Crystal Structures of a Complexed and Peptide-Free Membrane Protein–Binding Domain: Molecular Basis of Peptide Recognition by PDZ

@article{Doyle1996CrystalSO,
  title={Crystal Structures of a Complexed and Peptide-Free Membrane Protein–Binding Domain: Molecular Basis of Peptide Recognition by PDZ},
  author={Declan Anthony Doyle and Alice Lee and John H. Lewis and Eunjoon Kim and Morgan Sheng and Roderick MacKinnon},
  journal={Cell},
  year={1996},
  volume={85},
  pages={1067-1076}
}
Modular PDZ domains, found in many cell junction-associated proteins, mediate the clustering of membrane ion channels by binding to their C-terminus. The X-ray crystallographic structures of the third PDZ domain from the synaptic protein PSD-95 in complex with and in the absence of its peptide ligand have been determined at 1.8 angstroms and 2.3 angstroms resolution, respectively. The structures reveal that a four-residue C-terminal stretch (X-Thr/Ser-X-Val-COO(-)) engages the PDZ domain… Expand
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This study systematically probed putative backbone hydrogen bonds between four different PDZ domains and peptides corresponding to natural protein ligands, demonstrating that hydrogen bonds contribute significantly to ligand binding and specifically addresses these for PDZ domain-peptide interactions. Expand
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Structural and dynamical evidence for allosteric effects in a PDZ domain, PDZ2 from the tyrosine phosphatase PTP-BL, upon binding to a target peptide is presented and it is revealed that binding is regulated by long-range interactions, which can be correlated with the structural rearrangements resulting from peptide binding. Expand
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References

SHOWING 1-10 OF 61 REFERENCES
Protein-peptide interactions.
TLDR
These various recognition motifs are illustrated by peptide interactions with antibodies, calmodulin, OppA periplasmic binding protein, PapD chaperone, MHC class I and class II molecules, and Src homology (SH) domains 2 and 3. Expand
Clustering of Shaker-type K+ channels by interaction with a family of membrane-associated guanylate kinases
TLDR
Functional and biochemical evidence is presented that cell-surface clustering of Shaker-subfamily K+ channels is mediated by the PSD-95 family of membrane-associated putative guanylate kinases, and the ability of PDZ domains to function as independent modules for protein–protein interaction, and their presence in other junction-associated molecules suggest that PDZ-domain-containing polypeptides may be widely involved in the organization of proteins at sites of membrane specialization. Expand
Interaction between the C terminus of NMDA receptor subunits and multiple members of the PSD-95 family of membrane-associated guanylate kinases
TLDR
Data suggest that PDZ domains can function as modules for protein-protein interactions and members of the PSD-95 family might serve to anchor NMDA receptors to the submembrane cytoskeleton and aid in the assembly of signal transduction complexes at postsynaptic sites. Expand
Molecular identification of a major palmitoylated erythrocyte membrane protein containing the src homology 3 motif.
TLDR
The complete amino acid sequence of a 55-kDa erythrocyte membrane protein was deduced from cDNA clones isolated from a human reticulocyte library, and Northern blot analysis indicated that p55 mRNA was constitutively expressed during erythropoiesis and underwent 2-fold amplification after induction of K562 erythroleukemia cells toward the ERYthropoietic lineage. Expand
Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect.
TLDR
Six "cavity-creating" mutants were constructed within the hydrophobic core of phage T4 lysozyme and the results suggest how to reconcile a number of conflicting reports concerning the strength of thehydrophobic effect in proteins. Expand
CASK: a novel dlg/PSD95 homolog with an N-terminal calmodulin-dependent protein kinase domain identified by interaction with neurexins
  • Y. Hata, S. Butz, T. Sudhof
  • Biology, Medicine
  • The Journal of neuroscience : the official journal of the Society for Neuroscience
  • 1996
TLDR
CASK is a membrane-associated protein that combines domains found in Ca2+ - activated protein kinases and in proteins specific for intercellular junctions, suggesting that it may be a signaling molecule operating at the plasma membrane, possibly in conjunction with neurexins. Expand
Structural basis for IL-4 receptor phosphopeptide recognition by thelRS-1 PTB domain
TLDR
The NMR structure of the PTB domain of insulin receptor substrate-1 (IRS-1) complexed to a tyrosine-phosphorylated peptide derived from the IL-4 receptor is presented and the phosphopeptide binding specificity is explained based on the structure and results of site-directed mutagenesis experiments. Expand
Molecular characterization and spatial distribution of SAP97, a novel presynaptic protein homologous to SAP90 and the Drosophila discs-large tumor suppressor protein
  • B. Muller, U. Kistner, +4 authors C. Garner
  • Biology, Medicine
  • The Journal of neuroscience : the official journal of the Society for Neuroscience
  • 1995
TLDR
Light and immunoelectron microscopic analysis of the rat hippocampal formation revealed that SAP97 is localized in the presynaptic nerve termini of excitatory synapses, suggesting that members of the SAP90/SAP97 subfamily may be involved in the site specific assembly, stability or functions of membrane specialization at sites of cell-cell contact. Expand
The tight junction protein ZO-1 is homologous to the Drosophila discs-large tumor suppressor protein of septate junctions.
TLDR
The results suggest a protein family specialized for signal transduction on the cytoplasmic surface of intercellular junctions, and provide biochemical evidence for similarity between invertebrate septate and vertebrate tight junctions. Expand
Molecular characterization and tissue distribution of ZO-2, a tight junction protein homologous to ZO-1 and the Drosophila discs-large tumor suppressor protein
TLDR
Immunohistochemical staining of frozen sections of whole tissue demonstrated that ZO-2 localized to the region of the tight junction in a number of epithelia, including liver, intestine, kidney, testis, and arterial endothelium, suggesting that this protein is a ubiquitous component of the Tight junction. Expand
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