› 1emh

X-ray diffraction
1.8Å resolution

CRYSTAL STRUCTURE OF HUMAN URACIL-DNA GLYCOSYLASE BOUND TO UNCLEAVED SUBSTRATE-CONTAINING DNA

Released:
DOI: 10.2210/pdb1emh/pdb
PDB entry 1emh coloured by chain, front view.
PDB entry 1emh coloured by chain, side view.
PDB entry 1emh coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Uracil-DNA glycosylase-DNA substrate and product structures: conformational strain promotes catalytic efficiency by coupled stereoelectronic effects.
Parikh SS, Walcher G, Jones GD, Slupphaug G, Krokan HE, Blackburn GM, Tainer JA
Proc Natl Acad Sci U S A 97 5083-8 (2000)
PMID: 10805771

Function and Biology Details

Reaction catalysed: 
Hydrolyzes single-stranded DNA or mismatched double-stranded DNA and polynucleotides, releasing free uracil
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-113749 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Uracil-DNA glycosylase Chain: A
Molecule details ›
Chain: A
Length: 223 amino acids
Theoretical weight: 25.54 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P13051 (Residues: 91-313; Coverage: 71%)
Gene names: DGU, UNG, UNG1, UNG15
Sequence domains: Uracil DNA glycosylase superfamily
Structure domains: Uracil-DNA glycosylase-like domain
DNA (5'-D(*TP*GP*TP*(P2U)P*AP*TP*CP*TP*T)-3') Chain: B
Molecule details ›
Chain: B
Length: 9 nucleotides
Theoretical weight: 2.7 KDa
Source organism: Homo sapiens
Expression system: Not provided
DNA (5'-D(*AP*AP*AP*GP*AP*TP*AP*AP*CP*A)-3') Chain: C
Molecule details ›
Chain: C
Length: 10 nucleotides
Theoretical weight: 3.07 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

No bound ligands
1 modified residue:
Ligand P2U 1 x P2U

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 14-BM-D
Spacegroup: P212121
Unit cell:
a: 48.655Å b: 64.815Å c: 94.964Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.216 0.216 0.233
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

25 review citations

Uracil in DNA--occurrence, consequences and repair.
Krokan et al. (2002)
24 more

50 mentions without citation

Detection of damaged DNA bases by DNA glycosylase enzymes.
Friedman et al. (2010)
49 more