4K3M

E.coli sliding clamp in complex with AcALDLF peptide

Summary for 4K3M

• Entry DOI: 10.2210/pdb4k3m/pdb
• Related: 1MMI 4K3K 4K3L 4K3O 4K3P 4K3Q 4K3R 4K3S
• Descriptor: DNA polymerase III subunit beta, ALDLF, DI(HYDROXYETHYL)ETHER, ... (7 entities in total)
• Functional Keywords: e. coli sliding clamp, transferase
• Biological source: Escherichia coli; More
• Cellular location: Cytoplasm: P0A988
• Total number of polymer chains: 3
• Total formula weight: 82932.16

Authors

Yin, Z.,Oakley, A.J. (deposition date: 2013-04-11, release date: 2013-05-01, Last modification date: 2023-11-08)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (1.85 Å)