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 philosopher believes that the value of his philosophy lies in its totality, in its structure: posterity discovers it in the stones with which he built and with which other structures are subsequently built that are frequently better—and so, in the fact that that structure can be demolished and yet still possess value as material.”
—Friedrich Nietzsche (1844–1900)
“Slumism is the pent-up anger of people living on the outside of affluence. Slumism is decay of structure and deterioration of the human spirit. Slumism is a virus which spreads through the body politic. As other “isms,” it breeds disorder and demagoguery and hate.”
—Hubert H. Humphrey (1911–1978)
“What is the most rigorous law of our being? Growth. No smallest atom of our moral, mental, or physical structure can stand still a year. It grows—it must grow; nothing can prevent it.”
—Mark Twain [Samuel Langhorne Clemens] (1835–1910)