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TitleBringing the ends together: cryo-EM structures of mycobacterial Ku in complex with DNA define its role in NHEJ synapsis.
Journal, issue, pagesNucleic Acids Res, Vol. 54, Issue 1, Year 2026
Publish dateJan 5, 2026
AuthorsJoydeep Baral / Ching-Seng Ang / Paul James McMillan / Kalyan Shobhana / Ayushi Saini / Elizabeth Hinde / Amit Kumar Das / Isabelle Rouiller /
PubMed AbstractNon-homologous end joining (NHEJ) is the sole pathway for repairing double-strand breaks in Mycobacterium tuberculosis during dormancy, relying on mycobacterial Ku (mKu) and ligase D, with mKu as the ...Non-homologous end joining (NHEJ) is the sole pathway for repairing double-strand breaks in Mycobacterium tuberculosis during dormancy, relying on mycobacterial Ku (mKu) and ligase D, with mKu as the rate-limiting factor. Despite its essential role, the lack of structural information on prokaryotic Ku has hindered understanding of the molecular mechanisms underlying bacterial two-component NHEJ machinery. Here, we present the first cryo-electron microscopy (cryo-EM) structures of mKu in DNA-bound and higher-order supercomplex forms, revealing a Ku-mediated DNA synapsis mechanism unique to prokaryotes. Integrating cryo-EM with hydrogen-deuterium exchange mass spectrometry, we define key mKu-mKu dimerization, DNA-binding, and synapsis interactions essential for efficient NHEJ, bridging structure with function. Structure-guided in silico mutagenesis, coupled with electrophoretic mobility shift assays, identifies residues essential for DNA binding and synaptic assembly, which are crucial for NHEJ. Förster resonance energy transfer confirms DNA-dependent mKu oligomerization in solution, while live-cell imaging captures its spatiotemporal dynamics during double-stranded DNA break repair. These findings provide fundamental insights into the architecture and function of prokaryotic NHEJ, positioning mKu as a potential therapeutic target against tuberculosis and offering a framework for understanding DNA repair across bacterial species.
External linksNucleic Acids Res / PubMed:41521670 / PubMed Central
MethodsEM (single particle)
Resolution3.7 - 4.1 Å
Structure data

42978

8v53

EMDB-42978, PDB-8v53:
CryoEM structure of Ku homodimer in complex with hairpin DNA
Method: EM (single particle) / Resolution: 4.1 Å

43184

8vf2

EMDB-43184, PDB-8vf2:
CryoEM structure of Ku homodimer super-complex with linear DNA
Method: EM (single particle) / Resolution: 3.7 Å

43185

8vf4

EMDB-43185, PDB-8vf4:
CryoEM structure of Ku homodimer super-complex with hairpin DNA
Method: EM (single particle) / Resolution: 4.1 Å

43186

8vf5

EMDB-43186, PDB-8vf5:
CryoEM structure of Ku homodimer in complex with linear DNA
Method: EM (single particle) / Resolution: 3.7 Å

Source
  • mycobacterium tuberculosis h37rv (bacteria)
  • synthetic construct (others)
KeywordsDNA BINDING PROTEIN / NHEJ / DNA repair / Mycobacterium tuberculosis / DNA synapsis / DNA BINDING PROTEIN/DNA / DNA Binding / Protein-DNA complex / DNA BINDING PROTEIN-DNA complex

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