5ED0

Structure of the Shigella flexneri VapC mutant D7N

5ED0 の概要

• エントリーDOI: 10.2210/pdb5ed0/pdb
• 関連するPDBエントリー: 5ECD
• 分子名称: tRNA(fMet)-specific endonuclease VapC (2 entities in total)
• 機能のキーワード: toxin, pin-domain, hydrolase
• 由来する生物種: Shigella flexneri
• タンパク質・核酸の鎖数: 12
• 化学式量合計: 187967.65

構造登録者

Xu, K.,Dedic, E.,Brodersen, D.E. (登録日: 2015-10-20, 公開日: 2016-02-17, 最終更新日: 2024-05-08)

主引用文献

Xu, K.,Dedic, E.,Brodersen, D.E.
Structural analysis of the active site architecture of the VapC toxin from Shigella flexneri.
Proteins, 84:892-899, 2016

PubMed Abstract: The VapC toxin from the Shigella flexneri 2a virulence plasmid pMYSH6000 belongs to the PIN domain protein family, which is characterized by a conserved fold with low amino acid sequence conservation. The toxin is a bona fide Mg(2+) -dependent ribonuclease and has been shown to target initiator tRNA(fMet) in vivo. Here, we present crystal structures of active site catalytic triad mutants D7A, D7N, and D98N of the VapC toxin in absence of antitoxin. In all structures, as well as in solution, VapC forms a dimer. In the D98N structure, a Hepes molecule occupies both active sites of the dimer and comparison with the structure of RNase H bound to a DNA/RNA hybrid suggests that the Hepes molecule mimics the position of an RNA nucleotide in the VapC active site. Proteins 2016; 84:892-899. © 2016 Wiley Periodicals, Inc.

PubMed: 26833558
DOI: 10.1002/prot.25002

実験手法

X-RAY DIFFRACTION (2.1 Å)