PDBsum entry 1n7f

Protein binding

PDB id: 1n7f

Contents

Protein chains

86 a.a. *

Ligands

ALA-THR-VAL-ARG-THR-TYR-SER-CYS ×2

Waters ×236

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Crystal structure of grip1 pdz6-Peptide complex reveals the structural basis for class ii pdz target recognition and pdz domain-Mediated multimerization.

Authors

Y.J.Im, S.H.Park, S.H.Rho, J.H.Lee, G.B.Kang, M.Sheng, E.Kim, S.H.Eom.

Ref.

J Biol Chem, 2003, 278, 8501-8507. [DOI no: 10.1074/jbc.M212263200]

PubMed id

12493751

Abstract

PDZ domains bind to short segments within target proteins in a sequence-specific fashion. Glutamate receptor-interacting protein (GRIP)/ABP family proteins contain six to seven PDZ domains and interact via the sixth PDZ domain (class II) with the C termini of various proteins including liprin-alpha. In addition the PDZ456 domain mediates the formation of homo- and heteromultimers of GRIP proteins. To better understand the structural basis of peptide recognition by a class II PDZ domain and PDZ-mediated multimerization, we determined the crystal structures of the GRIP1 PDZ6 domain alone and in complex with a synthetic C-terminal octapeptide of human liprin-alpha at resolutions of 1.5 and 1.8 A, respectively. Remarkably, unlike other class II PDZ domains, Ile-736 at alphaB5 rather than conserved Leu-732 at alphaB1 makes a direct hydrophobic contact with the side chain of the Tyr at the -2 position of the ligand. Moreover, the peptide-bound structure of PDZ6 shows a slight reorientation of helix alphaB, indicating that the second hydrophobic pocket undergoes a conformational adaptation to accommodate the bulkiness of the Tyr side chain, and forms an antiparallel dimer through an interface located at a site distal to the peptide-binding groove. This configuration may enable formation of GRIP multimers and efficient clustering of GRIP-binding proteins.

Figure 3.
Fig. 3. The peptide-binding site. A, ball and stick model of the peptide binding pocket and its specific ligand (ATVRTYSC). Only the last four residues of the peptide are shown (green), and for clarity only side chains of the residues involved in the peptide binding are shown. Dashed lines represent hydrogen bonds around the carboxylate binding site. A water molecule, shown as a red ball, forms a hydrogen bond with one of the ligand C-terminal carboxylic oxygen atoms. The majority of the hydrogen bonds are between the peptide backbone and the carboxylate-binding loop or strand B. B, molecular surfaces of GRIP PDZ6 showing the hydrophobic binding pocket and the bound peptide. The hydrophobic residues are colored white, and the hydrophobic side chains within the binding pocket are colored in gray scale. The polar, acidic, and basic residues are colored yellow, red, and blue respectively. The two hydrophobic binding pockets are indicated by circles. The side chains of hydrophobic ligand residues Cys-0 and Try-1 dip into the hydrophobic binding pockets. C, conformational changes upon peptide binding. Superposition of the peptide-free and peptide-bound structures was done using the six -strands, which do not undergo conformational change upon peptide binding. The peptide-free and peptide-bound PDZ structures are shown in white and gray, respectively. The segments that undergo large conformational changes upon peptide binding are colored black. D, ball and stick model showing a conformational change of Ile-736. Peptide-bound PDZ6 is colored dark blue; self-associated PDZ6 is colored green. The peptide ligand and C-terminal tail of the PDZ6 construct are colored pale blue and yellow, respectively. The bulky hydrophobic side chain of Tyr-2 makes hydrophobic contact with Ile-736.

Figure 4.
Fig. 4. Dimerization of GRIP PDZ6. A, dimeric structure of PDZ6 domain. PDZ6 domains form a dimer via interaction of antiparallel A strands and A- D loops. Peptide ligands bound to the opposite side of the PDZ6 dimer are represented in ball-and-stick. B, self-association of two GRIP PDZ6 domains related by a 2-fold crystallographic axis was observed in the peptide-free PDZ6 crystal. Each C terminus serves as a ligand for a neighboring PDZ molecule. C, effects of mutations on dimerization. Molecular weights of mutants Y671D and R731D and a wild type PDZ domain were estimated by size exclusion chromatography (Superdex 75 HR 16/60 column). The mutated residues, Y671D and R718D, were shown in ball and stick with van der Waals radius in A and B. The elution profiles of a wild type, Y671D and R718D mutants. This result suggests that the dimer in solution is the form shown in A. D, the variable residues within the PDZ6 domains of GRIP homologues are represented in ball-and-stick. Only one variable residue, Ile-669, which is Val in GRIP2, is located in the dimeric interface.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 8501-8507) copyright 2003.