6G15

Crystal structure of pppGpp bound RbgA from S. aureus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural basis for (p)ppGpp-mediated inhibition of the GTPase RbgA.

Pausch, P.Steinchen, W.Wieland, M.Klaus, T.Freibert, S.A.Altegoer, F.Wilson, D.N.Bange, G.

(2018) J. Biol. Chem. --: --

  • DOI: 10.1074/jbc.RA118.003070
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Efficient adaptation to environmental changes is pivotal for all bacterial cells. Almost all bacterial species depend on the conserved stringent response system to prompt timely transcriptional and metabolic responses according to stress conditions a ...

    Efficient adaptation to environmental changes is pivotal for all bacterial cells. Almost all bacterial species depend on the conserved stringent response system to prompt timely transcriptional and metabolic responses according to stress conditions and nutrient depletion. The stringent response relies on the stress-dependent synthesis of the second messenger nucleotides and alarmones (p)ppGpp, which pleiotropically target and reprogram processes that consume cellular resources, such as ribosome biogenesis. Here we show that (p)ppGpp acts on the ribosome biogenesis GTPase A (RbgA) of Gram-positive bacteria. Using X-ray crystallography, hydrogen-deuterium exchange mass spectrometry (HDX-MS) and kinetic analysis, we demonstrate that the alarmones (p)ppGpp bind to RbgA in a manner similar to that of binding by GDP and GTP and therby act as competitive inhibitors. Our structural analysis of Staphylococcus aureus RbgA bound to ppGpp and pppGpp at 1.8 Å and 1.65 Å resolution, respectively, suggested that the alarmones (p)ppGpp prevent the active GTPase conformation of RbgA by sterically blocking the association of its G2 motif via their 3'-pyrophosphate moieties. Taken together, our structural and biochemical characterization of RbgA in the context of the alarmone-mediated stringent response reveals how (p)ppGpp affects the function of RbgA and reprograms this GTPase to arrest the ribosomal large subunit.


    Organizational Affiliation

    Philipps-University Marburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribosome biogenesis GTPase A
A, B
301Staphylococcus aureus (strain USA300)Mutation(s): 0 
Find proteins for A0A0H2XK72 (Staphylococcus aureus (strain USA300))
Go to UniProtKB:  A0A0H2XK72
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C1Z
Query on C1Z

Download SDF File 
Download CCD File 
A, B
guanosine 3'-diphosphate 5'-triphosphate
C10 H18 N5 O20 P5
KCPMACXZAITQAX-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.218 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 72.084α = 90.00
b = 78.467β = 90.00
c = 125.022γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PHASERphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2018-03-20 
  • Released Date: 2018-11-07 
  • Deposition Author(s): Pausch, P., Bange, G.

Revision History 

  • Version 1.0: 2018-11-07
    Type: Initial release