Linkage between the Bacterial Acid Stress and Stringent Responses: The Structure of the Inducible Lysine Decarboxylase

Experimental Data Snapshot

  • Resolution: 4.10 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.276 
  • R-Value Observed: 0.278 

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Linkage between the bacterial acid stress and stringent responses: the structure of the inducible lysine decarboxylase.

Kanjee, U.Gutsche, I.Alexopoulos, E.Zhao, B.El Bakkouri, M.Thibault, G.Liu, K.Ramachandran, S.Snider, J.Pai, E.F.Houry, W.A.

(2011) EMBO J 30: 931-944

  • DOI: https://doi.org/10.1038/emboj.2011.5
  • Primary Citation of Related Structures:  
    3N75, 3Q16

  • PubMed Abstract: 

    The Escherichia coli inducible lysine decarboxylase, LdcI/CadA, together with the inner-membrane lysine-cadaverine antiporter, CadB, provide cells with protection against mild acidic conditions (pH∼5). To gain a better understanding of the molecular processes underlying the acid stress response, the X-ray crystal structure of LdcI was determined. The structure revealed that the protein is an oligomer of five dimers that associate to form a decamer. Surprisingly, LdcI was found to co-crystallize with the stringent response effector molecule ppGpp, also known as the alarmone, with 10 ppGpp molecules in the decamer. ppGpp is known to mediate the stringent response, which occurs in response to nutrient deprivation. The alarmone strongly inhibited LdcI enzymatic activity. This inhibition is important for modulating the consumption of lysine in cells during acid stress under nutrient limiting conditions. Hence, our data provide direct evidence for a link between the bacterial acid stress and stringent responses.

  • Organizational Affiliation

    Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysine decarboxylase, inducible
A, B, C, D, E
715Escherichia coli K-12Mutation(s): 0 
Gene Names: cadAldcI
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
Experimental Data & Validation

Experimental Data

  • Resolution: 4.10 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.276 
  • R-Value Observed: 0.278 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 270.29α = 90
b = 181.29β = 125.06
c = 169.93γ = 90
Software Package:
Software NamePurpose
MxDCdata collection
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-02-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2023-12-06
    Changes: Data collection