6FVL

DNA polymerase sliding clamp from Escherichia coli with bound P7 peptide

Summary for 6FVL

• Entry DOI: 10.2210/pdb6fvl/pdb
• Descriptor: Beta sliding clamp, P7 peptide, PENTAETHYLENE GLYCOL, ... (5 entities in total)
• Functional Keywords: dna sliding clamp, dna binding protein
• Biological source: Escherichia coli (strain K12); More
• Total number of polymer chains: 8
• Total formula weight: 170921.60

Authors

Martiel, I.,Andre, C.,Olieric, V.,Guichard, G.,Burnouf, D. (deposition date: 2018-03-04, release date: 2019-04-10, Last modification date: 2024-10-23)

Primary citation

Andre, C.,Martiel, I.,Wolff, P.,Landolfo, M.,Lorber, B.,Silva da Veiga, C.,Dejaegere, A.,Dumas, P.,Guichard, G.,Olieric, V.,Wagner, J.G.,Burnouf, D.Y.
Peptide Interactions on Bacterial Sliding Clamps.
Acs Infect Dis., 2019

PubMed Abstract: Bacterial sliding clamps control the access of DNA polymerases to the replication fork and are appealing targets for antibacterial drug development. It is therefore essential to decipher the polymerase-clamp binding mode across various bacterial species. Here, two residues of the E. coli clamp binding pocket, S and M, and their cognate residues in M. tuberculosis and B. subtilis clamps, were mutated. The effects of these mutations on the interaction of a model peptide with these variant clamps were evaluated by thermodynamic, molecular dynamics, X-rays crystallography, and biochemical analyses. M and corresponding residues in Gram positive clamps occupy a strategic position where a mobile residue is essential for an efficient peptide interaction. S has a more subtle function that modulates the pocket folding dynamics, while the equivalent residue in B. subtilis is essential for polymerase activity and might therefore be a Gram positive-specific molecular marker. Finally, the peptide binds through an induced-fit process to Gram negative and positive pockets, but the complex stability varies according to a pocket-specific network of interactions.

PubMed: 30912430
DOI: 10.1021/acsinfecdis.9b00089

Experimental method

X-RAY DIFFRACTION (1.975 Å)