› 1hd7

X-ray diffraction
1.95Å resolution

A Second Divalent Metal Ion in the Active Site of a New Crystal Form of Human Apurinic/Apyridinimic Endonuclease, Ape1, and its Implications for the Catalytic Mechanism

Released:
DOI: 10.2210/pdb1hd7/pdb
Model geometry
Fit model/data
PDB entry 1hd7 coloured by chain, front view.
PDB entry 1hd7 coloured by chain, side view.
PDB entry 1hd7 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Two divalent metal ions in the active site of a new crystal form of human apurinic/apyrimidinic endonuclease, Ape1: implications for the catalytic mechanism.
Beernink PT, Segelke BW, Hadi MZ, Erzberger JP, Wilson DM, Rupp B
J Mol Biol 307 1023-34 (2001)
PMID: 11286553

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:
Sequence domains:
Structure domain:

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 Chain: A
Molecule details ›
Chain: A
Length: 318 amino acids
Theoretical weight: 35.61 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P27695 (Residues: 1-318; Coverage: 100%)
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 PB 1 x PB
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SSRL BEAMLINE BL1-5
Spacegroup: C2
Unit cell:
a: 128.39Å b: 44.85Å c: 78.14Å
α: 90° β: 124.54° γ: 90°
R-values:
R R work R free
0.205 0.205 0.255
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

17 review citations

APE1/Ref-1 role in redox signaling: translational applications of targeting the redox function of the DNA repair/redox protein APE1/Ref-1.
Kelley et al. (2012)
16 more

8 mentions without citation

Human AP endonuclease 1: a potential marker for the prediction of environmental carcinogenesis risk.
Park et al. (2014)
7 more