› 3ogd

X-ray diffraction
2.8Å resolution

AlkA Undamaged DNA Complex: Interrogation of a G*:C base pair

Released:
DOI: 10.2210/pdb3ogd/pdb
PDB entry 3ogd coloured by chain, front view.
PDB entry 3ogd coloured by chain, side view.
PDB entry 3ogd coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Structure of Escherichia coli AlkA in complex with undamaged DNA.
Bowman BR, Lee S, Wang S, Verdine GL
J Biol Chem 285 35783-91 (2010)
PMID: 20843803

Function and Biology Details

Reaction catalysed: 
Hydrolysis of alkylated DNA, releasing 3-methyladenine, 3-methylguanine, 7-methylguanine and 7-methyladenine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116646 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA-3-methyladenine glycosylase 2 Chain: A
Molecule details ›
Chain: A
Length: 289 amino acids
Theoretical weight: 32.13 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P04395 (Residues: 2-282; Coverage: 100%)
Gene names: JW2053, aidA, alkA, b2068
Sequence domains:
Structure domains:
5'-D(*GP*CP*AP*GP*TP*CP*AP*TP*G)-3' Chain: B
Molecule details ›
Chain: B
Length: 9 nucleotides
Theoretical weight: 2.76 KDa
Source organism: Escherichia coli K-12
Expression system: Not provided
5'-D(*CP*AP*(BRU)P*GP*AP*CP*(BRU)P*GP*C)-3' Chain: C
Molecule details ›
Chain: C
Length: 9 nucleotides
Theoretical weight: 2.85 KDa
Source organism: Escherichia coli K-12
Expression system: Not provided

Ligands and Environments

No bound ligands
1 modified residue:
Ligand BRU 2 x BRU

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: I4122
Unit cell:
a: 139.7Å b: 139.7Å c: 95.3Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.218 0.215 0.269
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 review citation

Computational investigations on target-site searching and recognition mechanisms by thymine DNA glycosylase during DNA repair process.
Wang et al. (2022)
13 other articles

3 mentions without citation

Recent advances in the structural mechanisms of DNA glycosylases.
Brooks et al. (2013)
2 more