7U1A

RFC:PCNA bound to dsDNA with a ssDNA gap of six nucleotides

Summary for 7U1A

• Entry DOI: 10.2210/pdb7u1a/pdb
• EMDB information: 25616 25617 26298
• Descriptor: Replication factor C subunit 1, PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER, MAGNESIUM ION, ... (12 entities in total)
• Functional Keywords: sliding clamp, dna replication&repair, aaa+, clamp loader, brct domain, replication, replication-dna complex, replication/dna
• Biological source: Saccharomyces cerevisiae (baker's yeast); More
• Total number of polymer chains: 11
• Total formula weight: 369265.94

Authors

Liu, X.,Gaubitz, C.,Pajak, J.,Kelch, B.A. (deposition date: 2022-02-20, release date: 2022-07-06, Last modification date: 2024-02-21)

Primary citation

Liu, X.,Gaubitz, C.,Pajak, J.,Kelch, B.A.
A second DNA binding site on RFC facilitates clamp loading at gapped or nicked DNA.
Elife, 11:-, 2022

PubMed Abstract: Clamp loaders place circular sliding clamp proteins onto DNA so that clamp-binding partner proteins can synthesize, scan, and repair the genome. DNA with nicks or small single-stranded gaps are common clamp-loading targets in DNA repair, yet these substrates would be sterically blocked given the known mechanism for binding of primer-template DNA. Here, we report the discovery of a second DNA binding site in the yeast clamp loader replication factor C (RFC) that aids in binding to nicked or gapped DNA. This DNA binding site is on the external surface and is only accessible in the open conformation of RFC. Initial DNA binding at this site thus provides access to the primary DNA binding site in the central chamber. Furthermore, we identify that this site can partially unwind DNA to create an extended single-stranded gap for DNA binding in RFC's central chamber and subsequent ATPase activation. Finally, we show that deletion of the BRCT domain, a major component of the external DNA binding site, results in defective yeast growth in the presence of DNA damage where nicked or gapped DNA intermediates occur. We propose that RFC's external DNA binding site acts to enhance DNA binding and clamp loading, particularly at DNA architectures typically found in DNA repair.

PubMed: 35731107
DOI: 10.7554/eLife.77483

Experimental method

ELECTRON MICROSCOPY (3.3 Å)