A distinctive PDZ:β-hairpin interaction mediates AFDN complex with SCRIB and promotes binding to KRAS

PSD-95/DLG/ZO-1 (PDZ) domains canonically recognize short C-terminal peptide motifs, but numerous non-canonical binding mechanisms have also been described. We previously identified a direct interaction between the cell polarity protein SCRIB and the RAS effector AFDN, mediated by the SCRIB PDZ1 and AFDN FHA domains, though a structural basis remained unresolved. Here, we use AlphaFold3 predictions to model the SCRIB:AFDN complex, revealing that binding is driven by a conserved β-hairpin motif C-terminal to the AFDN FHA domain. This β-hairpin engages the canonical peptide-binding groove of SCRIB PDZ1, contributing an antiparallel strand to extend the PDZ β-sandwich, inserting a phenylalanine into the hydrophobic pocket, and forming contacts that recapitulate a canonical PDZ:peptide complex. We validate the interface with nuclear magnetic resonance spectroscopy (NMR) and biochemical assays and show that point mutations at either side of the interface can abolish complex formation. Unexpectedly, disruption of full-length AFDN:SCRIB binding in cells results in loss of interaction with the KRAS oncoprotein. The identified β-hairpin motif is highly conserved across deuterostomes but absent from most invertebrate AFDN orthologs, including Drosophila melanogaster - the organism in which AFDN/Canoe and SCRIB/Scribbled functions have been most extensively characterized. The complex closely resembles the only previously described PDZ:β-hairpin structure, between the PDZ domain of Syntrophin and a motif from nNOS/NOS1. A proteome-wide search identifies hundreds of candidate internal PDZ-binding sites conforming to this β-hairpin motif, suggesting the mechanism may be significantly more widespread than currently appreciated.