› 3szq

X-ray diffraction
2.35Å resolution

Structure of an S. pombe APTX/DNA/AMP/Zn complex

Released:
DOI: 10.2210/pdb3szq/pdb
PDB 3szq coloured by chain and viewed from the front.
PDB 3szq coloured by chain and viewed from the side.
PDB 3szq coloured by chain and viewed from the top.
Source organism: Schizosaccharomyces pombe 972h-
Primary publication:
Structure of an aprataxin-DNA complex with insights into AOA1 neurodegenerative disease.
Tumbale P, Appel CD, Kraehenbuehl R, Robertson PD, Williams JS, Krahn J, Ahel I, Williams RS
OpenAccess logo Nat Struct Mol Biol 18 1189-95 (2011)
PMID: 21984210

Function and Biology Details

Reactions catalysed: 
(DNA)-3'-diphospho-5'-guanosine + H(2)O = (DNA)-3'-phosphate + GMP
Adenosine-5'-diphospho-5'-(DNA) + H(2)O = AMP + phospho-5'-(DNA)
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Aprataxin-like protein Chain: A
Molecule details ›
Chain: A
Length: 206 amino acids
Theoretical weight: 23.9 KDa
Source organism: Schizosaccharomyces pombe 972h-
Expression system: Escherichia coli
UniProt:
  • Canonical: O74859 (Residues: 31-232; Coverage: 87%)
Gene names: SPCC18.09c, hnt3
Sequence domains:
Structure domains: HIT-like
5'-D(*CP*CP*CP*TP*G)-3' Chain: B
Molecule details ›
Chain: B
Length: 5 nucleotides
Theoretical weight: 1.46 KDa
Source organism: Schizosaccharomyces pombe 972h-
Expression system: Not provided
5'-D(*TP*AP*TP*CP*GP*GP*AP*AP*TP*CP*AP*GP*GP*G)-3' Chain: C
Molecule details ›
Chain: C
Length: 14 nucleotides
Theoretical weight: 4.34 KDa
Source organism: Schizosaccharomyces pombe 972h-
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand AMP 1 x AMP
Ligand BME 2 x BME
Ligand ZN 1 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: I432
Unit cell:
a: 157.05Å b: 157.05Å c: 157.05Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.167 0.165 0.211
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

12 review citations

Structural insight into DNA joining: from conserved mechanisms to diverse scaffolds.
Williamson et al. (2020)
11 more

3 mentions without citation

Molecular underpinnings of Aprataxin RNA/DNA deadenylase function and dysfunction in neurological disease.
Schellenberg et al. (2015)
2 more