5dfh

X-ray diffraction
1.95Å resolution

Human APE1 mismatch product complex

Released:
Primary publication:
Capturing snapshots of APE1 processing DNA damage.
OpenAccess logo Nat. Struct. Mol. Biol. (2015)
PMID: 26458045

Function and Biology Details

Reaction catalysed:
The C-O-P bond 3' to the apurinic or apyrimidinic site in DNA is broken by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned

Structure analysis Details

Assemblies composition:
hetero tetramer (preferred)
monomeric
Entry contents:
1 distinct polypeptide molecule
3 distinct DNA molecules
Macromolecules (4 distinct):
DNA-(apurinic or apyrimidinic site) lyase, mitochondrial Chains: A, B
Molecule details ›
Chains: A, B
Length: 276 amino acids
Theoretical weight: 31.19 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
Structure domains: Endonuclease/exonuclease/phosphatase
DNA (5'-D(P*(3DR)P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3') Chain: D
Molecule details ›
Chain: D
Length: 11 nucleotides
Theoretical weight: 3.21 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3') Chain: V
Molecule details ›
Chain: V
Length: 21 nucleotides
Theoretical weight: 6.47 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*T)-3') Chain: C
Molecule details ›
Chain: C
Length: 10 nucleotides
Theoretical weight: 3.08 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: P1
Unit cell:
a: 44.434Å b: 61.603Å c: 72.277Å
α: 83.86° β: 78.76° γ: 88.19°
R-values:
R R work R free
0.18 0.179 0.219
Expression systems:
  • Escherichia coli
  • Not provided