5Z7C

crystal structure of cyclic GMP-AMP specifc phosphodiesterases in V.cholerae (V-cGAP3)

5Z7C の概要

• エントリーDOI: 10.2210/pdb5z7c/pdb
• 分子名称: 3'3'-cGAMP-specific phosphodiesterase 3 (2 entities in total)
• 機能のキーワード: cyclic dinucleotides, phosphodiesterase., metal binding protein
• 由来する生物種: Vibrio cholerae O1 biovar El Tor str. N16961
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 51564.65

構造登録者

Deng, M.J.,Ye, Z.Y.,Su, X.D. (登録日: 2018-01-28, 公開日: 2019-01-02, 最終更新日: 2024-10-23)

主引用文献

Deng, M.J.,Tao, J.,E, C.,Ye, Z.Y.,Jiang, Z.,Yu, J.,Su, X.D.
Novel Mechanism for Cyclic Dinucleotide Degradation Revealed by Structural Studies of Vibrio Phosphodiesterase V-cGAP3.
J. Mol. Biol., 430:5080-5093, 2018

PubMed Abstract: 3'3'-cyclic GMP-AMP (3'3'-cGAMP) belongs to a family of the bacterial secondary messenger cyclic dinucleotides. It was first discovered in the Vibrio cholerae seventh pandemic strains and is involved in efficient intestinal colonization and chemotaxis regulation. Phosphodiesterases (PDEs) that degrade 3'3'-cGAMP play important regulatory roles in the relevant signaling pathways, and a previous study has identified three PDEs in V. cholerae, namely, V-cGAP1, V-cGAP2, and V-cGAP3, functioning in 3'3'-cGAMP degradation. We report the crystal structure, biochemical, and structural analyses of V-cGAP3, providing a foundation for understanding the mechanism of 3'3'-cGAMP degradation and regulation in general. Our crystal and molecular dynamic (MD)-simulated structures revealed that V-cGAP3 contains tandem HD-GYP domains within its N- and C-terminal domains, with similar three-dimensional topologies despite their low-sequence identity. Biochemical and structural analyses showed that the N-terminal domain plays a mechanism of positive regulation for the catalytic C-terminal domain. We also demonstrated that the other homologous Vibrio PDEs, V-cGAP1/2, likely function via a similar mechanism.

PubMed: 30365951
DOI: 10.1016/j.jmb.2018.10.010

実験手法

X-RAY DIFFRACTION (2.76 Å)