4TSZ

Crystal structure of DNA polymerase sliding clamp from Pseudomonas aeruginosa with ligand

Summary for 4TSZ

• Entry DOI: 10.2210/pdb4tsz/pdb
• Related PRD ID: PRD_001111
• Descriptor: DNA polymerase III subunit beta, ACE-GLN-ALC-ASP-LEU-ZCL peptide (3 entities in total)
• Functional Keywords: transferase
• Biological source: Pseudomonas aeruginosa; More
• Total number of polymer chains: 32
• Total formula weight: 666355.47

Authors

Olieric, V.,Burnouf, D.,Ennifar, E.,Wolff, P. (deposition date: 2014-06-19, release date: 2014-09-10, Last modification date: 2016-12-21)

Primary citation

Wolff, P.,Amal, I.,Olieric, V.,Chaloin, O.,Gygli, G.,Ennifar, E.,Lorber, B.,Guichard, G.,Wagner, J.,Dejaegere, A.,Burnouf, D.Y.
Differential Modes of Peptide Binding onto Replicative Sliding Clamps from Various Bacterial Origins.
J.Med.Chem., 57:7565-7576, 2014

PubMed Abstract: Bacterial sliding clamps are molecular hubs that interact with many proteins involved in DNA metabolism through their binding, via a conserved peptidic sequence, into a universally conserved pocket. This interacting pocket is acknowledged as a potential molecular target for the development of new antibiotics. We previously designed short peptides with an improved affinity for the Escherichia coli binding pocket. Here we show that these peptides differentially interact with other bacterial clamps, despite the fact that all pockets are structurally similar. Thermodynamic and modeling analyses of the interactions differentiate between two categories of clamps: group I clamps interact efficiently with our designed peptides and assemble the Escherichia coli and related orthologs clamps, whereas group II clamps poorly interact with the same peptides and include Bacillus subtilis and other Gram-positive clamps. These studies also suggest that the peptide binding process could occur via different mechanisms, which depend on the type of clamp.

PubMed: 25170813
DOI: 10.1021/jm500467a

Experimental method

X-RAY DIFFRACTION (2 Å)