The assembled human DNA clamp, a trimer of the protein PCNA.

A DNA clamp, also known as a sliding clamp, is a protein fold that serves as a processivity-promoting factor in DNA replication. As a critical component of the DNA polymerase III holoenzyme, the clamp protein binds DNA polymerase and prevents the enzyme from dissociating from the template DNA strand. Because the rate-limiting step in the DNA synthesis reaction is the association of the polymerase with the DNA template, the presence of the sliding clamp dramatically increases the number of nucleotides that the polymerase can add to the growing strand per association event because the clamp-polymerase protein-protein interactions are stronger and more specific than the direct interactions between the polymerase and the template DNA strand. The DNA clamp protein's presence can increase the rate of DNA synthesis up to 1,000-fold versus a nonprocessive polymerase. Image File history File links Download high-resolution version (1108x1196, 527 KB) File links The following pages on the English Wikipedia link to this file (pages on other projects are not listed): Wikipedia:Picture of the day/Archive User talk:Ravedave User:My Cat inn/sandbox Wikipedia:WikiProject Molecular and... Image File history File links Download high-resolution version (1108x1196, 527 KB) File links The following pages on the English Wikipedia link to this file (pages on other projects are not listed): Wikipedia:Picture of the day/Archive User talk:Ravedave User:My Cat inn/sandbox Wikipedia:WikiProject Molecular and... Trimer might refer to: trimer (chemistry), a reaction product composed of three identical molecules trimer (biochemistry), a compound of three macromolecules non-covalently bound This is a disambiguation page: a list of articles associated with the same title. ... Proliferating Cell Nuclear Antigen, commonly known as PCNA, is a protein that acts as a cofactor for DNA polymerase delta in eukaryotic cells. ... A representation of the 3D structure of myoglobin, showing coloured alpha helices. ... In biochemistry, the tertiary structure of a protein is its overall shape. ... Processivity is the frequency with which an enzyme dissociates from the template during DNA replication. ... This article or section is in need of attention from an expert on the subject. ... Pol III can also refer to KNM Pol III, a Norwegian guard vessel from WW2 DNA polymerase III holoenzyme is the primary enzyme complex involved in prokaryotic DNA replication. ... 3D structure of the DNA-binding helix-hairpin-helix motifs in human DNA polymerase beta A DNA polymerase is an enzyme that assists in DNA replication. ... Ribbon diagram of the enzyme TIM, surrounded by the space-filling model of the protein. ... The structure of part of a DNA double helix. ... The rate-determining step is a chemistry term for the slowest step in a chemical reaction. ... A nucleotide is a chemical compound that consists of a heterocyclic base, a sugar, and one or more phosphate groups. ... Protein-protein interactions refer to the association of protein molecules and the study of these associations from the perspective of biochemistry and networks. ...

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 toroid-shaped clamp between the DNA and the protein surface. The DNA clamp fold is found in both prokaryotes and eukaryotes and has a rough twofold internal symmetry. Because of the toroidal shape of the assembled multimer, the clamp cannot dissociate from the template strand without also dissociating into monomers. abcdefg An α+β protein fold is a class of structural domains in which the secondary structure is composed of α-helices and β-strands that occur separately along the backbone. ... A nucleotide is a chemical compound that consists of a heterocyclic base, a sugar, and one or more phosphate groups. ... DNA split along the replication fork The replication fork is a structure which forms when DNA is ready to replicate itself. ... Water is an odourless substance that is essential to all known forms of life and is known as the universal solvent. ... Prokaryotes (from Old Greek pro- before + karyon nut or kernel, referring to the cell nucleus, + suffix -otos, pl. ... Kingdoms Animalia - Animals Fungi Plantae - Plants Protista A eukaryote (IPA: ) is an organism with a complex cell or cells, in which the genetic material is organized into a membrane-bound nucleus or nuclei. ... In chemistry, a monomer (from Greek mono one and meros part) is a small molecule that may become chemically bonded to other monomers to form a polymer. ...

Assembly

Sliding clamps are loaded onto their associated DNA template strands by specialized proteins known as "sliding clamp loaders", which also disassemble the clamps after replication has completed. The binding sites for these initiator proteins overlap with the binding sites for the DNA polymerase, so the clamp cannot simultaneously associate with a clamp loader and with a polymerase. Thus the clamp will not be actively disassembled while the polymerase remains bound. Although DNA clamps play a less significant role in associating with other DNA-interacting proteins, such as nucleosome assembly factors, Okazaki fragment ligases, and DNA repair proteins, all of these proteins also share a binding site on the DNA clamp that overlaps with the clamp loader site, ensuring that the clamp will not be removed while any enzyme is still working on the DNA. The activity of the clamp loader requires ATP hydrolysis to "close" the clamp around the DNA. A nucleosome is a unit made of DNA and histones. ... śś¼Wiki markup: {{}} | [] [[]] [[Category:]] #REDIRECT [[]] Cite error 4; Invalid <ref> tag; refs with no name must have content • (templates) Okazaki fragment is a relatively short fragment of DNA (with an RNA primer at the 5 terminus) created on the lagging strand during DNA replication. ... DNA damage resulting in multiple broken chromosomes DNA repair is a process constantly operating in cells; it is essential to survival because it protects the genome from damage and harmful mutations. ... This is the reaction by which chemical energy that has been stored and transported in the high-energy phosphodiester bonds in ATP is released, for example in the muscles, to produce work. ...

References

• Watson JD, Baker TA, Bell SP, Gann A, Levine M, Losick R. (2004). Molecular Biology of the Gene 5th ed. Benjamin Cummings: Cold Spring Harbor Laboratory Press.
• Gulbis, J.M., Kelman, Z., Hurwitz, J., O`Donnell, M., Kuriyan, J. (1996). Structure of the C-terminal region of p21(WAF1/CIP1) complexed with human PCNA. Cell 87:297-306.

External links

• SCOP DNA clamp fold
• CATH box architecture