3D1F: Crystal structure of E. coli sliding clamp (beta) bound to a polymerase III peptide

DNA polymerases attach to the DNA sliding clamp through a common overlapping binding site. We identify a small-molecule compound that binds the protein-binding site in the Escherichia coli beta-clamp and differentially affects the activity of DNA polymerases II, III, and IV. To understand the molecular basis of this discrimination, the cocrystal structure of the chemical inhibitor is solved in complex with beta and is compared with the structures of Pol II, Pol III, and Pol IV peptides bound to beta. The analysis reveals that the small molecule localizes in a region of the clamp to which the DNA polymerases attach in different ways. The results suggest that the small molecule may be useful in the future to probe polymerase function with beta, and that the beta-clamp may represent an antibiotic target.
PDB ID: 3D1FDownload
MMDB ID: 65749
PDB Deposition Date: 2008/5/5
Updated in MMDB: 2017/11
Experimental Method:
x-ray diffraction
Resolution: 2  Å
Source Organism:
Escherichia coli
Similar Structures:
Biological Unit for 3D1F: tetrameric; determined by author and by software (PISA)
Molecular Components in 3D1F
Label Count Molecule
Proteins (4 molecules)
DNA Polymerase III Subunit Beta(Gene symbol: dnaN)
Molecule annotation
Nonapeptide From Polymerase III C-terminal
Molecule annotation
Chemicals (4 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB