4iem

X-ray diffraction
2.39Å resolution

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Entry contents:
1 distinct polypeptide molecule
3 distinct DNA molecules
Macromolecules (4 distinct):
DNA-(apurinic or apyrimidinic site) lyase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 317 amino acids
Theoretical weight: 35.48 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P27695 (Residues: 2-318; Coverage: 100%)
Gene names: APE, APE1, APEX, APEX1, APX, HAP1, REF1
Sequence domains: Endonuclease/Exonuclease/phosphatase family
Structure domains: Endonuclease/exonuclease/phosphatase
DNA (5'-D(*GP*CP*TP*AP*C)-3') Chains: E, H, K, N
Molecule details ›
Chains: E, H, K, N
Length: 5 nucleotides
Theoretical weight: 1.48 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(P*(3DR)P*GP*AP*TP*CP*G)-3') Chains: F, I, L, O
Molecule details ›
Chains: F, I, L, O
Length: 6 nucleotides
Theoretical weight: 1.7 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*CP*GP*AP*TP*CP*GP*GP*TP*AP*GP*C)-3') Chains: G, J, M, P
Molecule details ›
Chains: G, J, M, P
Length: 11 nucleotides
Theoretical weight: 3.37 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: ALS BEAMLINE 5.0.1
Spacegroup: P21
Unit cell:
a: 104.639Å b: 74.09Å c: 112.138Å
α: 90° β: 111.98° γ: 90°
R-values:
R R work R free
0.21 0.208 0.246
Expression systems:
  • Escherichia coli
  • Not provided