Inducible lysine decarboxylase LdcI decamer, pH 7.0

Experimental Data Snapshot

  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report

This is version 1.0 of the entry. See complete history


Supramolecular assembly of the Escherichia coli LdcI upon acid stress.

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.

(2021) Proc Natl Acad Sci U S A 118

  • DOI: https://doi.org/10.1073/pnas.2014383118
  • Primary Citation of Related Structures:  
    6YN5, 6YN6

  • 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 Escherichia coli 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 E. coli 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.

  • Organizational Affiliation

    Institut de Biologie Structurale (IBS), Université Grenoble Alpes (UGA), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), CNRS, F-38044 Grenoble, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Inducible lysine decarboxylase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
711Escherichia coli K-12Mutation(s): 0 
Gene Names: cadAldcIb4131JW4092
Find proteins for P0A9H3 (Escherichia coli (strain K12))
Explore P0A9H3 
Go to UniProtKB:  P0A9H3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A9H3
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on LLP
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
Experimental Data & Validation

Experimental Data

  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
European Research Council (ERC)Chap4Resp
European Molecular Biology Organization (EMBO)ALTF441-2017
Marie Sklodowska-Curie Actions, FragNET ITNRespViRALI

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-13
    Type: Initial release