› 2oxm

X-ray diffraction
2.5Å resolution

Crystal structure of a UNG2/modified DNA complex that represent a stabilized short-lived extrahelical state in ezymatic DNA base flipping

Released:
DOI: 10.2210/pdb2oxm/pdb
PDB entry 2oxm coloured by chain, front view.
PDB entry 2oxm coloured by chain, side view.
PDB entry 2oxm coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Enzymatic capture of an extrahelical thymine in the search for uracil in DNA.
Parker JB, Bianchet MA, Krosky DJ, Friedman JI, Amzel LM, Stivers JT
Nature 449 433-7 (2007)
PMID: 17704764

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-115743 (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
DNA (5'-D(*TP*GP*TP*TP*AP*TP*CP*TP*T)-3') Chain: B
Molecule details ›
Chain: B
Length: 9 nucleotides
Theoretical weight: 2.71 KDa
Source organism: Homo sapiens
Expression system: Not provided
DNA (5'-D(*AP*AP*AP*GP*AP*TP*(4MF)P*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
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU300
Spacegroup: P212121
Unit cell:
a: 48.467Å b: 65.567Å c: 98.472Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.257 0.254 0.328
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

22 review citations

Early steps in the DNA base excision/single-strand interruption repair pathway in mammalian cells.
Hegde et al. (2008)
21 more

14 mentions without citation

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