› 4z7z

X-ray diffraction
1.83Å resolution

Structure of the enzyme-product complex resulting from TDG action on a GT mismatch in the presence of excess base

Released:
DOI: 10.2210/pdb4z7z/pdb
PDB entry 4z7z coloured by chain, front view.
PDB entry 4z7z coloured by chain, side view.
PDB entry 4z7z coloured by chain, top view.
Source organisms:
Primary publication:
Thymine DNA glycosylase exhibits negligible affinity for nucleobases that it removes from DNA.
Malik SS, Coey CT, Varney KM, Pozharski E, Drohat AC
Nucleic Acids Res 43 9541-52 (2015)
PMID: 26358812

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-118368 (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: 8.47 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand EDO 1 x EDO
Ligand ACY 1 x ACY
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL12-2
Spacegroup: C2
Unit cell:
a: 90.729Å b: 53.46Å c: 82.033Å
α: 90° β: 95.54° γ: 90°
R-values:
R R work R free
0.195 0.193 0.237
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

4 review citations

TET-mediated active DNA demethylation: mechanism, function and beyond.
Wu et al. (2017)
3 more

1 mention without citation

Thymine DNA glycosylase exhibits negligible affinity for nucleobases that it removes from DNA.
Malik et al. (2015)