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9vnq

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Bacillus Subtilis Ku core homodimer complexed with double strand DNA

Structural highlights

9vnq is a 6 chain structure with sequence from Bacillus subtilis and Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 2.74Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

KU_BACSU With LigD forms a non-homologous end joining (NHEJ) DNA repair enzyme, which repairs dsDNA breaks with reduced fidelity. Binds linear dsDNA with 5'- and 3'- overhangs but not closed circular dsDNA nor ssDNA. Recruits and stimulates the ligase activity of LigD (By similarity). Probably involved in DNA repair during spore germination.[HAMAP-Rule:MF_01875]^[1]

Publication Abstract from PubMed

DNA double-strand breaks (DSBs) pose a severe threat to genomic integrity, and cells rely on two major pathways for repair: homologous recombination and non-homologous end joining (NHEJ). While eukaryotic NHEJ requires a multi-component assembly including the Ku70/80 heterodimer, bacterial NHEJ operates with a simpler toolkit comprising a Ku homodimer and the multifunctional LigD. Despite this simplicity, the mechanism by which broken DNA ends are bridged together has remained unclear in bacterial NHEJ. Here, we present a cryo-electron microscopy structure of the Bacillus subtilis Ku (bsKu)-DNA complex at 2.74 A resolution, capturing two blunt DNA ends bridged by a Ku protein alone. Supported by further biochemical assays, we propose an integrated model in which oligomeric arrays of Ku homodimers bridge and stabilize two DNA ends, facilitating efficient DSB repair in Bacillus subtilis. This work reveals a bsKu-mediated DNA bridging mechanism distinct from the eukaryotic system and provides critical structural insight into prokaryotic DNA repair.

Structure of Bacillus subtilis Ku-mediated DNA synaptic complex.,Kim WJ, Kim J, Jo M, Kim Y, Kim MS Nucleic Acids Res. 2025 Oct 21:gkaf1036. doi: 10.1093/nar/gkaf1036. PMID:41118517^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Wang ST, Setlow B, Conlon EM, Lyon JL, Imamura D, Sato T, Setlow P, Losick R, Eichenberger P. The forespore line of gene expression in Bacillus subtilis. J Mol Biol. 2006 Apr 21;358(1):16-37. PMID:16497325 doi:10.1016/j.jmb.2006.01.059
↑ Kim WJ, Kim J, Jo M, Kim Y, Kim MS. Structure of Bacillus subtilis Ku-mediated DNA synaptic complex. Nucleic Acids Res. 2025 Oct 21:gkaf1036. PMID:41118517 doi:10.1093/nar/gkaf1036