› 4lyl

X-ray diffraction
1.93Å resolution

Crystal structure of uracil-DNA glycosylase from cod (Gadus morhua) in complex with the proteinaceous inhibitor UGI

Released:
DOI: 10.2210/pdb4lyl/pdb
PDB entry 4lyl coloured by chain, front view.
PDB entry 4lyl coloured by chain, side view.
PDB entry 4lyl coloured by chain, top view.
Source organisms:
Primary publication:
Structural and biophysical analysis of interactions between cod and human uracil-DNA N-glycosylase (UNG) and UNG inhibitor (Ugi).
Assefa NG, Niiranen L, Johnson KA, Leiros HK, Smalås AO, Willassen NP, Moe E
Acta Crystallogr D Biol Crystallogr 70 2093-100 (2014)
PMID: 25084329

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 analysis Details

Assemblies composition:
hetero dimer (preferred)
hetero tetramer
Assembly name:
PDBe Complex ID:
PDB-CPX-147057 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Uracil-DNA glycosylase Chains: A, C, E, G, I, K, M, O
Molecule details ›
Chains: A, C, E, G, I, K, M, O
Length: 223 amino acids
Theoretical weight: 25.29 KDa
Source organism: Gadus morhua
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9I983 (Residues: 82-301; Coverage: 73%)
Gene names: UNG, UNG1, ung1
Sequence domains: Uracil DNA glycosylase superfamily
Structure domains: Uracil-DNA glycosylase-like domain
Uracil-DNA glycosylase inhibitor Chains: B, D, F, H, J, L, N, P
Molecule details ›
Chains: B, D, F, H, J, L, N, P
Length: 84 amino acids
Theoretical weight: 9.48 KDa
Source organism: Bacillus phage PBS2
Expression system: Escherichia coli
UniProt:
  • Canonical: P14739 (Residues: 1-84; Coverage: 100%)
Gene name: UGI
Sequence domains: Uracil-DNA glycosylase inhibitor
Structure domains: Bacteriophage PBS2, uracil-glycosylase inhibitor

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: P21
Unit cell:
a: 98.21Å b: 86.92Å c: 175.37Å
α: 90° β: 90.35° γ: 90°
R-values:
R R work R free
0.239 0.237 0.283
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Applications and Prospects of CRISPR/Cas9-Mediated Base Editing in Plant Breeding.
Li et al. (2023)
1 other article

2 mentions without citation

An unconventional family 1 uracil DNA glycosylase in Nitratifractor salsuginis.
Li et al. (2017)
1 more