› 6iob

X-ray diffraction
2Å resolution

The structure of the H109A mutant of UdgX in complex with uracil

Released:
DOI: 10.2210/pdb6iob/pdb
PDB entry 6iob coloured by chain, front view.
PDB entry 6iob coloured by chain, side view.
PDB entry 6iob coloured by chain, top view.
Source organism: Mycolicibacterium smegmatis MC2 155
Primary publication:
Suicide inactivation of the uracil DNA glycosylase UdgX by covalent complex formation.
Tu J, Chen R, Yang Y, Cao W, Xie W
Nat Chem Biol 15 615-622 (2019)
PMID: 31101915

Function and Biology Details

Reaction catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-125239 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Type-4 uracil-DNA glycosylase Chain: A
Molecule details ›
Chain: A
Length: 212 amino acids
Theoretical weight: 22.42 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
Expression system: Escherichia coli
UniProt:
  • Canonical: I7F541 (Residues: 7-215; Coverage: 97%)
Gene name: MSMEI_0259
Sequence domains: Uracil DNA glycosylase superfamily

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: NFPSS BEAMLINE BL19U1
Spacegroup: P21
Unit cell:
a: 39.151Å b: 51.158Å c: 40.957Å
α: 90° β: 92.19° γ: 90°
R-values:
R R work R free
0.197 0.195 0.254
Expression system: Escherichia coli

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Citations

3 review citations

Bacterial DNA excision repair pathways.
Wozniak et al. (2022)
2 more