8VAL

Structure of the E. coli clamp loader bound to the beta clamp in a Open-DNAp/t conformation

Summary for 8VAL

• Entry DOI: 10.2210/pdb8val/pdb
• Related: 8VAM 8VAN 8VAP 8VAQ 8VAR 8VAS 8VAT
• EMDB information: 43094
• Descriptor: DNA polymerase III subunit delta, MAGNESIUM ION, DNA polymerase III subunit tau, ... (10 entities in total)
• Functional Keywords: bacterial clamp loader complex, replication, transferase-dna complex, transferase/dna
• Biological source: Escherichia coli; More
• Total number of polymer chains: 9
• Total formula weight: 300396.58

Authors

Landeck, J.T.,Kelch, B.A. (deposition date: 2023-12-11, release date: 2024-03-27, Last modification date: 2024-05-01)

Primary citation

Landeck, J.T.,Pajak, J.,Norman, E.K.,Sedivy, E.L.,Kelch, B.A.
Differences between bacteria and eukaryotes in clamp loader mechanism, a conserved process underlying DNA replication.
J.Biol.Chem., 300:107166-107166, 2024

PubMed Abstract: Clamp loaders are pentameric ATPases that place circular sliding clamps onto DNA, where they function in DNA replication and genome integrity. The central activity of a clamp loader is the opening of the ring-shaped sliding clamp and the subsequent binding to primer-template (p/t)-junctions. The general architecture of clamp loaders is conserved across all life, suggesting that their mechanism is retained. Recent structural studies of the eukaryotic clamp loader replication factor C (RFC) revealed that it functions using a crab-claw mechanism, where clamp opening is coupled to a massive conformational change in the loader. Here we investigate the clamp loading mechanism of the Escherichia coli clamp loader at high resolution using cryo-electron microscopy. We find that the E. coli clamp loader opens the clamp using a crab-claw motion at a single pivot point, whereas the eukaryotic RFC loader uses motions distributed across the complex. Furthermore, we find clamp opening occurs in multiple steps, starting with a partly open state with a spiral conformation, and proceeding to a wide open clamp in a surprising planar geometry. Finally, our structures in the presence of p/t-junctions illustrate how the clamp closes around p/t-junctions and how the clamp loader initiates release from the loaded clamp. Our results reveal mechanistic distinctions in a macromolecular machine that is conserved across all domains of life.

PubMed: 38490435
DOI: 10.1016/j.jbc.2024.107166

Experimental method

ELECTRON MICROSCOPY (3.7 Å)