› 5clb

X-ray diffraction
1.77Å resolution

Alkylpurine DNA glycosylase AlkD bound to DNA containing a 3-methyladenine analog (9-mer A)

Released:
DOI: 10.2210/pdb5clb/pdb
PDB entry 5clb coloured by chain, front view.
PDB entry 5clb coloured by chain, side view.
PDB entry 5clb coloured by chain, top view.
Source organisms:
Primary publication:
The DNA glycosylase AlkD uses a non-base-flipping mechanism to excise bulky lesions.
Mullins EA, Shi R, Parsons ZD, Yuen PK, David SS, Igarashi Y, Eichman BF
Nature 527 254-8 (2015)
PMID: 26524531

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-238527 (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(*AP*AP*GP*CP*AP*(DZM)P*AP*CP*C)-3') Chain: B
Molecule details ›
Chain: B
Length: 9 nucleotides
Theoretical weight: 2.73 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*TP*GP*GP*TP*TP*TP*GP*CP*T)-3') Chain: C
Molecule details ›
Chain: C
Length: 9 nucleotides
Theoretical weight: 2.75 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

No bound ligands
1 modified residue:
Ligand DZM 1 x DZM

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-F
Spacegroup: C2
Unit cell:
a: 127.439Å b: 55.405Å c: 47.969Å
α: 90° β: 105.7° γ: 90°
R-values:
R R work R free
0.165 0.163 0.203
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

12 review citations

Base excision repair of oxidative DNA damage: from mechanism to disease.
Whitaker et al. (2017)
11 more

2 mentions without citation

The DNA glycosylase AlkD uses a non-base-flipping mechanism to excise bulky lesions.
Mullins et al. (2015)
1 more