› 4zbx

X-ray diffraction
1.7Å resolution

Family 4 uracil-DNA glycosylase from Sulfolobus tokodaii (free form, X-ray wavelength=0.9000)

Released:
DOI: 10.2210/pdb4zbx/pdb
PDB entry 4zbx coloured by chain, front view.
PDB entry 4zbx coloured by chain, side view.
PDB entry 4zbx coloured by chain, top view.
Source organism: Sulfurisphaera tokodaii str. 7
Primary publication:
Crystal structure of family 4 uracil-DNA glycosylase from Sulfolobus tokodaii and a function of tyrosine 170 in DNA binding.
Kawai A, Higuchi S, Tsunoda M, Nakamura KT, Yamagata Y, Miyamoto S
FEBS Lett 589 2675-82 (2015)
PMID: 26318717

Function and Biology Details

Reaction catalysed: 
Hydrolyzes single-stranded DNA or mismatched double-stranded DNA and polynucleotides, releasing free uracil
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-188792 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Type-4 uracil-DNA glycosylase Chain: A
Molecule details ›
Chain: A
Length: 194 amino acids
Theoretical weight: 22.36 KDa
Source organism: Sulfurisphaera tokodaii str. 7
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q96YD0 (Residues: 1-194; Coverage: 88%)
Gene name: STK_22380
Sequence domains: Uracil DNA glycosylase superfamily
Structure domains: Uracil-DNA glycosylase-like domain

Ligands and Environments

2 bound ligands:
Ligand SF4 1 x SF4
Ligand MES 1 x MES
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL44XU
Spacegroup: P212121
Unit cell:
a: 52.189Å b: 52.25Å c: 74.453Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.171 0.169 0.216
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 citation in other articles

Molecular Basis of Substrate Recognition of Endonuclease Q from the Euryarchaeon Pyrococcus furiosus.
Shiraishi et al. (2020)
1 more