› 3uo7

X-ray diffraction
3Å resolution

Crystal structure of Human Thymine DNA Glycosylase Bound to Substrate 5-carboxylcytosine

Released:
DOI: 10.2210/pdb3uo7/pdb
PDB entry 3uo7 coloured by chain, front view.
PDB entry 3uo7 coloured by chain, side view.
PDB entry 3uo7 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-116999 (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: 22.73 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*AP*TP*GP*AP*GP*CP*AP*GP*TP*GP*GP*A)-3' Chain: C
Molecule details ›
Chain: C
Length: 23 nucleotides
Theoretical weight: 7.11 KDa
Source organism: Homo sapiens
Expression system: Not provided
5'-D(*CP*CP*AP*CP*TP*GP*CP*TP*CP*AP*(1CC)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: 7.05 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-B
Spacegroup: P65
Unit cell:
a: 164.352Å b: 164.352Å c: 57.569Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.232 0.227 0.28
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

79 review citations

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

14 mentions without citation

Recent advances in the structural mechanisms of DNA glycosylases.
Brooks et al. (2013)
13 more