› 3rzj

X-ray diffraction
2.5Å resolution

Duplex Interrogation by a Direct DNA Repair Protein in the Search of Damage

Released:
DOI: 10.2210/pdb3rzj/pdb
PDB entry 3rzj coloured by chain, front view.
PDB entry 3rzj coloured by chain, side view.
PDB entry 3rzj coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Duplex interrogation by a direct DNA repair protein in search of base damage.
Yi C, Chen B, Qi B, Zhang W, Jia G, Zhang L, Li CJ, Dinner AR, Yang CG, He C
Nat Struct Mol Biol 19 671-6 (2012)
PMID: 22659876

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-116845 (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: 23.78 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
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*CP*TP*(ME6)P*AP*CP*TP*GP*CP*G)-3' Chain: B
Molecule details ›
Chain: B
Length: 13 nucleotides
Theoretical weight: 3.93 KDa
Source organism: Homo sapiens
Expression system: Not provided
5'-D(*TP*CP*GP*CP*AP*GP*TP*GP*AP*GP*AP*CP*A)-3' Chain: C
Molecule details ›
Chain: C
Length: 13 nucleotides
Theoretical weight: 4 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand MN 1 x MN
Ligand AKG 1 x AKG
Ligand XL3 1 x XL3
1 modified residue:
Ligand ME6 1 x ME6

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-D
Spacegroup: P6522
Unit cell:
a: 77.779Å b: 77.779Å c: 229.016Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.229 0.227 0.259
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

16 review citations

Bacterial sigma factors: a historical, structural, and genomic perspective.
Feklístov et al. (2014)
15 more

8 mentions without citation

Duplex interrogation by a direct DNA repair protein in search of base damage.
Yi et al. (2012)
7 more