› 5uug

X-ray diffraction
1.71Å resolution

Bacillus cereus DNA glycosylase AlkD bound to a yatakemycin-adenine nucleobase adduct and DNA containing an abasic site (9-mer product complex)

Released:
DOI: 10.2210/pdb5uug/pdb
PDB entry 5uug coloured by chain, front view.
PDB entry 5uug coloured by chain, side view.
PDB entry 5uug coloured by chain, top view.
Source organisms:
Primary publication:
Toxicity and repair of DNA adducts produced by the natural product yatakemycin.
Mullins EA, Shi R, Eichman BF
Nat Chem Biol 13 1002-1008 (2017)
PMID: 28759018

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-238529 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA alkylation repair protein Chain: A
Molecule details ›
Chain: A
Length: 241 amino acids
Theoretical weight: 28.58 KDa
Source organism: Bacillus cereus
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: Q816E8 (Residues: 1-237; Coverage: 100%)
Gene name: BC_4913
Sequence domains: DNA alkylation repair enzyme
Structure domains: Leucine-rich Repeat Variant
DNA (5'-D(*AP*GP*GP*CP*AP*(ORP)P*AP*GP*C)-3') Chain: B
Molecule details ›
Chain: B
Length: 9 nucleotides
Theoretical weight: 2.66 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*TP*GP*CP*TP*TP*TP*GP*CP*C)-3') Chain: C
Molecule details ›
Chain: C
Length: 9 nucleotides
Theoretical weight: 2.7 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand CA 1 x CA
Ligand YTA 1 x YTA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-G
Spacegroup: C2
Unit cell:
a: 124.715Å b: 55.661Å c: 47.991Å
α: 90° β: 112.2° γ: 90°
R-values:
R R work R free
0.138 0.136 0.177
Expression systems:
  • Escherichia coli K-12
  • Not provided

Quick links

Citations

8 review citations

Emerging Roles of DNA Glycosylases and the Base Excision Repair Pathway.
Mullins et al. (2019)
7 more

2 mentions without citation

Toxicity and repair of DNA adducts produced by the natural product yatakemycin.
Mullins et al. (2017)
1 more