› 5jxy

X-ray diffraction
1.71Å resolution

Enzyme-substrate complex of TDG catalytic domain bound to a G/U analog

Released:
DOI: 10.2210/pdb5jxy/pdb
PDB entry 5jxy coloured by chain, front view.
PDB entry 5jxy coloured by chain, side view.
PDB entry 5jxy coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis of damage recognition by thymine DNA glycosylase: Key roles for N-terminal residues.
Coey CT, Malik SS, Pidugu LS, Varney KM, Pozharski E, Drohat AC
Nucleic Acids Res 44 10248-10258 (2016)
PMID: 27580719

Function and Biology Details

Reaction catalysed: 
Hydrolyzes mismatched double-stranded DNA and polynucleotides, releasing free thymine
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-118885 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
G/T mismatch-specific thymine DNA glycosylase Chain: A
Molecule details ›
Chain: A
Length: 204 amino acids
Theoretical weight: 23.07 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q13569 (Residues: 111-308; Coverage: 48%)
Gene name: TDG
Sequence domains: Uracil DNA glycosylase superfamily
Structure domains: Uracil-DNA glycosylase-like domain
DNA (28-MER) Chain: C
Molecule details ›
Chain: C
Length: 28 nucleotides
Theoretical weight: 8.65 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (28-MER) Chain: D
Molecule details ›
Chain: D
Length: 28 nucleotides
Theoretical weight: 8.59 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

No bound ligands
1 modified residue:
Ligand UF2 1 x UF2

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL12-2
Spacegroup: C2
Unit cell:
a: 88.45Å b: 53.27Å c: 82.54Å
α: 90° β: 95.63° γ: 90°
R-values:
R R work R free
0.2 0.198 0.231
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

5 review citations

Base excision repair of oxidative DNA damage: from mechanism to disease.
Whitaker et al. (2017)
4 more