg

X-ray diffraction
1.93Å resolution

Crystal structure of Thermotoga maritima (Tm) Endonuclease V (E89Q) in complex with a 12mer DNA containing an inosine followed by a ribo-adenosine

Released:
DOI: 10.2210/pdb6ozg/pdb
PDB entry 6ozg coloured by chain, front view.
PDB entry 6ozg coloured by chain, side view.
PDB entry 6ozg coloured by chain, top view.
Source organisms:
Primary publication:
Evolution of Inosine-Specific Endonuclease V from Bacterial DNase to Eukaryotic RNase.
Wu J, Samara NL, Kuraoka I, Yang W
Mol Cell 76 44-56.e3 (2019)
PMID: 31444105

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 dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-505837 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA/RNA hybrid molecule
Macromolecules (2 distinct):
Endonuclease V Chains: A, B
Molecule details ›
Chains: A, B
Length: 224 amino acids
Theoretical weight: 25.49 KDa
Source organism: Thermotoga maritima
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9X2H9 (Residues: 1-224; Coverage: 100%)
Gene names: TM_1865, nfi
Sequence domains: Endonuclease V
DNA/RNA (5'-D(*AP*AP*TP*GP*A)-R(P*A)-D(P*GP*AP*T)-R(P*NP*N)-D(P*T)-3') Chains: C, D
Molecule details ›
Chains: C, D
Length: 12 nucleotides
Theoretical weight: 3.5 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand MG 3 x MG
Ligand GOL 2 x GOL
Ligand EDO 3 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-BM
Unit cell:
a: 63.495Å b: 82.487Å c: 108.569Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.179 0.177 0.209
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

6 review citations

Function and Molecular Mechanism of the DNA Damage Response in Immunity and Cancer Immunotherapy.
Ye et al. (2021)
5 more