A Specificity Map for the PDZ Domain Family

Abstract

PDZ domains are protein–protein interaction modules that recognize specific C-terminal sequences to assemble protein complexes in multicellular organisms. By scanning billions of random peptides, we accurately map binding specificity for approximately half of the over 330 PDZ domains in the human and Caenorhabditis elegans proteomes. The domains recognize features of the last seven ligand positions, and we find 16 distinct specificity classes conserved from worm to human, significantly extending the canonical two-class system based on position −2. Thus, most PDZ domains are not promiscuous, but rather are fine-tuned for specific interactions. Specificity profiling of 91 point mutants of a model PDZ domain reveals that the binding site is highly robust, as all mutants were able to recognize C-terminal peptides. However, many mutations altered specificity for ligand positions both close and far from the mutated position, suggesting that binding specificity can evolve rapidly under mutational pressure. Our specificity map enables the prediction and prioritization of natural protein interactions, which can be used to guide PDZ domain cell biology experiments. Using this approach, we predicted and validated several viral ligands for the PDZ domains of the SCRIB polarity protein. These findings indicate that many viruses produce PDZ ligands that disrupt host protein complexes for their own benefit, and that highly pathogenic strains target PDZ domains involved in cell polarity and growth.

Unusual binding interactions in PDZ domain crystal structures help explain binding mechanisms

“…PDZ domains show a varied selectivity for up to seven C-terminal residues. 1,2 The canonical binding mode involves the C-terminus of the protein target binding to the PDZ domain in a shallow groove, with the side-chains of the C-terminal residue (P0) and third-last residue (P-2) pointing toward the groove and being the most significant for recognition of the protein target by the PDZ domain. 3 Various classification schemes have been devised to aid in the prediction of target protein identity based on the sequence of PDZ domains.…”

“…The classification schemes all assume a canonical binding, however, systematic mutation of the ERBB2IP-1 PDZ domain showed that residues not immediately adjacent to the binding groove influence the selectivity. 1 Furthermore, kinetic analysis of the second PDZ domain of PTP-BL showed evidence for two stages in the binding mechanism, with initial formation of a weaker complex followed by a conformational change to a lower-energy state 4,5 ; the nature of the identified intermediate was unknown.…”

Prostacyclin receptors: Transcriptional regulation and novel signalling mechanisms

“…The frequently encountered postsynaptic density-95, disks large, zonula occludens-1 (PDZ) domain mediates protein:protein interactions by binding to the PDZ ligand located most typically, but not exclusively, at the extreme C termini of target proteins [108][109][110] . Through the formation of multiprotein complexes, PDZ interactions can participate in the coordination of key intra-and intercellular signaling systems, including intracellular routing or localization of proteins, cell polarity, as well as in the regulation of cell:cell interactions [108][109][110] .…”

“…Through the formation of multiprotein complexes, PDZ interactions can participate in the coordination of key intra-and intercellular signaling systems, including intracellular routing or localization of proteins, cell polarity, as well as in the regulation of cell:cell interactions [108][109][110] . Structurally, the PDZ domain is composed of compact globular modules containing six anti-parallel β-strands (βA-βF) and two α-helices (αA and αB) with a highly conserved GLGF motif within its hydrophobic binding pocket that is responsible for the sequencespecific recognition of the PDZ ligand within the target protein(s).…”

Cluster based prediction of PDZ-peptide interactions

“…As was recently shown by two high-throughput experiments, PDZ domains can be classified into 16 different specificity classes [15, 16] with similar ligand binding profiles. Stiffler et al .…”