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TitleThe E. coli DnaX clamp loader sharply bends DNA to load β-clamp at nicks and small gaps.
Journal, issue, pagesMol Cell, Vol. 86, Issue 11, Page 2055-2069.e10, Year 2026
Publish dateJun 4, 2026
AuthorsFengwei Zheng / Nina Y Yao / Roxana E Georgescu / Meinan Lyu / Michael E O'Donnell / Huilin Li /
PubMed AbstractDNA sliding clamps are essential for processive DNA synthesis in all domains of life and are loaded by ATP-dependent clamp loaders that recognize recessed 3' ends. How clamp loaders function at nicks ...DNA sliding clamps are essential for processive DNA synthesis in all domains of life and are loaded by ATP-dependent clamp loaders that recognize recessed 3' ends. How clamp loaders function at nicks and small single-stranded DNA (ssDNA) gaps-common DNA repair intermediates-remains unclear. Here, we show that the bacterial E. coli DnaX clamp loader uses a mechanism distinct from its eukaryotic counterpart. Whereas eukaryotic replication factor C (RFC) unwinds DNA at the recessed 3' end and stabilizes the 5'-dsDNA (double-stranded DNA) at a shoulder site, the bacterial DnaX-complex neither unwinds DNA nor stably binds the 5'-dsDNA in vitro. Instead, cryo-EM structures reveal that the β-clamp contains a conserved external DNA-binding site that bends gapped DNA by ∼150°, promoting insertion of 3'-dsDNA into the clamp. This DNA-bending mechanism enables efficient β-clamp loading at nicks and small gaps and reveals a distinct bacterial strategy likely important for DNA repair.
External linksMol Cell / PubMed:42140189 / PubMed Central
MethodsEM (single particle)
Resolution2.54 - 5.5 Å
Structure data

EMDB-71019: Consensus map of E. coli clamp loader DnaX-complex loading beta-clamp onto 10-nt gapped DNA in state 1 the DNA recognition state
Method: EM (single particle) / Resolution: 2.54 Å

EMDB-71020: Focus refined map of E. coli clamp loader sub-complex Psi-Chi
Method: EM (single particle) / Resolution: 5.5 Å

Source
  • Escherichia coli (E. coli)
  • DNA molecule (others)

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