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

PDB id:

1be9

Name:

Peptide recognition

Title:

The third pdz domain from the synaptic protein psd-95 in com a c-terminal peptide derived from cript.

Structure:

Psd-95. Chain: a. Fragment: the third pdz domain of psd-95. Engineered: yes. Cript. Chain: b. Fragment: c-terminal peptide

Source:

Rattus norvegicus. Norway rat. Organism_taxid: 10116. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

Biol. unit:

Dodecamer (from PQS)

Resolution:

1.82Å R-factor: 0.207 R-free: 0.278

Authors:

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

Key ref:

D.A.Doyle et al. (1996). Crystal structures of a complexed and peptide-free membrane protein-binding domain: molecular basis of peptide recognition by PDZ. Cell, 85, 1067-1076. PubMed id: 8674113 DOI: 10.1016/S0092-8674(00)81307-0

Date:

20-May-98 Release date: 21-Oct-98

Protein chain

P31016  (DLG4_RAT) -  Disks large homolog 4

Seq: 724 a.a.

Struc: 115 a.a.*

* PDB and UniProt seqs differ at 15 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 

• Biochemical function: protein binding (1 term)

DOI no: 10.1016/S0092-8674(00)81307-0

Cell 85:1067-1076 (1996)

PubMed id: 8674113

Crystal structures of a complexed and peptide-free membrane protein-binding domain: molecular basis of peptide recognition by PDZ.

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

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.

Selected figure(s)

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.

Figures were selected by an automated process.