› 6ksf

X-ray diffraction
2.4Å resolution

Crystal Structure of ALKBH1 bound to 21-mer DNA bulge

Released:
DOI: 10.2210/pdb6ksf/pdb
PDB entry 6ksf coloured by chain, front view.
PDB entry 6ksf coloured by chain, side view.
PDB entry 6ksf coloured by chain, top view.
Source organisms:
Primary publication:
Mammalian ALKBH1 serves as an N6-mA demethylase of unpairing DNA.
Zhang M, Yang S, Nelakanti R, Zhao W, Liu G, Li Z, Liu X, Wu T, Xiao A, Li H
Cell Res 30 197-210 (2020)
PMID: 32051560

Function and Biology Details

Reactions catalysed: 
DNA-base-CH(3) + 2-oxoglutarate + O(2) = DNA-base + formaldehyde + succinate + CO(2)
N(6)-methyladenine in DNA + 2-oxoglutarate + O(2) = adenine in DNA + formaldehyde + succinate + CO(2)
The C-O-P bond 3' to the apurinic or apyrimidinic site in DNA is broken by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-120175 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Nucleic acid dioxygenase ALKBH1 Chain: A
Molecule details ›
Chain: A
Length: 336 amino acids
Theoretical weight: 38.09 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0CB42 (Residues: 20-355; Coverage: 86%)
Gene names: Abh, Alkbh, Alkbh1
Sequence domains: 2OG-Fe(II) oxygenase superfamily
DNA (5'-D(*DGP*DCP*DTP*DGP*DAP*DGP*DTP*DGP*DCP*DCP*DCP*DGP*DCP*DGP*DTP*DGP*DCP*DTP*DGP*DGP*DAP*DTP*DCP*DC)-3') Chain: B
Molecule details ›
Chain: B
Length: 24 nucleotides
Theoretical weight: 7.38 KDa
Source organism: Homo sapiens
Expression system: Not provided
DNA (5'-D(*DGP*DGP*DAP*DTP*DCP*DCP*DAP*DGP*DCP*DAP*DCP*DGP*DCP*DCP*DAP*DCP*DTP*DCP*DAP*DGP*DC)-3') Chain: C
Molecule details ›
Chain: C
Length: 21 nucleotides
Theoretical weight: 6.38 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand CL 2 x CL
Ligand SIN 1 x SIN
Ligand XL3 1 x XL3
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P41212
Unit cell:
a: 67.482Å b: 67.482Å c: 263.641Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.23 0.228 0.272
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

16 review citations

The epitranscriptome beyond m6A.
Wiener et al. (2021)
15 more

2 mentions without citation

The role of demethylase AlkB homologs in cancer.
Li et al. (2023)
1 more