3W9S

Crystal Structure Analysis of the N-terminal Receiver domain of Response Regulator PmrA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Basis of a Physical Blockage Mechanism for the Interaction of Response Regulator PmrA with Connector Protein PmrD from Klebsiella Pneumoniae

Lou, S.C.Lou, Y.C.Rajasekaran, M.Chang, Y.W.Hsiao, C.D.Chen, C.

(2013) J.Biol.Chem. 288: 25551-25561

  • DOI: 10.1074/jbc.M113.481978

  • PubMed Abstract: 
  • 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 c ...

    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.


    Organizational Affiliation

    Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
OmpR family response regulator in two-component regulatory system with BasS
A, B
131N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
BEF
Query on BEF

Download SDF File 
Download CCD File 
A, B
BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.165 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 49.994α = 90.00
b = 49.994β = 90.00
c = 145.859γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
PHENIXrefinement
SOLVEphasing
HKL-2000data scaling
HKL-2000data reduction
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-04-15 
  • Released Date: 2013-07-24 
  • Deposition Author(s): Chen, C., Luo, S.

Revision History 

  • Version 1.0: 2013-07-24
    Type: Initial release
  • Version 1.1: 2013-09-18
    Type: Database references