The Link Clamp and Its Role in DNA Replication

The Link Clamp and Its Role in DNA Replication

Link Clamp

During the course of DNA replication, the 12.12.link clamp link clamp is used to stabilise the DNA molecule between polymerases and clamp loaders.12.link clamp The tightening of the clamp is accomplished by the interaction between the conserved b-clamp binding motif and its peptide partners. This interaction is governed by strict regulation. In order to function correctly, the b-clamp must not only ensure that its peptide binding partner is properly positioned, but it also needs to make sure that the bond is strong enough to withstand the high clamping forces applied by the polymerases. The complex interplay between bacterial processivity factors and their various clamp-binding peptide partners is well established and has been characterised at an unprecedented level in recent years.

The central residues in the b-clamp binding motifs are generally quite conserved across bacteria, but the peripheral side chains of these motifs have the potential to vary considerably between proteins.12.link clamp This variation is particularly prominent for the Arg-152 and His-175 residues of the b-clamp surface. These residues are the key determinants of the position and stability of the various peptide-clamp binding motifs.

In the case of the UmuC peptide, the differences between the positioning of its central and peripheral amino acids are striking.12.link clamp As a result, the glycine residue in the UmuC b-clamp binding motif (UmuC#359 in Figure 3) does not insert into the clamp hydrophobic pocket in the same way that it does in other peptide-clamp structures.

By contrast, the Pol II b-clamp binding motif has a side chain at position 359 similar to that of UmuC#359 but which forms a hydrogen bond with clamp Arg-152 (Pol II#359 in Figure 2).12.link clamp Similarly, the Glu-23 side chain of the Pol III b-clamp binding motif makes contact with the Arg-152 hydrogen atom through a water molecule, rather than directly forming a salt bridge like the Asn-359 side chain of UmuC.

The results from the two different crystal structures of a Pol II-UmuC peptide complex suggest that these differences are not just an artifact of differences in the structural alignments of the binding sites but that a change in the central position of the glycine residue in the b-clamp binding motif can significantly alter the interaction with the peptide.12.link clamp This is consistent with the hypothesis that the polarity of the peptide and the position of its backbone oxygens in the hydrophobic pocket affect the binding of the peptide to the b-clamp. In addition, the polarity of the peptide backbone may also influence the ability of the Leu-358 side chain to form intimate contacts with the clamp surface. The polarity of the peptide backbone is also likely to have an impact on the positioning of the conserved phenylalanine in the Pol IV b-clamp binding motif. The polarity of this residue determines whether it inserts into the b-clamp binding pocket at subsite 1, or is oriented towards the solvent as observed in other peptide-clamp complexes.

Link Clamp