› 4ykl

X-ray diffraction
2.25Å resolution

Hnt3 in complex with DNA and guanosine

Released:
DOI: 10.2210/pdb4ykl/pdb
PDB entry 4ykl coloured by chain, front view.
PDB entry 4ykl coloured by chain, side view.
PDB entry 4ykl coloured by chain, top view.
Source organisms:
Primary publication:
DNA3'pp5'G de-capping activity of aprataxin: effect of cap nucleoside analogs and structural basis for guanosine recognition.
Chauleau M, Jacewicz A, Shuman S
Nucleic Acids Res 43 6075-83 (2015)
PMID: 26007660

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-118323 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
Aprataxin-like protein Chain: B
Molecule details ›
Chain: B
Length: 200 amino acids
Theoretical weight: 23.23 KDa
Source organism: Schizosaccharomyces pombe 972h-
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O74859 (Residues: 33-232; Coverage: 86%)
Gene names: SPCC18.09c, hnt3
Sequence domains:
Structure domains: HIT-like
DNA (5'-D(*GP*AP*AP*TP*CP*AP*TP*AP*AP*C)-3') Chain: A
Molecule details ›
Chain: A
Length: 10 nucleotides
Theoretical weight: 3.04 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand ZN 1 x ZN
Ligand GMP 1 x GMP
Ligand GOL 4 x GOL
Ligand CL 2 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P321
Unit cell:
a: 119.083Å b: 119.083Å c: 36.564Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.184 0.18 0.24
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

1 review citation

RNA damage in biological conflicts and the diversity of responding RNA repair systems.
Burroughs et al. (2016)
2 other articles