› 3rzl

X-ray diffraction
2.6Å resolution

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

Released:
DOI: 10.2210/pdb3rzl/pdb
PDB 3rzl coloured by chain and viewed from the front.
PDB 3rzl coloured by chain and viewed from the side.
PDB 3rzl coloured by chain and viewed from the top.
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
OpenAccess logo 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:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA oxidative demethylase ALKBH2 Chains: A, D
Molecule details ›
Chains: A, D
Length: 208 amino acids
Theoretical weight: 23.72 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(*AP*TP*GP*TP*AP*TP*CP*AP*CP*TP*GP*CP*G)-3' Chains: B, E
Molecule details ›
Chains: B, E
Length: 13 nucleotides
Theoretical weight: 3.97 KDa
Source organism: Homo sapiens
Expression system: Not provided
5'-D(*TP*CP*GP*CP*AP*GP*TP*IP*AP*TP*AP*CP*A)-3' Chains: C, F
Molecule details ›
Chains: C, F
Length: 13 nucleotides
Theoretical weight: 3.96 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand XL3 2 x XL3
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P212121
Unit cell:
a: 55.934Å b: 65.006Å c: 167.896Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.224 0.221 0.289
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

11 review citations

Multi-substrate selectivity based on key loops and non-homologous domains: new insight into ALKBH family.
Xu et al. (2021)
10 more

1 mention without citation

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