PDBsum entry 1v1t

Cell adhesion

PDB id: 1v1t

Contents

Protein chain

164 a.a. *

Ligands

ASN-GLU-TYR-LYS-VAL ×2

BEZ

Waters ×281

* Residue conservation analysis

PDB id:

1v1t

Name:

Cell adhesion

Title:

Crystal structure of the pdz tandem of human syntenin in complex with tneykv peptide

Structure:

Syntenin 1. Chain: a, b. Fragment: pdz tandem, residues 108-273. Synonym: syndecan binding protein 1, melanoma differentiation associated protein-9, mda-9, scaffold protein pbp1, pro-tgf-alpha cytoplasmic domain-interacting protein 18, tacip18. Engineered: yes. Tneykv peptide. Chain: s, t.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 511693. Other_details: gene, sdcbp or mda9 or sycl. Synthetic: yes. Synthetic construct. Organism_taxid: 32630

Biol. unit:

Tetramer (from PDB file)

Resolution:

1.80Å R-factor: 0.183 R-free: 0.229

Authors:

J.Grembecka,T.Cierpicki,Y.Devedjiev,D.R.Cooper,U.Derewenda, Z.S.Derewenda

Key ref:

J.Grembecka et al. (2006). The binding of the PDZ tandem of syntenin to target proteins. Biochemistry, 45, 3674-3683. PubMed id: 16533050 DOI: 10.1021/bi052225y

Date:

23-Apr-04 Release date: 14-Jun-05

Protein chains

O00560  (SDCB1_HUMAN) -  Syntenin-1 from Homo sapiens

Seq: 298 a.a.

Struc: 164 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

DOI no: 10.1021/bi052225y

Biochemistry 45:3674-3683 (2006)

PubMed id: 16533050

The binding of the PDZ tandem of syntenin to target proteins.

J.Grembecka, T.Cierpicki, Y.Devedjiev, U.Derewenda, B.S.Kang, J.H.Bushweller, Z.S.Derewenda.

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.