› 6w4t

X-ray diffraction
2.77Å resolution

APE1 Y269A phosphorothioate substrate complex with abasic DNA

Released:
DOI: 10.2210/pdb6w4t/pdb
PDB entry 6w4t coloured by chain, front view.
PDB entry 6w4t coloured by chain, side view.
PDB entry 6w4t coloured by chain, top view.
Source organisms:
Primary publication:
AP-endonuclease 1 sculpts DNA through an anchoring tyrosine residue on the DNA intercalating loop.
Hoitsma NM, Whitaker AM, Beckwitt EC, Jang S, Agarwal PK, Van Houten B, Freudenthal BD
Nucleic Acids Res 48 7345-7355 (2020)
PMID: 32542366

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:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-120805 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA repair nuclease/redox regulator APEX1, mitochondrial Chains: A, B
Molecule details ›
Chains: A, B
Length: 276 amino acids
Theoretical weight: 31.06 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P27695 (Residues: 43-318; Coverage: 87%)
Gene names: APE, APE1, APEX, APEX1, APX, HAP1, REF1
Sequence domains: Endonuclease/Exonuclease/phosphatase family
DNA (5'-D(P*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*(48Z)P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3') Chains: C, P
Molecule details ›
Chains: C, P
Length: 21 nucleotides
Theoretical weight: 6.35 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3') Chains: F, V
Molecule details ›
Chains: F, V
Length: 21 nucleotides
Theoretical weight: 6.45 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 4.2.2
Spacegroup: P212121
Unit cell:
a: 45.659Å b: 148.315Å c: 153.235Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.224 0.221 0.274
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

2 review citations

Understanding APE1 cellular functions by the structural preference of exonuclease activities.
Liu et al. (2021)
1 more

1 mention without citation

AP-endonuclease 1 sculpts DNA through an anchoring tyrosine residue on the DNA intercalating loop.
Hoitsma et al. (2020)