1YBO

Crystal structure of the PDZ tandem of human syntenin with syndecan peptide

Summary for 1YBO

• Entry DOI: 10.2210/pdb1ybo/pdb
• Descriptor: Syntenin 1, Syndecan-4 (3 entities in total)
• Functional Keywords: pdz domain, scaffolding protein, adhesion complex, structural protein
• Biological source: Homo sapiens (human); More
• Cellular location: Cell junction, focal adhesion : O00560; Isoform 1: Membrane ; Single- pass type I membrane protein . Isoform 2: Secreted: P31431
• Total number of polymer chains: 4
• Total formula weight: 39982.03

Authors

Grembecka, J.,Cooper, D.R.,Cierpicki, T.,Kang, B.S.,Devedjiev, Y.,Derewenda, Z. (deposition date: 2004-12-21, release date: 2006-01-10, Last modification date: 2023-08-23)

Primary citation

Grembecka, J.,Cierpicki, T.,Devedjiev, Y.,Derewenda, U.,Kang, B.S.,Bushweller, J.H.,Derewenda, Z.S.
The binding of the PDZ tandem of syntenin to target proteins
Biochemistry, 45:3674-3683, 2006

PubMed Abstract: PDZ domains are among the most abundant protein modules in the known genomes. Their main function is to provide scaffolds for membrane-associated protein complexes by binding to the cytosolic, C-terminal fragments of receptors, channels, and other integral membrane proteins. Here, using both heteronuclear NMR and single crystal X-ray diffraction, we show how peptides with different sequences, including those corresponding to the C-termini of syndecan, neurexin, and ephrin B, can simultaneously bind to both PDZ domains of the scaffolding protein syntenin. The PDZ2 domain binds these peptides in the canonical fashion, and an induced fit mechanism allows for the accommodation of a range of side chains in the P(0) and P(-)(2) positions. However, binding to the PDZ1 domain requires that the target peptide assume a noncanonical conformation. These data help explain how syntenin, and perhaps other PDZ-containing proteins, may preferentially bind to dimeric and clustered targets, and provide a mechanistic explanation for the previously reported cooperative ligand binding by syntenin's two PDZ domains.

PubMed: 16533050
DOI: 10.1021/bi052225y

Experimental method

X-RAY DIFFRACTION (2.3 Å)