› 2yg9

X-ray diffraction
1.95Å resolution

Structure of an unusual 3-Methyladenine DNA Glycosylase II (Alka) from Deinococcus radiodurans

Released:
DOI: 10.2210/pdb2yg9/pdb
PDB entry 2yg9 coloured by chain, front view.
PDB entry 2yg9 coloured by chain, side view.
PDB entry 2yg9 coloured by chain, top view.
Source organism: Deinococcus radiodurans
Primary publication:
Structure-function studies of an unusual 3-methyladenine DNA glycosylase II (AlkA) from Deinococcus radiodurans.
Moe E, Hall DR, Leiros I, Monsen VT, Timmins J, McSweeney S
Acta Crystallogr D Biol Crystallogr 68 703-12 (2012)
PMID: 22683793

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:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-193239 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
DNA-3-methyladenine glycosylase II Chains: A, B
Molecule details ›
Chains: A, B
Length: 225 amino acids
Theoretical weight: 23.83 KDa
Source organism: Deinococcus radiodurans
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9RRB0 (Residues: 1-225; Coverage: 100%)
Gene name: DR_2584
Sequence domains: HhH-GPD superfamily base excision DNA repair protein
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand CL 4 x CL
Ligand GOL 1 x GOL
Ligand NI 2 x NI
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-1
Spacegroup: C2
Unit cell:
a: 108.311Å b: 51.372Å c: 90.039Å
α: 90° β: 99.71° γ: 90°
R-values:
R R work R free
0.173 0.17 0.231
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 review citations

Conservation and diversity of radiation and oxidative stress resistance mechanisms in Deinococcus species.
Lim et al. (2019)
1 more

2 mentions without citation

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