4Q2O

PDLIM4 PDZ in Complex with a Phage-Derived Peptide

4Q2O の概要

• エントリーDOI: 10.2210/pdb4q2o/pdb
• 関連するPDBエントリー: 4Q2N 4Q2P 4Q2Q
• 分子名称: PDZ and LIM domain protein 4 (2 entities in total)
• 機能のキーワード: pdz, protein binding
• 由来する生物種: Homo sapiens (human)
• タンパク質・核酸の鎖数: 6
• 化学式量合計: 61822.06

構造登録者

Appleton, B.A.,Wiesmann, C. (登録日: 2014-04-09, 公開日: 2014-09-10, 最終更新日: 2024-11-20)

主引用文献

Ernst, A.,Appleton, B.A.,Ivarsson, Y.,Zhang, Y.,Gfeller, D.,Wiesmann, C.,Sidhu, S.S.
A structural portrait of the PDZ domain family.
J.Mol.Biol., 426:3509-3519, 2014

PubMed Abstract: PDZ (PSD-95/Discs-large/ZO1) domains are interaction modules that typically bind to specific C-terminal sequences of partner proteins and assemble signaling complexes in multicellular organisms. We have analyzed the existing database of PDZ domain structures in the context of a specificity tree based on binding specificities defined by peptide-phage binding selections. We have identified 16 structures of PDZ domains in complex with high-affinity ligands and have elucidated four additional structures to assemble a structural database that covers most of the branches of the PDZ specificity tree. A detailed comparison of the structures reveals features that are responsible for the diverse specificities across the PDZ domain family. Specificity differences can be explained by differences in PDZ residues that are in contact with the peptide ligands, but these contacts involve both side-chain and main-chain interactions. Most PDZ domains bind peptides in a canonical conformation in which the ligand main chain adopts an extended β-strand conformation by interacting in an antiparallel fashion with a PDZ β-strand. However, a subset of PDZ domains bind peptides with a bent main-chain conformation and the specificities of these non-canonical domains could not be explained based on canonical structures. Our analysis provides a structural portrait of the PDZ domain family, which serves as a guide in understanding the structural basis for the diverse specificities across the family.

PubMed: 25158098
DOI: 10.1016/j.jmb.2014.08.012

実験手法

X-RAY DIFFRACTION (2.1 Å)