Structure
The DNA clamp fold is an α+β protein that assembles into a multimeric structure that completely encircles the DNA double helix as the polymerase adds nucleotides to the growing strand. The DNA clamp assembles on the DNA at the replication fork and "slides" along the DNA with the advancing polymerase, aided by a layer of water molecules in the central pore of the clamp between the DNA and the protein surface. Because of the toroidal shape of the assembled multimer, the clamp cannot dissociate from the template strand without also dissociating into monomers.
The DNA clamp fold is found in bacteria, archaea, eukaryotes and some viruses. In bacteria, the sliding clamp is a homodimer composed of two identical beta subunits of DNA polymerase III and hence is referred to as the beta clamp. In archaea and eukaryotes, it is a trimer composed of three molecules of PCNA. The T4 bacteriophage also uses a sliding clamp, called gp45 that is a trimer similar in structure to PCNA but lacks sequence homology to either PCNA or the bacterial beta clamp.
| Kingdom | Sliding clamp protein | Aggregation state | Associated polymerase |
|---|---|---|---|
| Bacteria | beta subunit of pol III | dimer | DNA polymerase III |
| Archaea | archaeal PCNA | trimer | pol ε |
| Eukaryote | PCNA | trimer | DNA polymerase delta |
| Virus | gp43 / gp45 | trimer | RB69 Pol / T4 Pol |
Read more about this topic: DNA Clamp
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