Molecular basis for pH sensing in the KDEL trafficking receptor

Trafficking receptors control protein localization through the recognition of specific signal sequences that specify unique cellular locations. Differences in luminal pH are important for the vectorial trafficking of cargo receptors. The KDEL receptor is responsible for maintaining the integrity of the ER by retrieving luminally localized folding chaperones in a pH-dependent mechanism. Structural studies have revealed the end states of KDEL receptor activation and the mechanism of selective cargo binding. However, precisely how the KDEL receptor responds to changes in luminal pH remains unclear. To explain the mechanism of pH sensing, we combine analysis of X-ray crystal structures of the KDEL receptor at neutral and acidic pH with advanced computational methods and cell-based assays. We show a critical role for ordered water molecules that allows us to infer a direct connection between protonation in different cellular compartments and the consequent changes in the affinity of the receptor for cargo. [Display omitted] •KDELR X-ray structures at neutral and acidic pH reveal distinct bridging waters•At neutral pH, only one water is observed, but at acidic pH two waters are seen•GCMC calculations show the two-water network is stabilized by a protonated histidine•The data reveal the mechanism of pH sensing in a trafficking receptor Wu et al. use a combination of X-ray crystal structures of the KDEL receptor at neutral and acidic pH with advanced computational methods and cell-based assays to explain at the atomic level how the cell performs pH-dependent retrieval of cargo proteins from the Golgi to the ER.