› 4uqm

X-ray diffraction
1.35Å resolution

Crystal structure determination of uracil-DNA N-glycosylase (UNG) from Deinococcus radiodurans in complex with DNA - new insights into the role of the Leucine-loop for damage recognition and repair

Released:
DOI: 10.2210/pdb4uqm/pdb
PDB entry 4uqm coloured by chain, front view.
PDB entry 4uqm coloured by chain, side view.
PDB entry 4uqm coloured by chain, top view.
Source organisms:
Primary publication:
Structure determination of uracil-DNA N-glycosylase from Deinococcus radiodurans in complex with DNA.
Pedersen HL, Johnson KA, McVey CE, Leiros I, Moe E
Acta Crystallogr D Biol Crystallogr 71 2137-49 (2015)
PMID: 26457437

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:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-118212 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Uracil-DNA glycosylase Chain: A
Molecule details ›
Chain: A
Length: 247 amino acids
Theoretical weight: 27.79 KDa
Source organism: Deinococcus radiodurans
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9RWH9 (Residues: 1-247; Coverage: 100%)
Gene names: DR_0689, ung
Sequence domains: Uracil DNA glycosylase superfamily
Structure domains: Uracil-DNA glycosylase-like domain
5'-D(*CP*CP*TP*AP*TP*CP*CP*AP*AAB*GP*TP*CP*TP*CP*CP*G)-3' Chain: B
Molecule details ›
Chain: B
Length: 16 nucleotides
Theoretical weight: 4.68 KDa
Source organism: synthetic construct
Expression system: Not provided
5'-D(*GP*CP*GP*GP*AP*GP*AP*CP*AP*TP*GP*GP*AP*CP*AP*G)-3' Chain: C
Molecule details ›
Chain: C
Length: 16 nucleotides
Theoretical weight: 5 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand CL 1 x CL
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: P21212
Unit cell:
a: 84.3Å b: 98.72Å c: 43.94Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.184 0.182 0.211
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

2 citation in other articles

Effects of Conserved Wedge Domain Residues on DNA Binding Activity of Deinococcus radiodurans RecG Helicase.
Jeong et al. (2021)
1 more

2 mentions without citation

A Decade of Biochemical and Structural Studies of the DNA Repair Machinery of Deinococcus radiodurans: Major Findings, Functional and Mechanistic Insight and Challenges.
Timmins et al. (2016)
1 more