› 2d3y

X-ray diffraction
1.55Å resolution

Crystal structure of uracil-DNA glycosylase from Thermus Thermophilus HB8

Released:
DOI: 10.2210/pdb2d3y/pdb
PDB entry 2d3y coloured by chain, front view.
PDB entry 2d3y coloured by chain, side view.
PDB entry 2d3y 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:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-177998 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
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

Ligands and Environments

3 bound ligands:
Ligand ACT 2 x ACT
Ligand SF4 1 x SF4
Ligand DU 1 x DU
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL45XU, SPRING-8 BEAMLINE BL44B2
Spacegroup: P212121
Unit cell:
a: 48.18Å b: 62.35Å c: 63.04Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.186 0.186 0.21
Expression system: Escherichia coli BL21(DE3)

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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

3 mentions without citation

Local conformational changes in the DNA interfaces of proteins.
Sunami et al. (2013)
2 more