all three subunits are involved in PCNA binding, and mutations in the PCNA order SCD-inhibitor binding motifs have shown that all three subunits are required for optimal PCNA binding. The equivalence of the apparent 8 Human DNA Polymerase Delta binding of the two human trimeric subassemblies would suggest that there may be multiple modes of interaction when the Pol d holoenzyme interacts with PCNA. The requirement for multiple conformations of Pol d in its binding to PCNA may arise because PCNA serves as a platform on which multiple proteins are involved in coordinated DNA transactions, for example in Okazaki fragment processing, where coordination of Pol d with Fen1 and other nucleases are required for removal of primers, as well as with DNA ligase for completion of the process. In other systems, structural analysis of PCNA binding proteins that need to coordinate their occupancy of PCNA has provided evidence that these proteins may have multiple conformations of binding with PCNA, e. g., in the case of S. solfataricus DNA polymerase, Fen1 and DNA ligase interactions with PCNA. However, the future elucidation of the structure of Pol d will be required to gain further insights into how the individual subunits may physically interact with the PCNA molecule. Thus, our data using the poly/oligo assays support a perspective in which the core enzyme has sufficient affinity for PCNA to carry out elongation of the oligo primer, and that addition of either PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/22202440 the p68 or p12 subunit is sufficient to increase the affinity for PCNA so that a maximal stimulation is observed. 
9 Human DNA Polymerase Delta However, interpretation of these data must bear in mind that these are derived from measurement of the response of the enzymes to PCNA with the poly/oligo template primer. This substrate consists of a sparsely primed 4000 nt poly template onto which PCNA is freely able slide onto the ends and does not require loading by RFC; the homopolymeric nature of the template also eliminates the possibility of formation of secondary structures that could lead to stalling of Pol d. With this in mind we have also analyzed the behavior of the Pol d complexes on sparsely primed M13 DNA. The comparisons of the behavior of the Pol d complexes reveal much greater differences. In this case, only the core+p68 trimer is able to perform synthesis of the 7.4 kb M13 in a manner comparable to the Pol d4 holoenzyme. This suggests that the p68 subunit plays a major role in PCNA binding. Our recent studies have established that the core+p68 trimer is a physiologically relevant enzyme, as the cellular content of Pol d4 is wholly converted to the core+p68 trimer during challenge by genotoxic agents or by replication stress. In other studies using the core+p68 trimer prepared by the methods reported here, we have shown that the core+p68 trimer exhibits altered properties which are consistent with the hypothesis that its formation may be useful to the cell undergoing genotoxic stress. The core+p68 trimer exhibits an increased discrimination against translesion synthesis across damaged templates, and a decreased tendency for extension of mismatched primers. Pre-steady kinetic analyses further showed that the core+p68 enzyme has altered kinetic constants that are consistent with an increased proofreading ability, viz. greater fidelity in nucleotide incorporation than the Pol d4 enzyme. The question that arises is whether the core+p68 trimer is also present under other cellular conditions. Recent studies
