4K3M

E.coli sliding clamp in complex with AcALDLF peptide

4K3M の概要

• エントリーDOI: 10.2210/pdb4k3m/pdb
• 関連するPDBエントリー: 1MMI 4K3K 4K3L 4K3O 4K3P 4K3Q 4K3R 4K3S
• 分子名称: DNA polymerase III subunit beta, ALDLF, DI(HYDROXYETHYL)ETHER, ... (7 entities in total)
• 機能のキーワード: e. coli sliding clamp, transferase
• 由来する生物種: Escherichia coli; 詳細
• 細胞内の位置: Cytoplasm: P0A988
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 82932.16

構造登録者

Yin, Z.,Oakley, A.J. (登録日: 2013-04-11, 公開日: 2013-05-01, 最終更新日: 2023-11-08)

主引用文献

Yin, Z.,Kelso, M.J.,Beck, J.L.,Oakley, A.J.
Structural and Thermodynamic Dissection of Linear Motif Recognition by the E. coli Sliding Clamp
J.Med.Chem., 56:8665-8673, 2013

PubMed Abstract: Protein-protein interactions based on linear motif (LM) recognition play roles in many cell regulatory processes. The E. coli sliding clamp is a protein mediator of replisome formation, which uses a common surface pocket composed of two subsites (I and II) to interact with LMs in multiple binding partners. A structural and thermodynamic dissection of sliding clamp-LM recognition has been performed, providing support for a sequential binding model. According to the model, a hydrophobic C-terminal LM dipeptide submotif acts as an anchor to establish initial contacts within subsite I, and this is followed by formation of a stabilizing hydrogen-bonding network between the flanking LM residues and subsite II. Differential solvation/desolvation during positioning of the submotifs is proposed as a driver for the sequential binding. Our model provides general insights into linear motif recognition and should guide the design of small-molecule inhibitors of the E. coli sliding clamp, an emerging antibacterial target.

PubMed: 24090409
DOI: 10.1021/jm401118f

実験手法

X-RAY DIFFRACTION (1.85 Å)