› 1q3f

X-ray diffraction
1.9Å resolution

Uracil DNA glycosylase bound to a cationic 1-aza-2'-deoxyribose-containing DNA

Released:
DOI: 10.2210/pdb1q3f/pdb
PDB entry 1q3f coloured by chain, front view.
PDB entry 1q3f coloured by chain, side view.
PDB entry 1q3f coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Electrostatic guidance of glycosyl cation migration along the reaction coordinate of uracil DNA glycosylase.
Bianchet MA, Seiple LA, Jiang YL, Ichikawa Y, Amzel LM, Stivers JT
Biochemistry 42 12455-60 (2003)
PMID: 14580190

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-114420 (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: 94-313; Coverage: 70%)
Gene names: DGU, UNG, UNG1, UNG15
Sequence domains: Uracil DNA glycosylase superfamily
Structure domains: Uracil-DNA glycosylase-like domain
5'-D(*TP*GP*TP*(NRI)P*AP*TP*CP*TP*T)-3' Chain: B
Molecule details ›
Chain: B
Length: 9 nucleotides
Theoretical weight: 2.59 KDa
Source organism: Homo sapiens
Expression system: Not provided
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

2 bound ligands:
Ligand URA 1 x URA
Ligand PO4 1 x PO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU300
Spacegroup: P212121
Unit cell:
a: 48.64Å b: 65.89Å c: 99.41Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.19 0.19 0.235
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

6 review citations

DNA glycosylase recognition and catalysis.
Fromme et al. (2004)
5 more

7 mentions without citation

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