6YN5

Inducible lysine decarboxylase LdcI decamer, pH 7.0

6YN5 の概要

• エントリーDOI: 10.2210/pdb6yn5/pdb
• EMDBエントリー: 10849
• 分子名称: Inducible lysine decarboxylase (1 entity in total)
• 機能のキーワード: acid stress-inducible, decarboxylase, laodc, lyase
• 由来する生物種: Escherichia coli (strain K12)
• タンパク質・核酸の鎖数: 10
• 化学式量合計: 811105.70

構造登録者

Jessop, M.,Felix, J.,Desfosses, A.,Effantin, G.,Gutsche, I. (登録日: 2020-04-10, 公開日: 2021-01-13, 最終更新日: 2025-04-09)

主引用文献

Jessop, M.,Liesche, C.,Felix, J.,Desfosses, A.,Baulard, M.,Adam, V.,Fraudeau, A.,Huard, K.,Effantin, G.,Kleman, J.P.,Bacia-Verloop, M.,Bourgeois, D.,Gutsche, I.
Supramolecular assembly of the Escherichia coli LdcI upon acid stress.
Proc.Natl.Acad.Sci.USA, 118:-, 2021

PubMed Abstract: Pathogenic and commensal bacteria often have to resist the harsh acidity of the host stomach. The inducible lysine decarboxylase LdcI buffers the cytosol and the local extracellular environment to ensure enterobacterial survival at low pH. Here, we investigate the acid stress-response regulation of LdcI by combining biochemical and biophysical characterization with negative stain and cryoelectron microscopy (cryo-EM) and wide-field and superresolution fluorescence imaging. Due to deleterious effects of fluorescent protein fusions on native LdcI decamers, we opt for three-dimensional localization of nanobody-labeled endogenous wild-type LdcI in acid-stressed cells and show that it organizes into distinct patches at the cell periphery. Consistent with recent hypotheses that in vivo clustering of metabolic enzymes often reflects their polymerization as a means of stimulus-induced regulation, we show that LdcI assembles into filaments in vitro at physiologically relevant low pH. We solve the structures of these filaments and of the LdcI decamer formed at neutral pH by cryo-EM and reveal the molecular determinants of LdcI polymerization, confirmed by mutational analysis. Finally, we propose a model for LdcI function inside the enterobacterial cell, providing a structural and mechanistic basis for further investigation of the role of its supramolecular organization in the acid stress response.

PubMed: 33372137
DOI: 10.1073/pnas.2014383118

実験手法

ELECTRON MICROSCOPY (2.7 Å)