Molecule of the Month: Sliding Clamps
Sliding clamps slide along DNA strands and keep DNA polymerase on track during replication
Exploring the Structure
Clamp Loader Complex (PDB entry 3u5z)
PDB entry 3u5z includes two copies of the complex of clamp, DNA and clamp loader, one with an open clamp (shown here) and one with a closed clamp. You'll notice that one of the DNA strands is longer--this corresponds to the template strand. The clamp will then assist DNA polymerase in extending the shorter strand. There are also sites for binding ATP between each of the five clamp-loader subunits. This structure includes molecules similar to ATP that can't be cleaved (shown in magenta). To compare the open and closed forms, click on the image for an interactive Jmol.
Topics for Further Discussion
- You can find structures for clamp loaders from other organisms in the PDB. Notice that they all have a similar structure, with five subunits in a helical arrangement.
- Some organisms use sliding clamps composed of three subunits, and others use sliding clamps with two subunits. You can find structures for both types in the PDB.
Related PDB-101 Resources
- Browse Protein Synthesis
- B. A. Kelch, D. L. Makino, M O'Donnell & J. Kuriyan (2012) Clamp loader ATPases and the evolution of DNA replication machinery. BMC Biology 10:34.
- T. R. Beattie & S. D. Bell (2011) The role of the DNA sliding clamp in Okazaki fragment maturation in archaea and eukaryotes. Biochemical Society Transactions 39:70-76.
June 2012, David Goodsellhttp://doi.org/10.2210/rcsb_pdb/mom_2012_6