A Structure-Based Model of Substrate Discrimination by a Noncanonical PDZ Tandem in the Intramembrane-Cleaving Protease RseP

During the extracytoplasmic stress response in Escherichia coli, the intramembrane protease RseP cleaves the anti-σE protein RseA only after the membrane-anchored protease DegS truncates the periplasmic part of RseA that suppresses the action of RseP. Here we analyzed the three-dimensional structure of the two tandemly arranged PSD-95/Dlg/ZO-1 (PDZ) domains (PDZ tandem) present in the periplasmic region of RseP and revealed that the two putative ligand-binding grooves constitute a single pocket-like structure that would lie just above the active center sequestrated within the membrane. Complete removal of the PDZ tandem from RseP led to the intramembrane cleavage of RseA without prior truncation by DegS. Furthermore, mutations expected to destabilize the tertiary structure of the PDZ tandem also caused the deregulation of the sequential cleavage. These observations suggest that the PDZ tandem serves as a size-exclusion filter to accommodate the truncated form of RseA into the active center. [Display omitted] •Two tandemly arranged PDZ domains of RseP form a unique pocket-like structure•Removal of the two PDZ domains abolishes the regulation of intramembrane cleavage•Structural alteration of the PDZ tandem is related to the deregulation•A model for substrate discrimination through the PDZ domains is proposed E. coli RseP is an intramembrane-cleaving protease involved in the extracytoplasmic stress response. Hizukuri et al. show that the two tandemly-arranged periplasmic PDZ domains in RseP form a “clam-shaped” conformation and propose that RseP discriminates its substrates by size-exclusion via the PDZ domains.