Versatile modes of peptide recognition by the ClpX N domain mediate alternative adaptor-binding specificities in different bacterial species

Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
Protein Science (Impact Factor: 2.85). 02/2010; 19(2):242-54. DOI: 10.1002/pro.306
Source: PubMed


ClpXP, an AAA+ protease, plays key roles in protein-quality control and many regulatory processes in bacteria. The N-terminal domain of the ClpX component of ClpXP is involved in recognition of many protein substrates, either directly or by binding the SspB adaptor protein, which delivers specific classes of substrates for degradation. Despite very limited sequence homology between the E. coli and C. crescentus SspB orthologs, each of these adaptors can deliver substrates to the ClpXP enzyme from the other bacterial species. We show that the ClpX N domain recognizes different sequence determinants in the ClpX-binding (XB) peptides of C. crescentus SspBalpha and E. coli SspB. The C. crescentus XB determinants span 10 residues and involve interactions with multiple side chains, whereas the E. coli XB determinants span half as many residues with only a few important side chain contacts. These results demonstrate that the N domain of ClpX functions as a highly versatile platform for peptide recognition, allowing the emergence during evolution of alternative adaptor-binding specificities. Our results also reveal highly conserved residues in the XB peptides of both E. coli SspB and C. crescentus SspBalpha that play no detectable role in ClpX-binding or substrate delivery.

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Available from: Peter Chien, Mar 28, 2014
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    • "In vitro studies of adaptor-mediated proteolysis catalysed by Clp proteases involve reactions in which the adaptor, such as SspB and ClpS, is present at equimolar or near equimolar amounts with respect to protease and substrate (Levchenko et al., 2000). In one case, SspB was present in 10-fold molar excess over ClpXP (Chowdhury et al., 2010), while in another study, ClpS was present in a ClpAPcatalysed proteolytic reaction in 0.5 molar equivalent to protease and substrate (Dougan et al., 2002). Thus, the adaptor–protease complex acts catalytically in the reaction that causes substrate degradation, but the adaptor acts stoichiometrically with respect to interaction with the protease. "
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