Structural basis for the differential interaction of Scribble PDZ domains with the guanine nucleotide exchange factor β-PIX

Abstract

Scribble is a highly conserved protein regulator of cell polarity that has been demonstrated to function as a tumor suppressor or, conversely, as an oncogene in a context-dependent manner, and it also controls many physiological processes ranging from immunity to memory. Scribble consists of a leucine-rich repeat domain and four PDZ domains, with the latter being responsible for most of Scribble's complex formation with other proteins. Given the similarities of the Scribble PDZ domain sequences in their binding grooves, it is common for these domains to show overlapping preferences for the same ligand. Yet, Scribble PDZ domains can still exhibit unique binding profiles toward other ligands. This raises the fundamental question as to how these PDZ domains discriminate ligands and exert specificities in Scribble complex formation. To better understand how Scribble PDZ domains direct cell polarity signaling, we investigated here their interactions with the well-characterized Scribble binding partner β-PIX, a guanine nucleotide exchange factor. We report the interaction profiles of all isolated Scribble PDZ domains with a β-PIX peptide. We show that Scribble PDZ1 and PDZ3 are the major interactors with β-PIX and reveal a distinct binding hierarchy in the interactions between the individual Scribble PDZ domains and β-PIX. Furthermore, using crystal structures of PDZ1 and PDZ3 bound to β-PIX, we define the structural basis for Scribble's ability to specifically engage β-PIX via its PDZ domains and provide a mechanistic platform for understanding Scribble-β-PIX-coordinated cellular functions such as directional cell migration.

Crystal structure of the human Scribble PDZ1 domain bound to the PDZ‐binding motif of APC

“…Clear and continuous electron density is visible for APC residues 2837–2843, with the remaining Gly presumed disordered. As shown previously the SCRIB PDZ1 domain comprises a compact globular fold comprising six β‐strands and two α‐helices that adopt a β‐sandwich structure, with the APC peptide bound in the canonical ligand binding groove located between the β2 strand and helix α2 (Fig. A).…”

“…Examination of the PDZ1:APC structure reveals that binding of APC does not significantly change the PDZ1 domain structure when superimposed onto the previously determined structures of a SCRIB PDZ1:β‐PIX complex or ligand free SCRIB PDZ1 (PDB ID http://www.rcsb.org/pdb/search/structidSearch.do?structureId=5VWC) , with an rmsd of 0.9 Å over 93 Cα atoms between SCRIB PDZ1:β‐PIX and APC complexes, and between PDZ1 alone and PDZ1:APC of 1.2 Å over 96 Cα atoms .…”

PDZ Domains as Drug Targets

“…Tetrahydroquinoline analogs 10-70 µm (K i ) NA Development [189] Shank3 GSSGDPAWDETNL and multimeric analogs 8-41 µm (K d ) NA Development [193] Disheveled 1 "J01-017a" 1.5 µm (K i ) Cancer Preclinical [215] Disheveled 2 KWYGWF 0.7 µm (K i ) Cancer Preclinical [42] Scribble PDZ1 RSWFETWV 0.7 µm (K d ) Cancer Development [239] Syntenin PDZ12…”

“…This binding motif has been reported as responsible for the interaction between Scribble and Fat1. [239] The preference and selectivity for PDZ1 and PDZ3 over PDZ2 and PDZ4 was validated in a cellular context using endogenously expressed β-PIX. This interaction, however, is not dependent on the C-terminal PDZ binding motif (HTEV), suggesting that Scribble recognizes an internal epitope in Drosophila.…”

“…The X-ray crystal structures of the β-PIX peptide binding to PDZ1 and PDZ3 highlight how the binding preference and specificity is achieved (Figure 10d). [239] Scribble is a promising target for the development of anticancer drugs; however, a major challenge is to design and develop PDZ selective inhibitors, which has so far not been achieved. In PDZ1, the Trp -5 forms a hydrophobic interaction by www.advancedsciencenews.com www.advtherap.com Figure 10.…”