› 3h8o

X-ray diffraction
2Å resolution

Structure determination of DNA methylation lesions N1-meA and N3-meC in duplex DNA using a cross-linked host-guest system

Released:
DOI: 10.2210/pdb3h8o/pdb
PDB entry 3h8o coloured by chain, front view.
PDB entry 3h8o coloured by chain, side view.
PDB entry 3h8o coloured by chain, top view.
Source organisms:
Primary publication:
Structure determination of DNA methylation lesions N1-meA and N3-meC in duplex DNA using a cross-linked protein-DNA system.
Lu L, Yi C, Jian X, Zheng G, He C
Nucleic Acids Res 38 4415-25 (2010)
PMID: 20223766

Function and Biology Details

Reaction catalysed: 
DNA-base-CH(3) + 2-oxoglutarate + O(2) = DNA-base + formaldehyde + succinate + CO(2)
Biochemical function:
  • not assigned
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116353 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA oxidative demethylase ALKBH2 Chain: A
Molecule details ›
Chain: A
Length: 209 amino acids
Theoretical weight: 23.71 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q6NS38 (Residues: 56-261; Coverage: 79%)
Gene names: ABH2, ALKBH2
Sequence domains: 2OG-Fe(II) oxygenase superfamily
Structure domains: Alpha-ketoglutarate-dependent dioxygenase AlkB-like
5'-D(*CP*TP*GP*TP*AP*TP*(2YR)P*AP*TP*(MA7)P*GP*CP*G)-3' Chain: B
Molecule details ›
Chain: B
Length: 13 nucleotides
Theoretical weight: 4.04 KDa
Source organism: synthetic construct
Expression system: Not provided
5'-D(*TP*CP*GP*CP*TP*AP*TP*AP*AP*TP*AP*CP*A)-3' Chain: C
Molecule details ›
Chain: C
Length: 13 nucleotides
Theoretical weight: 3.93 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand GOL 1 x GOL
1 modified residue:
Ligand MA7 1 x MA7

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-B
Spacegroup: P6522
Unit cell:
a: 79.11Å b: 79.11Å c: 242.27Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.204 0.202 0.237
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

9 review citations

Structural studies on human 2-oxoglutarate dependent oxygenases.
McDonough et al. (2010)
8 more

8 mentions without citation

New insights into Hoogsteen base pairs in DNA duplexes from a structure-based survey.
Zhou et al. (2015)
7 more