Flexible linkers leash the substrate binding domain of SspB to a peptide module that stabilizes delivery complexes with the AAA plus ClpXP protease

SspB dimers bind proteins bearing the ssrA-degradation tag and stimulate their degradation by the ClpXP protease. Here, E. coli SspB is shown to contain a dimeric substrate binding domain of 110-120 N-terminal residues, which binds ssrA-tagged substrates but does not stimulate their degradation. The C-terminal 40-50 residues of SspB are unstructured but are required for SspB to form substrate-delivery complexes with ClpXP. A synthetic peptide containing the 10 C-terminal residues of SspB binds ClpX, stimulates its ATPase activity, and prevents SspB-mediated delivery of GFP-ssrA for ClpXP degradation. This tripartite structure-an ssrA-tag binding and dimerization domain, a flexible linker, and a short peptide module that docks with ClpX-allows SspB to deliver tagged substrates to ClpXP without interfering with their denaturation or degradation.