› 3s6i

X-ray diffraction
2.28Å resolution

Schizosaccaromyces pombe 3-methyladenine DNA glycosylase (Mag1) in complex with abasic-DNA.

Released:
DOI: 10.2210/pdb3s6i/pdb
PDB entry 3s6i coloured by chain, front view.
PDB entry 3s6i coloured by chain, side view.
PDB entry 3s6i coloured by chain, top view.
Source organism: Schizosaccharomyces pombe 972h-
Primary publication:
Analysis of substrate specificity of Schizosaccharomyces pombe Mag1 alkylpurine DNA glycosylase.
Adhikary S, Eichman BF
EMBO Rep 12 1286-92 (2011)
PMID: 21960007

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-116865 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA-3-methyladenine glycosylase 1 Chains: A, D
Molecule details ›
Chains: A, D
Length: 228 amino acids
Theoretical weight: 26.42 KDa
Source organism: Schizosaccharomyces pombe 972h-
Expression system: Escherichia coli
UniProt:
  • Canonical: Q92383 (Residues: 1-228; Coverage: 100%)
Gene names: SPAPB24D3.04c, mag1
Sequence domains: HhH-GPD superfamily base excision DNA repair protein
Structure domains:
(5'-D(*TP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*T)-3') Chains: B, E
Molecule details ›
Chains: B, E
Length: 11 nucleotides
Theoretical weight: 3.19 KDa
Source organism: Schizosaccharomyces pombe 972h-
Expression system: Not provided
(5'-D(*AP*AP*GP*AP*CP*TP*TP*GP*GP*AP*C)-3') Chains: C, F
Molecule details ›
Chains: C, F
Length: 11 nucleotides
Theoretical weight: 3.38 KDa
Source organism: Schizosaccharomyces pombe 972h-
Expression system: Not provided

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-BM, APS BEAMLINE 21-ID-D
Spacegroup: P21
Unit cell:
a: 54.317Å b: 112.298Å c: 61.113Å
α: 90° β: 99.55° γ: 90°
R-values:
R R work R free
0.236 0.185 0.225
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 review citation

Structural Biology of the HEAT-Like Repeat Family of DNA Glycosylases.
Shi et al. (2018)
9 other articles

4 mentions without citation

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