› 3ufj

X-ray diffraction
2.97Å resolution

Human Thymine DNA Glycosylase Bound to Substrate Analog 2'-fluoro-2'-deoxyuridine

Released:
DOI: 10.2210/pdb3ufj/pdb
PDB entry 3ufj coloured by chain, front view.
PDB entry 3ufj coloured by chain, side view.
PDB entry 3ufj coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Lesion processing by a repair enzyme is severely curtailed by residues needed to prevent aberrant activity on undamaged DNA.
Maiti A, Noon MS, MacKerell AD, Pozharski E, Drohat AC
Proc Natl Acad Sci U S A 109 8091-6 (2012)
PMID: 22573813

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-508054 (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: 204 amino acids
Theoretical weight: 23.07 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
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' Chains: C, E
Molecule details ›
Chains: C, E
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*(UF2)P*GP*TP*AP*CP*AP*GP*AP*GP*CP*TP*GP*T)-3' Chains: D, F
Molecule details ›
Chains: D, F
Length: 23 nucleotides
Theoretical weight: 7.02 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

No bound ligands
1 modified residue:
Ligand UF2 2 x UF2

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL7-1
Spacegroup: P65
Unit cell:
a: 162.537Å b: 162.537Å c: 54.959Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.265 0.263 0.304
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

4 review citations

MBD4 and TDG: multifaceted DNA glycosylases with ever expanding biological roles.
Sjolund et al. (2013)
3 more

11 mentions without citation

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