3D1G

Structure of a small molecule inhibitor bound to a DNA sliding clamp

Summary for 3D1G

• Entry DOI: 10.2210/pdb3d1g/pdb
• Related: 2POL 3BEP 3D1E 3D1F
• Descriptor: DNA polymerase III subunit beta, [(5R)-5-(2,3-dibromo-5-ethoxy-4-hydroxybenzyl)-4-oxo-2-thioxo-1,3-thiazolidin-3-yl]acetic acid (3 entities in total)
• Functional Keywords: chemical probe, dna polymerase, dna sliding clamp, dna replication, rational drug design, antibiotic target, transferase, transcription
• Biological source: Escherichia coli
• Cellular location: Cytoplasm : P0A988
• Total number of polymer chains: 2
• Total formula weight: 82259.41

Authors

Georgescu, R.E.,Yurieva, O.,Seung-Sup, K.,Kuriyan, J.,Kong, X.-P.,O'Donnell, M. (deposition date: 2008-05-05, release date: 2008-07-29, Last modification date: 2023-08-30)

Primary citation

Georgescu, R.E.,Yurieva, O.,Kim, S.S.,Kuriyan, J.,Kong, X.P.,O'Donnell, M.
Structure of a small-molecule inhibitor of a DNA polymerase sliding clamp.
Proc.Natl.Acad.Sci.Usa, 105:11116-11121, 2008

PubMed Abstract: 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.

PubMed: 18678908
DOI: 10.1073/pnas.0804754105

Experimental method

X-RAY DIFFRACTION (1.64 Å)