PDBsum entry 1oby

Cell adhesion

PDB id: 1oby

Contents

Protein chain

75 a.a. *

Ligands

ASN-GLU-PHE-TYR-ALA

THR-ASN-GLU-PHE-TYR-ALA

SO4 ×3

Waters ×145

* Residue conservation analysis

PDB id:

1oby

Name:

Cell adhesion

Title:

Crystal structure of the complex of pdz2 of syntenin with a syndecan-4 peptide.

Structure:

Syntenin 1. Chain: a, b. Fragment: pdz2, residues 197-270. Synonym: syndecan binding protein 1, melanoma differentiation associated protein-9, mda-9, scaffold protein pbp1, tacip18, pro-tgf- alpha cytoplasmic domain-interacting protein 18. Engineered: yes. Syndecan-4. Chain: p, q.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Atcc: 72537. Expressed in: escherichia coli. Expression_system_taxid: 511693. Synthetic: yes. Organism_taxid: 9606

Biol. unit:

Tetramer (from PDB file)

Resolution:

1.85Å R-factor: 0.175 R-free: 0.226

Authors:

B.S.Kang,D.R.Cooper,Y.Devedjiev,U.Derewenda,Z.S.Derewenda

Key ref:

B.S.Kang et al. (2003). Molecular roots of degenerate specificity in syntenin's PDZ2 domain: reassessment of the PDZ recognition paradigm. Structure, 11, 845-853. PubMed id: 12842047 DOI: 10.1016/S0969-2126(03)00125-4

Date:

31-Jan-03 Release date: 11-Jul-03

Protein chains

O00560  (SDCB1_HUMAN) -  Syntenin-1 from Homo sapiens

Seq: 298 a.a.

Struc: 75 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DOI no: 10.1016/S0969-2126(03)00125-4

Structure 11:845-853 (2003)

PubMed id: 12842047

Molecular roots of degenerate specificity in syntenin's PDZ2 domain: reassessment of the PDZ recognition paradigm.

B.S.Kang, D.R.Cooper, Y.Devedjiev, U.Derewenda, Z.S.Derewenda.

ABSTRACT

Crystal structures of the PDZ2 domain of the scaffolding protein syntenin, both unbound and in complexes with peptides derived from C termini of IL5 receptor (alpha chain) and syndecan, reveal the molecular roots of syntenin's degenerate specificity. Three distinct binding sites (S(0), S(-1), and S(-2)), with affinities for hydrophobic side chains, function in a combinatorial way: S(-1) and S(-2) act together to bind syndecan, while S(0) and S(-1) are involved in the binding of IL5Ralpha. Neither mode of interaction is consistent with the prior classification scheme, which defined the IL5Ralpha interaction as class I (-S/T-X-phi) and the syndecan interaction as class II (-phi-X-phi). These results, in conjunction with other emerging structural data on PDZ domains, call for a revision of their classification and of the existing model of their mechanism.

Selected figure(s)

Figure 3.
Figure 3. Schematics of PDZ Interactions(A) Canonical PDZ binding of C-terminal sequence depends on the residues P[0] and P[ -2] binding pockets S[0] and S[ -2].(B) All three C-terminal residues are involved in the interaction to PDZ binding groove.(C) The C-terminal binding depends on the binding at S[ -1] and S[ -2] of PDZ as seen in PDZ2-syndecan-4 peptide complex.(D) The C-terminal binding depends on the binding at S[0] and S[ -1] as seen in syntenin PDZ2-interleukin 5 receptor a subunit peptide complex.(E) Syntrophin PDZ interaction by the residues from b-finger conformation of nNOS.(F) Interaction of internal residue at pocket S[ -2] while C-terminal residues binds at S[0] as seen in syntenin PDZ2-PDZ2 interaction.

The above figure is reprinted by permission from Cell Press: Structure (2003, 11, 845-853) copyright 2003.

Figure was selected by an automated process.