The binding of the PDZ tandem of syntenin to target proteins.

PDZ domains are among the most abundant protein modules in the known genomes. Their main function is to provide scaffolds for membrane-associated protein complexes by binding to the cytosolic, C-terminal fragments of receptors, channels, and other integral membrane proteins. Here, using both heteronuclear NMR and single crystal X-ray diffraction, we show how peptides with different sequences, including those corresponding to the C-termini of syndecan, neurexin, and ephrin B, can simultaneously bind to both PDZ domains of the scaffolding protein syntenin. The PDZ2 domain binds these peptides in the canonical fashion, and an induced fit mechanism allows for the accommodation of a range of side chains in the P(0) and P(-)(2) positions. However, binding to the PDZ1 domain requires that the target peptide assume a noncanonical conformation. These data help explain how syntenin, and perhaps other PDZ-containing proteins, may preferentially bind to dimeric and clustered targets, and provide a mechanistic explanation for the previously reported cooperative ligand binding by syntenin's two PDZ domains.

[1]  Seong-Hwan Rho,et al.  Crystal Structure of GRIP1 PDZ6-Peptide Complex Reveals the Structural Basis for Class II PDZ Target Recognition and PDZ Domain-mediated Multimerization* , 2003, The Journal of Biological Chemistry.

[2]  John Armstrong,et al.  Cytokine-Specific Transcriptional Regulation Through an IL-5Rα Interacting Protein , 2001, Science.

[3]  Martin Niethammer,et al.  Supramodular structure and synergistic target binding of the N-terminal tandem PDZ domains of PSD-95. , 2003, Journal of molecular biology.

[4]  R. Huganir,et al.  PDZ Proteins Bind, Cluster, and Synaptically Colocalize with Eph Receptors and Their Ephrin Ligands , 1998, Neuron.

[5]  Mingjie Zhang,et al.  Organization of signaling complexes by PDZ-domain scaffold proteins. , 2003, Accounts of chemical research.

[6]  G. Murshudov,et al.  Refinement of macromolecular structures by the maximum-likelihood method. , 1997, Acta crystallographica. Section D, Biological crystallography.

[7]  Sachdev S Sidhu,et al.  Origins of PDZ Domain Ligand Specificity , 2003, The Journal of Biological Chemistry.

[8]  G. Reekmans,et al.  Syntenin, a PDZ protein that binds syndecan cytoplasmic domains. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[9]  J. Navaza,et al.  AMoRe: an automated package for molecular replacement , 1994 .

[10]  M. Sheng,et al.  PDZ domains and the organization of supramolecular complexes. , 2001, Annual review of neuroscience.

[11]  W. Lim,et al.  Unexpected modes of PDZ domain scaffolding revealed by structure of nNOS-syntrophin complex. , 1999, Science.

[12]  S. Grzesiek,et al.  NMRPipe: A multidimensional spectral processing system based on UNIX pipes , 1995, Journal of biomolecular NMR.

[13]  M. Humphries,et al.  Cytoplasmic interactions of syndecan-4 orchestrate adhesion receptor and growth factor receptor signalling. , 2002, The Biochemical journal.

[14]  David R Cooper,et al.  Molecular roots of degenerate specificity in syntenin's PDZ2 domain: reassessment of the PDZ recognition paradigm. , 2003, Structure.

[15]  L. Chan,et al.  Autoinhibition of X11/Mint scaffold proteins revealed by the closed conformation of the PDZ tandem , 2005, Nature Structural &Molecular Biology.

[16]  Zhenbao Yu,et al.  Solution structure and backbone dynamics of the functional cytoplasmic subdomain of human ephrin B2, a cell-surface ligand with bidirectional signaling properties. , 2002, Biochemistry.

[17]  Z. Otwinowski,et al.  [20] Processing of X-ray diffraction data collected in oscillation mode. , 1997, Methods in enzymology.

[18]  G. Reekmans,et al.  Characterization of syntenin, a syndecan-binding PDZ protein, as a component of cell adhesion sites and microfilaments. , 2001, Molecular biology of the cell.

[19]  S. Eom,et al.  Crystal Structure of the Shank PDZ-Ligand Complex Reveals a Class I PDZ Interaction and a Novel PDZ-PDZ Dimerization* , 2003, Journal of Biological Chemistry.

[20]  J. Qin,et al.  Structure of an ultraweak protein-protein complex and its crucial role in regulation of cell morphology and motility. , 2005, Molecular cell.

[21]  J. Baselga,et al.  A role for a PDZ protein in the early secretory pathway for the targeting of proTGF-alpha to the cell surface. , 1999, Molecular cell.

[22]  L. Cantley,et al.  Recognition of Unique Carboxyl-Terminal Motifs by Distinct PDZ Domains , 1997, Science.

[23]  Ann Marie Craig,et al.  CRIPT, a Novel Postsynaptic Protein that Binds to the Third PDZ Domain of PSD-95/SAP90 , 1998, Neuron.

[24]  Wei Feng,et al.  Tandem PDZ repeats in glutamate receptor–interacting proteins have a novel mode of PDZ domain–mediated target binding , 2003, Nature Structural Biology.

[25]  T. Pawson,et al.  The Carboxyl Terminus of B Class Ephrins Constitutes a PDZ Domain Binding Motif* , 1999, The Journal of Biological Chemistry.

[26]  T. Leung,et al.  Crystal structure of the PDZ1 domain of human Na(+)/H(+) exchanger regulatory factor provides insights into the mechanism of carboxyl-terminal leucine recognition by class I PDZ domains. , 2001, Journal of molecular biology.

[27]  K. Prehoda,et al.  Internal recognition through PDZ domain plasticity in the Par-6–Pals1 complex , 2004, Nature Structural &Molecular Biology.

[28]  T. Südhof,et al.  The Making of Neurexins , 1998, Journal of neurochemistry.

[29]  P. Steinlein,et al.  Identification of Syntenin as a Protein of the Apical Early Endocytic Compartment in Madin-Darby Canine Kidney Cells* , 1999, The Journal of Biological Chemistry.

[30]  Paola Vaccaro,et al.  PDZ domains: troubles in classification , 2002, FEBS letters.

[31]  J. Zou,et al.  Improved methods for building protein models in electron density maps and the location of errors in these models. , 1991, Acta crystallographica. Section A, Foundations of crystallography.

[32]  I. Bezprozvanny,et al.  Classification of PDZ domains , 2001, FEBS letters.

[33]  G. David,et al.  Syntenin-Syndecan Binding Requires Syndecan-Synteny and the Co-operation of Both PDZ Domains of Syntenin* , 2000, The Journal of Biological Chemistry.

[34]  Seth G. N. Grant,et al.  PDZ Domain Proteins: Plug and Play! , 2003, Science's STKE.

[35]  F. Rathjen,et al.  The Neural Cell Recognition Molecule Neurofascin Interacts with Syntenin-1 but Not with Syntenin-2, Both of Which Reveal Self-associating Activity* , 2001, The Journal of Biological Chemistry.