› 3uob

X-ray diffraction
3.01Å resolution

Crystal structure of Human Thymine DNA Glycosylase Bound to Substrate Analog 2'-deoxy-2'-beta-fluoro-cytidine

Released:
DOI: 10.2210/pdb3uob/pdb
PDB entry 3uob coloured by chain, front view.
PDB entry 3uob coloured by chain, side view.
PDB entry 3uob coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Thymine DNA glycosylase specifically recognizes 5-carboxylcytosine-modified DNA.
Zhang L, Lu X, Lu J, Liang H, Dai Q, Xu GL, Luo C, Jiang H, He C
Nat Chem Biol 8 328-30 (2012)
PMID: 22327402

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 tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-117000 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
G/T mismatch-specific thymine DNA glycosylase Chains: A, B
Molecule details ›
Chains: A, B
Length: 201 amino acids
Theoretical weight: 22.77 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
5'-D(*CP*AP*GP*CP*TP*CP*TP*GP*TP*AP*CP*GP*TP*GP*AP*GP*CP*AP*GP*TP*GP*GP*A)-3' Chain: C
Molecule details ›
Chain: C
Length: 23 nucleotides
Theoretical weight: 7.12 KDa
Source organism: Homo sapiens
Expression system: Not provided
5'-D(*CP*CP*AP*CP*TP*GP*CP*TP*CP*AP*(1FC)P*GP*TP*AP*CP*AP*GP*AP*GP*CP*TP*GP*T)-3' Chain: D
Molecule details ›
Chain: D
Length: 23 nucleotides
Theoretical weight: 7.06 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-E
Spacegroup: P65
Unit cell:
a: 163.418Å b: 163.418Å c: 54.701Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.225 0.219 0.276
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

82 review citations

Function and information content of DNA methylation.
Schübeler D. (2015)
81 more

7 mentions without citation

TET enzymes, TDG and the dynamics of DNA demethylation.
Kohli et al. (2013)
6 more