5EAZ

crystal form I of YfiB belonging to space groups P21

5EAZ の概要

• エントリーDOI: 10.2210/pdb5eaz/pdb
• 関連するPDBエントリー: 5EB0 5EB1 5EB2 5EB3
• 分子名称: YfiB, SULFATE ION (3 entities in total)
• 機能のキーワード: ompa/pal-like outer-membrane lipoprotein, membrane protein
• 由来する生物種: Pseudomonas aeruginosa PAO1
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 59602.70

構造登録者

Xu, M.,Yang, X.,Yang, X.-A.,Zhou, L.,Liu, T.-Z.,Fan, Z.,Jiang, T. (登録日: 2015-10-17, 公開日: 2016-05-18, 最終更新日: 2023-11-08)

主引用文献

Xu, M.,Yang, X.,Yang, X.-A.,Zhou, L.,Liu, T.-Z.,Fan, Z.,Jiang, T.
Structural insights into the regulatory mechanism of the Pseudomonas aeruginosa YfiBNR system
Protein Cell, 7:403-416, 2016

PubMed Abstract: YfiBNR is a recently identified bis-(3'-5')-cyclic dimeric GMP (c-di-GMP) signaling system in opportunistic pathogens. It is a key regulator of biofilm formation, which is correlated with prolonged persistence of infection and antibiotic drug resistance. In response to cell stress, YfiB in the outer membrane can sequester the periplasmic protein YfiR, releasing its inhibition of YfiN on the inner membrane and thus provoking the diguanylate cyclase activity of YfiN to induce c-di-GMP production. However, the detailed regulatory mechanism remains elusive. Here, we report the crystal structures of YfiB alone and of an active mutant YfiB(L43P) complexed with YfiR with 2:2 stoichiometry. Structural analyses revealed that in contrast to the compact conformation of the dimeric YfiB alone, YfiB(L43P) adopts a stretched conformation allowing activated YfiB to penetrate the peptidoglycan (PG) layer and access YfiR. YfiB(L43P) shows a more compact PG-binding pocket and much higher PG binding affinity than wild-type YfiB, suggesting a tight correlation between PG binding and YfiB activation. In addition, our crystallographic analyses revealed that YfiR binds Vitamin B6 (VB6) or L-Trp at a YfiB-binding site and that both VB6 and L-Trp are able to reduce YfiB(L43P)-induced biofilm formation. Based on the structural and biochemical data, we propose an updated regulatory model of the YfiBNR system.

PubMed: 27113583
DOI: 10.1007/s13238-016-0264-7

実験手法

X-RAY DIFFRACTION (2.151 Å)