› 1emj

X-ray diffraction
2Å resolution

URACIL-DNA GLYCOSYLASE BOUND TO DNA CONTAINING A 4'-THIO-2'DEOXYURIDINE ANALOG PRODUCT

Released:
DOI: 10.2210/pdb1emj/pdb
PDB entry 1emj coloured by chain, front view.
PDB entry 1emj coloured by chain, side view.
PDB entry 1emj 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-113750 (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*(ASU)P*AP*TP*CP*TP*T)-3') Chain: B
Molecule details ›
Chain: B
Length: 9 nucleotides
Theoretical weight: 2.62 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

1 bound ligand:
Ligand URA 1 x URA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL7-1
Spacegroup: P212121
Unit cell:
a: 48.554Å b: 64.853Å c: 96.01Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.228 0.228 0.257
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

29 review citations

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

7 mentions without citation

Uracil-DNA glycosylases-structural and functional perspectives on an essential family of DNA repair enzymes.
Schormann et al. (2014)
6 more