Structure of a small-molecule inhibitor of a DNA polymerase sliding clamp

The Rockefeller University and Howard Hughes Medical Institute, 1230 York Avenue, P. O. Box 228, New York, NY 10065, USA.
Proceedings of the National Academy of Sciences (Impact Factor: 9.67). 09/2008; 105(32):11116-21. DOI: 10.1073/pnas.0804754105
Source: PubMed


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.

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    • "There is a pressing need for new classes of antibiotics (Bassetti et al., 2013). The bacterial SC is an emerging target for the development of new antibacterial agents (Georgescu et al., 2008; Wijffels et al., 2011). Its structure is highly conserved: studies indicate that clamps from several bacterial species have similar overall structures and CBM-binding sites (Burnouf et al., 2004; Argiriadi et al., 2006; Gui et al., 2011). "
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    Chemistry & biology 03/2014; 21(4). DOI:10.1016/j.chembiol.2014.02.009 · 6.65 Impact Factor
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    • "Because transposases are frequently toxic and insoluble when overexpressed, we exploited the fact that β-binding motifs are often located on highly flexible, peptide-like, structures at the C-terminus of the protein (Dalrymple et al. 2001; Bunting et al. 2003; López de Saro et al. 2003). Further, unlike most protein–protein interactions, which implicate relatively large surface areas, interactions with β are mostly circumscribed to the motif binding to a hydrophobic pocket on β (Georgescu et al. 2008). We synthesized N-biotinylated peptides (20 aa) derived from sequences of transposases containing putative β-binding motifs (fig. "
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    Genome Biology and Evolution 03/2014; 6(3). DOI:10.1093/gbe/evu052 · 4.23 Impact Factor
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    • "Given the agreement between the UmuC binding motif (QLNLF) and the consensus proposed by Dalrymple and others (2001) (QL[S/D]LF), it might be supposed that the UmuC motif would follow a very similar profile to that seen for Pol II (QLGLF) in complex with the β-clamp [14]. In the broadest context, the UmuC peptide binds to β-clamp as has been observed previously, occupying both binding sites on the clamp dimer, since crystal packing does not occlude either site. "
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