› 1oe5

X-ray diffraction
2.3Å resolution

Xenopus SMUG1, an anti-mutator uracil-DNA Glycosylase

Released:
DOI: 10.2210/pdb1oe5/pdb
PDB entry 1oe5 coloured by chain, front view.
PDB entry 1oe5 coloured by chain, side view.
PDB entry 1oe5 coloured by chain, top view.
Source organism: Xenopus laevis
Primary publication:
Structure and specificity of the vertebrate anti-mutator uracil-DNA glycosylase SMUG1.
Wibley JE, Waters TR, Haushalter K, Verdine GL, Pearl LH
Mol Cell 11 1647-59 (2003)
PMID: 12820976

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-114304 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Single-strand selective monofunctional uracil DNA glycosylase Chains: A, B
Molecule details ›
Chains: A, B
Length: 247 amino acids
Theoretical weight: 27.75 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9YGN6 (Residues: 35-281; Coverage: 88%)
Gene name: smug1
Sequence domains: Uracil DNA glycosylase superfamily
Structure domains: Uracil-DNA glycosylase-like domain
5'-D(*CP*CP*CP*GP*TP*GP*AP*GP*TP*CP*CP*G)-3' Chain: E
Molecule details ›
Chain: E
Length: 12 nucleotides
Theoretical weight: 3.64 KDa
Source organism: Xenopus laevis
Expression system: Not provided
5'-D(*CP*3DRP*GP*GP*AP*CP*TP*3DRP*AP*CP*GP*GP*GP)-3' Chain: F
Molecule details ›
Chain: F
Length: 13 nucleotides
Theoretical weight: 3.76 KDa
Source organism: Xenopus laevis
Expression system: Not provided

Ligands and Environments

5 bound ligands:
Ligand URA 1 x URA
Ligand GOL 1 x GOL
Ligand IPA 2 x IPA
Ligand EPE 2 x EPE
Ligand DUR 1 x DUR
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-1
Spacegroup: C2
Unit cell:
a: 120.596Å b: 85.653Å c: 78.467Å
α: 90° β: 118.56° γ: 90°
R-values:
R R work R free
0.166 0.163 0.229
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

25 review citations

Repair and genetic consequences of endogenous DNA base damage in mammalian cells.
Barnes et al. (2004)
24 more

7 mentions without citation

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