› 4b23

X-ray diffraction
2Å resolution

Unprecedented sculpting of DNA at abasic sites by DNA glycosylase homolog Mag2

Released:
DOI: 10.2210/pdb4b23/pdb
PDB entry 4b23 coloured by chain, front view.
PDB entry 4b23 coloured by chain, side view.
PDB entry 4b23 coloured by chain, top view.
Source organisms:
Primary publication:
Sculpting of DNA at abasic sites by DNA glycosylase homolog mag2.
Dalhus B, Nilsen L, Korvald H, Huffman J, Forstrøm RJ, McMurray CT, Alseth I, Tainer JA, Bjørås M
Structure 21 154-166 (2013)
PMID: 23245849

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-117230 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Alkylbase DNA glycosidase-like protein mag2 Chain: A
Molecule details ›
Chain: A
Length: 232 amino acids
Theoretical weight: 26.36 KDa
Source organism: Schizosaccharomyces pombe
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: O94468 (Residues: 1-213; Coverage: 100%)
Gene names: SPBC23G7.11, mag2
Sequence domains: HhH-GPD superfamily base excision DNA repair protein
Structure domains:
5'-D(*GP*CP*TP*AP*CP*(3DR)P*AP*AP*TP*CP*GP)-3' Chain: X
Molecule details ›
Chain: X
Length: 11 nucleotides
Theoretical weight: 3.21 KDa
Source organism: synthetic construct
Expression system: Not provided
5'-D(*CP*GP*AP*TP*TP*GP*GP*TP*AP*GP*CP)-3' Chain: Y
Molecule details ›
Chain: Y
Length: 11 nucleotides
Theoretical weight: 3.39 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU
Spacegroup: I222
Unit cell:
a: 68.48Å b: 84.52Å c: 125.75Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.248 0.248 0.29
Expression systems:
  • Escherichia coli BL21
  • Not provided

Quick links

Citations

2 review citations

Envisioning the dynamics and flexibility of Mre11-Rad50-Nbs1 complex to decipher its roles in DNA replication and repair.
Lafrance-Vanasse et al. (2015)
1 more

1 mention without citation

Sculpting of DNA at abasic sites by DNA glycosylase homolog mag2.
Dalhus et al. (2013)