› 5kub

X-ray diffraction
1.73Å resolution

Bacillus cereus DNA glycosylase AlkD bound to 7-methylguanine nucleobase and DNA containing an oxocarbenium-intermediate analog

Released:
DOI: 10.2210/pdb5kub/pdb
PDB entry 5kub coloured by chain, front view.
PDB entry 5kub coloured by chain, side view.
PDB entry 5kub coloured by chain, top view.
Source organisms:
Primary publication:
A Catalytic Role for C-H/π Interactions in Base Excision Repair by Bacillus cereus DNA Glycosylase AlkD.
Parsons ZD, Bland JM, Mullins EA, Eichman BF
J Am Chem Soc 138 11485-8 (2016)
PMID: 27571247

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-118969 (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
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(*CP*CP*CP*GP*AP*(NRI)P*AP*GP*TP*CP*CP*G)-3') Chain: B
Molecule details ›
Chain: B
Length: 12 nucleotides
Theoretical weight: 3.5 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*CP*GP*GP*AP*CP*TP*CP*TP*CP*GP*GP*G)-3') Chain: C
Molecule details ›
Chain: C
Length: 12 nucleotides
Theoretical weight: 3.68 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand MY6 1 x MY6
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-F
Spacegroup: P21
Unit cell:
a: 38.45Å b: 93.603Å c: 47.991Å
α: 90° β: 112.54° γ: 90°
R-values:
R R work R free
0.143 0.141 0.18
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

4 review citations

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