› 4lnd

X-ray diffraction
1.92Å resolution

Crystal structure of human apurinic/apyrimidinic endonuclease 1 with essential Mg2+ cofactor

Released:
DOI: 10.2210/pdb4lnd/pdb
PDB entry 4lnd coloured by chain, front view.
PDB entry 4lnd coloured by chain, side view.
PDB entry 4lnd coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure of human apurinic/apyrimidinic endonuclease 1 with the essential Mg2+ cofactor.
Manvilla BA, Pozharski E, Toth EA, Drohat AC
Acta Crystallogr D Biol Crystallogr 69 2555-62 (2013)
PMID: 24311596

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:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-151054 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
DNA repair nuclease/redox regulator APEX1, mitochondrial Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 286 amino acids
Theoretical weight: 32.1 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P27695 (Residues: 39-318; Coverage: 88%)
Gene names: APE, APE1, APEX, APEX1, APX, HAP1, REF1
Sequence domains: Endonuclease/Exonuclease/phosphatase family
Structure domains: Endonuclease/exonuclease/phosphatase

Ligands and Environments

1 bound ligand:
Ligand MG 3 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL7-1
Spacegroup: C2
Unit cell:
a: 165.795Å b: 90.94Å c: 94.03Å
α: 90° β: 123.22° γ: 90°
R-values:
R R work R free
0.218 0.217 0.241
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 review citations

Posttranscriptional regulation by RNA-binding proteins during epithelial-to-mesenchymal transition.
Aparicio et al. (2013)
1 more

6 mentions without citation

High-resolution crystal structures reveal plasticity in the metal binding site of apurinic/apyrimidinic endonuclease I.
He et al. (2014)
5 more