Structural basis of a physical blockage mechanism for the interaction of response regulator PmrA with connector protein PmrD from Klebsiella pneumoniae

J Biol Chem. 2013 Aug 30;288(35):25551-25561. doi: 10.1074/jbc.M113.481978. Epub 2013 Jul 16.


In bacteria, the two-component system is the most prevalent for sensing and transducing environmental signals into the cell. The PmrA-PmrB two-component system, responsible for sensing external stimuli of high Fe(3+) and mild acidic conditions, can control the genes involved in lipopolysaccharide modification and polymyxin resistance in pathogens. In Klebsiella pneumoniae, the small basic connector protein PmrD protects phospho-PmrA and prolongs the expression of PmrA-activated genes. We previously determined the phospho-PmrA recognition mode of PmrD. However, how PmrA interacts with PmrD and prevents its dephosphorylation remains unknown. To address this question, we solved the x-ray crystal structure of the N-terminal receiver domain of BeF3(-)-activated PmrA (PmrA(N)) at 1.70 Å. With this structure, we applied the data-driven docking method based on NMR chemical shift perturbation to generate the complex model of PmrD-PmrA(N), which was further validated by site-directed spin labeling experiments. In the complex model, PmrD may act as a blockade to prevent phosphatase from contacting with the phosphorylation site on PmrA.

Keywords: Drug Resistance; Molecular Docking; NMR; Protein-protein Interaction; Receiver Domain; Response Regulator; Signal Transduction; Site-directed Mutagenesis; Site-directed Spin Labeling; Two-component System.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / biosynthesis
  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / genetics
  • Crystallography, X-Ray
  • Gene Expression Regulation, Bacterial / physiology
  • Iron / chemistry*
  • Iron / metabolism
  • Klebsiella pneumoniae / chemistry*
  • Klebsiella pneumoniae / genetics
  • Klebsiella pneumoniae / metabolism
  • Nuclear Magnetic Resonance, Biomolecular
  • Phosphorylation / physiology
  • Protein Binding
  • Protein Structure, Quaternary
  • Protein Structure, Tertiary


  • Bacterial Proteins
  • pmrA protein, Bacteria
  • Iron

Associated data

  • PDB/3W9S