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

EMBO J. 2011 Mar 2;30(5):931-44. doi: 10.1038/emboj.2011.5. Epub 2011 Jan 28.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Amino Acid Transport Systems / chemistry*
  • Amino Acid Transport Systems / metabolism
  • Antiporters / chemistry*
  • Antiporters / metabolism
  • Carboxy-Lyases / chemistry*
  • Carboxy-Lyases / metabolism
  • Catalytic Domain
  • Crystallography, X-Ray
  • Enzyme Inhibitors / pharmacology
  • Escherichia coli / enzymology*
  • Escherichia coli Proteins / chemistry*
  • Escherichia coli Proteins / metabolism
  • Hydrogen-Ion Concentration
  • Molecular Sequence Data
  • Protein Conformation
  • Protein Multimerization
  • Stress, Physiological*


  • Amino Acid Transport Systems
  • Antiporters
  • CadB protein, E Coli
  • Enzyme Inhibitors
  • Escherichia coli Proteins
  • Carboxy-Lyases
  • lysine decarboxylase