Intramolecular autoinhibition of human PEX13 modulates peroxisomal import

Targeting and import of peroxisomal proteins depends on PEX5, PEX14 and PEX13. We present a biochemical and structural characterization of the PEX13 C-terminal region. By combining NMR spectroscopy, X-ray crystallography and biochemical methods, we show that the PEX13 SH3 domain mediates intramolecular interactions with a newly identified proximal FxxxF motif and also binds to WxxxF peptide motifs from the PEX5 NTD, demonstrating evolutionary conservation of this interaction from yeast to human. Strikingly, the C-terminal FxxxF motif autoinhibits the WxxxF/Y binding surface on the PEX13 SH3 domain. This is supported by high-resolution crystal structures, which show FxxxF or WxxxF/Y binding to the same, non-canonical surface on the SH3 domain. The FxxxF motif also binds the PEX14 NTD with micromolar affinity. Surprisingly, the canonical binding surface for PxxP motifs on the human PEX13 SH3 fold does not recognize PxxP motifs in PEX14, distinct from the yeast ortholog. The dynamic network of PEX13, PEX14 and PEX5 interactions mediated by diaromatic peptide motifs fine-tunes and modulates peroxisomal matrix import in cells.