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Structure paper

TitleStructural and mechanistic insights into the DNA glycosylase AAG-mediated base excision in nucleosome.
Journal, issue, pagesCell Discov, Vol. 9, Issue 1, Page 62, Year 2023
Publish dateJun 20, 2023
AuthorsLvqin Zheng / Bin Tsai / Ning Gao /
PubMed AbstractThe engagement of a DNA glycosylase with a damaged DNA base marks the initiation of base excision repair. Nucleosome-based packaging of eukaryotic genome obstructs DNA accessibility, and how DNA ...The engagement of a DNA glycosylase with a damaged DNA base marks the initiation of base excision repair. Nucleosome-based packaging of eukaryotic genome obstructs DNA accessibility, and how DNA glycosylases locate the substrate site on nucleosomes is currently unclear. Here, we report cryo-electron microscopy structures of nucleosomes bearing a deoxyinosine (DI) in various geometric positions and structures of them in complex with the DNA glycosylase AAG. The apo nucleosome structures show that the presence of a DI alone perturbs nucleosomal DNA globally, leading to a general weakening of the interface between DNA and the histone core and greater flexibility for the exit/entry of the nucleosomal DNA. AAG makes use of this nucleosomal plasticity and imposes further local deformation of the DNA through formation of the stable enzyme-substrate complex. Mechanistically, local distortion augmentation, translation/rotational register shift and partial opening of the nucleosome are employed by AAG to cope with substrate sites in fully exposed, occluded and completely buried positions, respectively. Our findings reveal the molecular basis for the DI-induced modification on the structural dynamics of the nucleosome and elucidate how the DNA glycosylase AAG accesses damaged sites on the nucleosome with different solution accessibility.
External linksCell Discov / PubMed:37339965 / PubMed Central
MethodsEM (single particle)
Resolution2.8 - 3.1 Å
Structure data

33171

7xfc

EMDB-33171, PDB-7xfc:
Structure of nucleosome-DI complex (-30I, Apo state)
Method: EM (single particle) / Resolution: 2.9 Å

33172

7xfh

EMDB-33172, PDB-7xfh:
Structure of nucleosome-AAG complex (A-30I, post-catalytic state)
Method: EM (single particle) / Resolution: 2.9 Å

33173

7xfi

EMDB-33173, PDB-7xfi:
Structure of nucleosome-DI complex (-50I, Apo state)
Method: EM (single particle) / Resolution: 2.9 Å

33174

7xfj

EMDB-33174, PDB-7xfj:
Structure of nucleosome-AAG complex (T-50I, post-catalytic state)
Method: EM (single particle) / Resolution: 3.0 Å

33175

7xfl

EMDB-33175, PDB-7xfl:
Structure of nucleosome-AAG complex (A-53I, free state)
Method: EM (single particle) / Resolution: 2.8 Å

33176

7xfm

EMDB-33176, PDB-7xfm:
Structure of nucleosome-AAG complex (A-53I, post-catalytic state)
Method: EM (single particle) / Resolution: 3.1 Å

33177

7xfn

EMDB-33177, PDB-7xfn:
Structure of nucleosome-DI complex (-55I, Apo state)
Method: EM (single particle) / Resolution: 2.8 Å

33322

7xnp

EMDB-33322, PDB-7xnp:
Structure of nucleosome-AAG complex (A-55I, post-catalytic state)
Method: EM (single particle) / Resolution: 2.9 Å

Source
  • xenopus laevis (African clawed frog)
  • homo sapiens (human)
KeywordsDNA BINDING PROTEIN/DNA / Nucleosome / AAG / DNA repair / Base excision repair / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex / Cryo-EM / Cyro-EM

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