› 4hsb

X-ray diffraction
1.9Å resolution

S. pombe 3-methyladenine DNA glycosylase-like protein Mag2 bound to damaged DNA

Released:
DOI: 10.2210/pdb4hsb/pdb
PDB entry 4hsb coloured by chain, front view.
PDB entry 4hsb coloured by chain, side view.
PDB entry 4hsb coloured by chain, top view.
Source organism: Schizosaccharomyces pombe 972h-
Primary publication:
Non-productive DNA damage binding by DNA glycosylase-like protein Mag2 from Schizosaccharomyces pombe.
Adhikary S, Cato MC, McGary KL, Rokas A, Eichman BF
DNA Repair (Amst) 12 196-204 (2013)
PMID: 23273506

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-117611 (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: 217 amino acids
Theoretical weight: 24.63 KDa
Source organism: Schizosaccharomyces pombe 972h-
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:
DNA (5'-D(P*GP*GP*AP*CP*TP*(3DR)P*AP*CP*GP*GP*G)-3') Chain: B
Molecule details ›
Chain: B
Length: 11 nucleotides
Theoretical weight: 3.29 KDa
Source organism: Schizosaccharomyces pombe 972h-
Expression system: Not provided
DNA (5'-D(P*CP*CP*CP*GP*TP*TP*AP*GP*TP*CP*C)-3') Chain: C
Molecule details ›
Chain: C
Length: 11 nucleotides
Theoretical weight: 3.29 KDa
Source organism: Schizosaccharomyces pombe 972h-
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand PEG 2 x PEG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-G
Spacegroup: P3221
Unit cell:
a: 54.891Å b: 54.891Å c: 153.457Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.194 0.192 0.234
Expression systems:
  • Escherichia coli BL21
  • Not provided

Quick links

Citations

3 citation in other articles

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

1 mention without citation

Non-productive DNA damage binding by DNA glycosylase-like protein Mag2 from Schizosaccharomyces pombe.
Adhikary et al. (2013)