DNA Replication: How Does a Sliding Clamp Slide?

Abstract

DNA sliding clamps are rings that tether certain enzymes to DNA. How clamp proteins slide on DNA has remained a mystery. A new crystal structure, together with molecular dynamics and NMR studies, has revealed how the human PCNA clamp slides on DNA.

Figure 1. Human PCNA–DNA crystal structure

(A) Front view of the PCNA trimer–DNA (PDB ID 5L7C) in space-filling representation; each subunit is a different shade of grey. The α helices lining the central chamber are in ribbon representation. In pink are the helices that interact with DNA (the blue strand), and in green are the remaining α helices (the six lysine side chains that interact with DNA are in pink space-filling representation). DNA is in blue and orange. (B) Cut away side-view of PCNA–DNA. The representation and colors of the protein and DNA are the same as in (A).

Figure 2. The PCNA tilt on DNA may function in different ways

(A) The PCNA tilt is maintained during diffusion on DNA, causing it to spin during diffusion along DNA. As it spins, the tilt will alternate between a forward and then backward tilt every five base pairs. If polymerase δ requires a specific tilt of PCNA on DNA for active synthesis, this type of diffusion will enable PCNA to maintain the specific tilt during diffusion, such that when PCNA samples the 3′ terminus it will be in the correct tilt for activity with polymerase δ. (B) Top: the PCNA inner chamber is lined by 12 α helices; five α helices carry the charged residues that track one strand of DNA. Thus there are two sites in one circular clamp and this could enable a ‘tilt switch’ in one step without diffusion. The middle diagram illustrates the use of this type of switch for bringing the exonuclease site into the correct orientation for removal of a mismatched nucleotide at the primer 3′ terminus. The bottom diagram illustrates a speculative case in which a translesion DNA polymerase may require a different PCNA tilt for activity relative to polymerase δ. In this case, a direct switch in tilt could alter specificity of PCNA for a replicative polymerase δ or a translesion DNA polymerase.