Crystal Structure of GRIP1 PDZ6-Peptide Complex Reveals the Structural Basis for Class II PDZ Target Recognition and PDZ Domain-mediated Multimerization

Young Jun Im,Seong Ho Park,Seong-Hwan Rho,Jun Hyuck Lee,Gil Bu Kang,Morgan Sheng,Eunjoon Kim,Soo Hyun Eom

doi:10.1074/jbc.m212263200

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.

Highlights

PDZ domains bind to short segments within target proteins in a sequence-specific fashion
Class I PDZ domains bind to a C-terminal motif with the sequence X-Ser/Thr-X-Val/Leu-COOH, where X represents any residue, while class II PDZ domains prefer X-⌽-X-⌽-COOH, where ⌽ is usually a large hydrophobic residue
Class III PDZ domains prefer the sequence X-Asp-X-Val-COOH in which a negatively charged amino acid is at the Ϫ2 position [3], while class IV domains prefer the sequence X-⌿-Asp/Glu-COOH in which an acidic residue is at the C-terminal position and where ⌿ represents an aromatic residue [4]

Summary

Introduction

PDZ domains bind to short segments within target proteins in a sequence-specific fashion. This is the first description of the crystal structure of a class II PDZ domain non-covalently complexed with its specific peptide ligand, showing an additional role of PDZ domains in the multimerization of PDZcontaining proteins.

Results

Conclusion