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:
“I’m a Sunday School teacher, and I’ve always known that the structure of law is founded on the Christian ethic that you shall love the Lord your God and your neighbor as yourself—a very high and perfect standard. We all know the fallibility of man, and the contentions in society, as described by Reinhold Niebuhr and many others, don’t permit us to achieve perfection.”
—Jimmy Carter (James Earl Carter, Jr.)
“What is the structure of government that will best guard against the precipitate counsels and factious combinations for unjust purposes, without a sacrifice of the fundamental principle of republicanism?”
—James Madison (1751–1836)
“Just as a new scientific discovery manifests something that was already latent in the order of nature, and at the same time is logically related to the total structure of the existing science, so the new poem manifests something that was already latent in the order of words.”
—Northrop Frye (b. 1912)