Proteomic identification and structural basis for the interaction between sorting nexin SNX17 and PDLIM family proteins

Abstract

The sorting nexin SNX17 controls endosome-to-cell surface recycling of diverse transmembrane cargo proteins including integrins, the amyloid precursor protein and lipoprotein receptors. This requires association with the multi-subunit Commander trafficking complex, which depends on the C-terminus of SNX17 through unknown mechanisms. Using affinity enrichment proteomics, we find that a C-terminal peptide of SNX17 is not only sufficient for Commander interaction but also associates with members of the actin-associated PDZ and LIM domain (PDLIM) family. We show that SNX17 contains a type III PSD95/Dlg/Zo1 (PDZ) binding motif (PDZbm) that binds specifically to the PDZ domains of PDLIM family proteins but not to other PDZ domains tested. The structure of the PDLIM7 PDZ domain bound to the SNX17 C-terminus was determined by NMR spectroscopy and reveals an unconventional perpendicular peptide interaction. Mutagenesis confirms the interaction is mediated by specific electrostatic contacts and a uniquely conserved proline-containing loop sequence in the PDLIM protein family. Our results define the mechanism of SNX17-PDLIM interaction and suggest that the PDLIM proteins may play a role in regulating the activity of SNX17 in conjunction with Commander and actin-rich endosomal trafficking domains.

Structure of the Commander endosomal trafficking complex linked to X-linked intellectual disability/Ritscher-Schinzel syndrome

“…Its subunits are conserved in eukaryotes from humans to single-celled choanoflagellates and are primarily localized to the outer leaflet of early endosomal compartments, where the complex is required for the plasma membrane recycling of many different cargos. Most of these, including a5b1 integrin, the amyloid precursor protein (APP) and various members of the lipoprotein receptor family such as LRP1 and LDLR, contain FxNxx[YF] sequence motifs (where F is a hydrophobic amino acid) that are recruited to Commander via the adaptor protein, sorting nexin 17 (SNX17) (6,20,(23)(24)(25)(26)(27)(28)(29). Other known transmembrane cargos such as the copper transporters ATP7A and ATP7B however, are trafficked via unknown mechanisms (30)(31)(32).…”

An Update on Coat Protein Complexes for Vesicle Formation in Plant Post-Golgi Trafficking

“…Previous studies suggested that the cargo sorting specificity is mediated by the core retromer subunit, but recent studies showed that SNX partners also participate in cargo recognition and membrane binding ( Leneva et al, 2021 ). In human, retromer complex cooperates with SNX3, SNX27, and SNX17 respectively for different cargoes ( Mcnally et al, 2017 ; Healy et al, 2021 ). For example, retromer-SNX3 recognizes the cargo through a Øx(L/M/V) motif, whereas retromer-SNX27 binds to the PDZ domain in β2-adrenoreceptor ( Lauffer et al, 2010 ).…”

“…In Arabidopsis thaliana , counterparts for SNX3 have been recently reported, but whether they perform a similar function in plants is still unclear. In addition, no SNX27 and SNX17 homologs have been identified yet ( Healy et al, 2021 ).…”

“…Subunits of the CCC complex in Arabidopsis genome have also been identified, including coiled-coil domain-containing protein 22 (CCDC22) and coiled-coil domain-containing protein 93 (CCDC93). However, it awaits further study to reveal whether they function together with plant “retriever” in endosome sorting ( Healy et al, 2021 ). Particularly, in human, commander complex also consists of 7 Commd proteins, but no homologs of these proteins can be found in Arabidopsis thaliana ( Healy et al, 2021 ).…”

“…However, it awaits further study to reveal whether they function together with plant “retriever” in endosome sorting ( Healy et al, 2021 ). Particularly, in human, commander complex also consists of 7 Commd proteins, but no homologs of these proteins can be found in Arabidopsis thaliana ( Healy et al, 2021 ).…”