PDBsum entry 1be9

Peptide recognition

PDB id: 1be9

Contents

Protein chain

115 a.a. *

Ligands

LYS-GLN-THR-SER-VAL

Waters ×146

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Crystal structures of a complexed and peptide-Free membrane protein-Binding domain: molecular basis of peptide recognition by pdz.

Authors

D.A.Doyle, A.Lee, J.Lewis, E.Kim, M.Sheng, R.Mackinnon.

Ref.

Cell, 1996, 85, 1067-1076. [DOI no: 10.1016/S0092-8674(00)81307-0]

PubMed id

8674113

Abstract

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 through antiparallel main chain interactions with a beta sheet of the domain. Recognition of the terminal carboxylate group of the peptide is conferred by a cradle of main chain amides provided by a Gly-Leu-Gly-Phe loop as well as by an arginine side chain. Specific side chain interactions and a prominent hydrophobic pocket explain the selective recognition of the C-terminal consensus sequence.

Figure 4.
Figure 4. Chemical Interactions Involved in Peptide Binding(A) Stereo view of the peptide-binding site demonstrating protein–peptide interactions via hydrogen bonds (dashed white lines) and the location of the Val 0 side chain in the hydrophobic pocket. Oxygen atoms are shown in red and nitrogen atoms in blue. The green sphere shows a well-ordered water molecule linking the carboxylate group to Arg-318. The picture was drawn with MOLSCRIPT and Raster3D.(B) Schematic view of the contacts identified in the crystal structure of the complex. Dashed lines represent hydrogen bonds, and the two closest atom-to-atom distances between the Val 0 side chain and all atoms in the hydrophobic pocket of the PDZ domain are drawn as solid black lines. The Val 0 side chain makes numerous other Van der Waals contacts within the range of 3.9 to 4.3 Å; however, for clarity they are not indicated in this diagram. The fixed orientation of the arginine guanidinium head group via hydrogen bonds with backbone carbonyl groups is also shown.

Figure 6.
Figure 6. Schematic Drawing of a PDZ and an IRS-1 PTB DomainA shared peptide-binding motif is highlighted in red. In both domains bound peptide, shown in yellow, forms an antiparallel β sheet with the β strand flanking the peptide-binding groove. The schematic of the IRS-1 PTB domain is based on [39].

The above figures are reprinted by permission from Cell Press: Cell (1996, 85, 1067-1076) copyright 1996.

Secondary reference #1

Title

Crystal structure of the hcask pdz domain reveals the structural basis of class ii pdz domain target recognition.

Authors

D.L.Daniels, A.R.Cohen, J.M.Anderson, A.T.Brünger.

Ref.

Nat Struct Biol, 1998, 5, 317-325.

PubMed id

9546224

Secondary reference #2

Title

Cript, A novel postsynaptic protein that binds to the third pdz domain of psd-95/sap90.

Authors

M.Niethammer, J.G.Valtschanoff, T.M.Kapoor, D.W.Allison, T.M.Weinberg, A.M.Craig, M.Sheng.

Ref.

Neuron, 1998, 20, 693-707. [DOI no: 10.1016/S0896-6273(00)81009-0]

PubMed id

9581762

Figure 5.
Figure 5. Concentration of CRIPT at Excitatory Synapses in Cultured Hippocampal Neurons(A–C) Double staining with antibodies against PSD-95 (A) and CRIPT (B) shows that these proteins colocalize (C) especially on dendritic spines (arrowheads).(D) Antibodies against CRIPT stain throughout the neuron, but immunoreactivity is concentrated in dendritic spines.(E–H) Staining with antibodies against CRIPT (green in [E–H]) and rhodamine phalloidin to label concentrations of F-actin in spines (red in [F] and [H]) shows localization of CRIPT to dendritic spines (E and F). Spiny immunoreactivity of CRIPT is lost after preincubation of the antibody with the immunogenic peptide (G and H).(I) Antibodies against the presynaptic marker SV2 (red) and CRIPT (green) show closely apposed signals, indicating that CRIPT punctate staining is synaptic (arrowheads).(J) The lack of colocalization in the staining for GAD (red) and CRIPT (green) indicates that CRIPT (arrowheads) is not concentrated at inhibitory synapses (arrows).Scale BARS = 10 μm.

Figure 6.
Figure 6. Immunogold EM Localization of CRIPT in Rat Brain(A) Immunogold labeling for CRIPT in CA1 region of hippocampus (F(ab′)2, conjugated to 10 nm gold particles). The postsynaptic portions of two asymmetric synapses are immunopositive.(B and C) Labeling of CRIPT in layer III of somatosensory cortex (12 nm gold in [B]; 18 nm gold in [C]). Labeling is concentrated over the postsynaptic density but may also be seen presynaptically.(D) Double labeling for CRIPT (12 nm gold, small dots) and PSD-95 (18 nm gold, large dots) in layer III of somatosensory cortex showing colocalization in an asymmetric synapse.(E) The distribution of immunogold particles along the axo-dendritic axis exhibited maximal density vert, similar 35 nm inside the postsynaptic membrane corresponding roughly to the inner edge of the postsynaptic density. Smaller peaks in density were seen at the presynaptic and postsynaptic membranes. Dashed line marks outer leaflet of postsynaptic membrane.(F) Lateral distribution of particle density along the synapse. To permit comparison of locations in synapses with differing active zone lengths, lateral positions were normalized (see Experimental Procedures). Labeling was fairly uniformly distributed across the synapse, declining sharply at its edge.Scale BARS = 250 nm, (A); 100 nm, (B–D).

The above figures are reproduced from the cited reference with permission from Cell Press

Secondary reference #3

Title

Crystal structure of a pdz domain.

Authors

J.H.Morais cabral, C.Petosa, M.J.Sutcliffe, S.Raza, O.Byron, F.Poy, S.M.Marfatia, A.H.Chishti, R.C.Liddington.

Ref.

Nature, 1996, 382, 649-652.

PubMed id

8757139