4K3M: E.coli Sliding Clamp in Complex With Acaldlf Peptide

Citation:
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.
PDB ID: 4K3MDownload
MMDB ID: 109748
PDB Deposition Date: 2013/4/11
Updated in MMDB: 2013/05
Experimental Method:
x-ray diffraction
Resolution: 1.85  Å
Source Organism:
Escherichia coli K-12
Similar Structures:
Biological Unit for 4K3M: trimeric; determined by author and by software (PISA)
Molecular Components in 4K3M
Label Count Molecule
Proteins (3 molecules)
2
DNA Polymerase III Subunit Beta(Gene symbol: dnaN)
Molecule annotation
1
Aldlf
Molecule annotation
Chemicals (13 molecules)
1
3
2
7
3
2
4
1
* Click molecule labels to explore molecular sequence information.

Citing MMDB
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