Replication Clamps and Clamp Loaders

Abstract

To achieve the high degree of processivity required for DNA replication, DNA polymerases associate with ring-shaped sliding clamps that encircle the template DNA and slide freely along it. The closed circular structure of sliding clamps necessitates an enzyme-catalyzed mechanism, which not only opens them for assembly and closes them around DNA, but specifically targets them to sites where DNA synthesis is initiated and orients them correctly for replication. Such a feat is performed by multisubunit complexes known as clamp loaders, which use ATP to open sliding clamp rings and place them around the 3′ end of primer–template (PT) junctions. Here we discuss the structure and composition of sliding clamps and clamp loaders from the three domains of life as well as T4 bacteriophage, and provide our current understanding of the clamp-loading process.

Regulating DNA Replication in Bacteria

“…During DNA elongation, the clamps remain on the lagging strand after Okazaki fragments are synthesized and the DNA polymerase III core is released (Yuzhakov et al 1996;Balakrishnan and Bambara 2013;Goodman and Woodgate 2013;Hedglin et al 2013;MacAlpine and Almouzni 2013). DNA-loaded, DNA polymerase-free clamps bind ADP-Hda, resulting in the activation of RIDA (Su'etsugu et al 2004.…”

Mechanism of asymmetric polymerase assembly at the eukaryotic replication fork

“…All cells, in eukaryotes, archaea and bacteria alike, use circular sliding clamps that tether the polymerases to DNA for highly stable synthesis (for example, eukaryotic proliferating cell nuclear antigen (PCNA)) 7,8 . Sliding clamps are opened and closed around DNA by a multiprotein clamp loader (for example, eukaryotic replication factor C (RFC)) 7,9 . Both Pol ε and Pol δ function with the PCNA clamp, yet their actions are confined to opposite strands of the replication fork.…”

Stability of the human polymerase δ holoenzyme and its implications in lagging strand DNA synthesis

“…Each subunit consists of two independent domains connected by an interdomain connecting loop (IDCL). The "front" face of the homotrimeric PCNA ring contains all IDCLs and is a platform for interaction with the eukaryotic replicative pols, e and δ, which are responsible for the faithful replication of the leading and lagging strands, respectively (1,2). Specifically, the well-conserved PCNA-interacting peptide (PIP) box within replicative pols makes extensive contact with an IDCL of PCNA and displays conserved residues that "plug" into the proximal hydrophobic patches.…”