› 6k19

X-ray diffraction
2.2Å resolution

Crystal structure of EXD2 exonuclease domain soaked in Mg

Released:
DOI: 10.2210/pdb6k19/pdb
PDB entry 6k19 coloured by chain, front view.
PDB entry 6k19 coloured by chain, side view.
PDB entry 6k19 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
The structure of human EXD2 reveals a chimeric 3' to 5' exonuclease domain that discriminates substrates via metal coordination.
Park J, Lee SY, Jeong H, Kang MG, Van Haute L, Minczuk M, Seo JK, Jun Y, Myung K, Rhee HW, Lee C
Nucleic Acids Res 47 7078-7093 (2019)
PMID: 31127291

Function and Biology Details

Reaction catalysed: 
Exonucleolytic cleavage in the 3'- to 5'-direction to yield nucleoside 5'-phosphates
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-192633 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Exonuclease 3'-5' domain-containing protein 2 Chains: A, B
Molecule details ›
Chains: A, B
Length: 220 amino acids
Theoretical weight: 24.4 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9NVH0 (Residues: 76-295; Coverage: 35%)
Gene names: C14orf114, EXD2, EXDL2
Sequence domains: 3'-5' exonuclease

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: PAL/PLS BEAMLINE 5C (4A)
Spacegroup: P212121
Unit cell:
a: 46.347Å b: 74.107Å c: 133.477Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.202 0.199 0.252
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Exonucleases: Degrading DNA to Deal with Genome Damage, Cell Death, Inflammation and Cancer.
Manils et al. (2022)
8 other articles

1 mention without citation

The structure of human EXD2 reveals a chimeric 3' to 5' exonuclease domain that discriminates substrates via metal coordination.
Park et al. (2019)