› 7lpj

X-ray diffraction
2.56Å resolution

APE1 Mn-bound phosphorothioate substrate complex with abasic ribonucleotide DNA

Released:
DOI: 10.2210/pdb7lpj/pdb
Model geometry
Fit model/data
PDB entry 7lpj coloured by chain, front view.
PDB entry 7lpj coloured by chain, side view.
PDB entry 7lpj coloured by chain, top view.
Source organisms:
Primary publication:
Altered APE1 activity on abasic ribonucleotides is mediated by changes in the nucleoside sugar pucker.
Hoitsma NM, Click TH, Agarwal PK, Freudenthal BD
OpenAccess logo Comput Struct Biotechnol J 19 3293-3302 (2021)
PMID: 34188778

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

Assemblies composition:
monomeric
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-219044 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA repair nuclease/redox regulator APEX1, mitochondrial Chains: B, D
Molecule details ›
Chains: B, D
Length: 276 amino acids
Theoretical weight: 31.16 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(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3') Chain: C
Molecule details ›
Chain: C
Length: 21 nucleotides
Theoretical weight: 6.45 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-R(P*(YA4))-D(P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3') Chain: E

Ligands and Environments

1 bound ligand:
Ligand MN 1 x MN
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: P1
Unit cell:
a: 44.171Å b: 60.901Å c: 73.32Å
α: 82.913° β: 77.583° γ: 86.245°
R-values:
R R work R free
0.189 0.183 0.248
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 review citation

Ribonucleotide Incorporation by Eukaryotic B-Family Replicases and Its Implications for Genome Stability.
Williams et al. (2022)
2 other articles

1 mention without citation

Altered APE1 activity on abasic ribonucleotides is mediated by changes in the nucleoside sugar pucker.
Hoitsma et al. (2021)