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
Famous quotes containing the word structure:
“The verbal poetical texture of Shakespeare is the greatest the world has known, and is immensely superior to the structure of his plays as plays. With Shakespeare it is the metaphor that is the thing, not the play.”
—Vladimir Nabokov (1899–1977)
“Women over fifty already form one of the largest groups in the population structure of the western world. As long as they like themselves, they will not be an oppressed minority. In order to like themselves they must reject trivialization by others of who and what they are. A grown woman should not have to masquerade as a girl in order to remain in the land of the living.”
—Germaine Greer (b. 1939)
“In the extent and proper structure of the Union, therefore, we behold a republican remedy for the diseases most incident to republican government.”
—James Madison (1751–1836)