› 4fnc

X-ray diffraction
2.49Å resolution

Human TDG in a post-reactive complex with 5-hydroxymethyluracil (5hmU)

Released:
DOI: 10.2210/pdb4fnc/pdb
PDB entry 4fnc coloured by chain, front view.
PDB entry 4fnc coloured by chain, side view.
PDB entry 4fnc coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Excision of 5-hydroxymethyluracil and 5-carboxylcytosine by the thymine DNA glycosylase domain: its structural basis and implications for active DNA demethylation.
Hashimoto H, Hong S, Bhagwat AS, Zhang X, Cheng X
Nucleic Acids Res 40 10203-14 (2012)
PMID: 22962365

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-117507 (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: Homo sapiens
Expression system: Not provided
DNA (29-MER) Chain: D
Molecule details ›
Chain: D
Length: 29 nucleotides
Theoretical weight: 8.78 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand HMU 1 x HMU
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: C2
Unit cell:
a: 90.96Å b: 53.72Å c: 81.56Å
α: 90° β: 96.49° γ: 90°
R-values:
R R work R free
0.226 0.224 0.266
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

32 review citations

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

6 mentions without citation

Excision of 5-hydroxymethyluracil and 5-carboxylcytosine by the thymine DNA glycosylase domain: its structural basis and implications for active DNA demethylation.
Hashimoto et al. (2012)
5 more