› 2ddg

X-ray diffraction
2.1Å resolution

Crystal structure of uracil-DNA glycosylase in complex with AP:G containing DNA

Released:
DOI: 10.2210/pdb2ddg/pdb
PDB entry 2ddg coloured by chain, front view.
PDB entry 2ddg coloured by chain, side view.
PDB entry 2ddg coloured by chain, top view.
Source organism: Thermus thermophilus HB8
Primary publication:
Crystal structure of family 5 uracil-DNA glycosylase bound to DNA.
Kosaka H, Hoseki J, Nakagawa N, Kuramitsu S, Masui R
J Mol Biol 373 839-50 (2007)
PMID: 17870091

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-115168 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Type-5 uracil-DNA glycosylase Chain: A
Molecule details ›
Chain: A
Length: 219 amino acids
Theoretical weight: 24.32 KDa
Source organism: Thermus thermophilus HB8
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q5SJ65 (Residues: 1-219; Coverage: 100%)
Gene names: TTHA1149, udgb
Sequence domains: Uracil DNA glycosylase superfamily
Structure domains: Uracil-DNA glycosylase-like domain
5'-D(*AP*TP*GP*TP*TP*GP*CP*(D1P)P*TP*TP*AP*GP*TP*CP*C)-3' Chain: C
Molecule details ›
Chain: C
Length: 15 nucleotides
Theoretical weight: 4.46 KDa
Source organism: Thermus thermophilus HB8
Expression system: Not provided
5'-D(*GP*GP*AP*CP*TP*AP*AP*GP*GP*CP*AP*AP*CP*A)-3' Chain: D
Molecule details ›
Chain: D
Length: 14 nucleotides
Theoretical weight: 4.32 KDa
Source organism: Thermus thermophilus HB8
Expression system: Not provided

Ligands and Environments

5 bound ligands:
Ligand ACT 2 x ACT
Ligand 2HP 2 x 2HP
Ligand SF4 1 x SF4
Ligand GOL 1 x GOL
Ligand EOH 4 x EOH
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E
Spacegroup: C2221
Unit cell:
a: 68.927Å b: 150.174Å c: 93.408Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.218 0.218 0.24
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

7 review citations

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

5 mentions without citation

Molecular mechanisms of the whole DNA repair system: a comparison of bacterial and eukaryotic systems.
Morita et al. (2010)
4 more