› 3spd

X-ray diffraction
1.91Å resolution

Crystal structure of aprataxin ortholog Hnt3 in complex with DNA

Released:
DOI: 10.2210/pdb3spd/pdb
PDB entry 3spd coloured by chain, front view.
PDB entry 3spd coloured by chain, side view.
PDB entry 3spd coloured by chain, top view.
Source organism: Schizosaccharomyces pombe 972h-
Primary publication:
Crystal structures of aprataxin ortholog Hnt3 reveal the mechanism for reversal of 5'-adenylated DNA.
Gong Y, Zhu D, Ding J, Dou CN, Ren X, Gu L, Jiang T, Wang DC
Nat Struct Mol Biol 18 1297-9 (2011)
PMID: 21984208

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116885 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Aprataxin-like protein Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 204 amino acids
Theoretical weight: 23.61 KDa
Source organism: Schizosaccharomyces pombe 972h-
Expression system: Escherichia coli
UniProt:
  • Canonical: O74859 (Residues: 33-232; Coverage: 86%)
Gene names: SPCC18.09c, hnt3
Sequence domains:
Structure domains: HIT-like
DNA (5'-D(*TP*AP*TP*TP*CP*CP*GP*AP*TP*AP*GP*TP*GP*AP*C)-3') Chains: E, G
Molecule details ›
Chains: E, G
Length: 15 nucleotides
Theoretical weight: 4.58 KDa
Source organism: Schizosaccharomyces pombe 972h-
Expression system: Not provided
DNA (5'-D(*GP*TP*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*AP*TP*GP*AP*G)-3') Chains: F, H
Molecule details ›
Chains: F, H
Length: 17 nucleotides
Theoretical weight: 5.25 KDa
Source organism: Schizosaccharomyces pombe 972h-
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand ZN 4 x ZN
Ligand SO4 16 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: R32
Unit cell:
a: 220.409Å b: 220.409Å c: 135.031Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.176 0.175 0.212
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 review citation

Repair of double-strand breaks by end joining.
Chiruvella et al. (2013)
4 other articles