› 6u16

X-ray diffraction
1.6Å resolution

Human thymine DNA glycosylase N140A mutant bound to DNA with 5-carboxyl-dC substrate

Released:
DOI: 10.2210/pdb6u16/pdb
PDB entry 6u16 coloured by chain, front view.
PDB entry 6u16 coloured by chain, side view.
PDB entry 6u16 coloured by chain, top view.
Source organisms:
Primary publication:
Excision of 5-Carboxylcytosine by Thymine DNA Glycosylase.
Pidugu LS, Dai Q, Malik SS, Pozharski E, Drohat AC
J Am Chem Soc 141 18851-18861 (2019)
PMID: 31693361

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-120668 (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: 227 amino acids
Theoretical weight: 25.83 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q13569 (Residues: 82-308; Coverage: 55%)
Gene name: TDG
Sequence domains: Uracil DNA glycosylase superfamily
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: 8.61 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand EDO 3 x EDO
2 modified residues:
Ligand CSO 1 x CSO
Ligand 1CC 1 x 1CC

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL12-2
Spacegroup: C2
Unit cell:
a: 94.57Å b: 53.23Å c: 81.32Å
α: 90° β: 94.84° γ: 90°
R-values:
R R work R free
0.188 0.186 0.21
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

2 review citations

The base excision repair process: comparison between higher and lower eukaryotes.
Hindi et al. (2021)
1 more

1 mention without citation

Excision of 5-Carboxylcytosine by Thymine DNA Glycosylase.
Pidugu et al. (2019)