6YN5

Inducible lysine decarboxylase LdcI decamer, pH 7.0

Summary for 6YN5

• Entry DOI: 10.2210/pdb6yn5/pdb
• EMDB information: 10849
• Descriptor: Inducible lysine decarboxylase (1 entity in total)
• Functional Keywords: acid stress-inducible, decarboxylase, laodc, lyase
• Biological source: Escherichia coli (strain K12)
• Total number of polymer chains: 10
• Total formula weight: 811105.70

Authors

Jessop, M.,Felix, J.,Desfosses, A.,Effantin, G.,Gutsche, I. (deposition date: 2020-04-10, release date: 2021-01-13)

Primary citation

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

Experimental method

ELECTRON MICROSCOPY (2.7 Å)