3D1G

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

3D1G の概要

• エントリーDOI: 10.2210/pdb3d1g/pdb
• 関連するPDBエントリー: 2POL 3BEP 3D1E 3D1F
• 分子名称: 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)
• 機能のキーワード: chemical probe, dna polymerase, dna sliding clamp, dna replication, rational drug design, antibiotic target, transferase, transcription
• 由来する生物種: Escherichia coli
• 細胞内の位置: Cytoplasm : P0A988
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 82259.41

構造登録者

Georgescu, R.E.,Yurieva, O.,Seung-Sup, K.,Kuriyan, J.,Kong, X.-P.,O'Donnell, M. (登録日: 2008-05-05, 公開日: 2008-07-29, 最終更新日: 2023-08-30)

主引用文献

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

実験手法

X-RAY DIFFRACTION (1.64 Å)