6FGJ

Crystal structure of the small alarmone synthethase 2 from Staphylococcus aureus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.251 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural and mechanistic divergence of the small (p)ppGpp synthetases RelP and RelQ.

Steinchen, W.Vogt, M.S.Altegoer, F.Giammarinaro, P.I.Horvatek, P.Wolz, C.Bange, G.

(2018) Sci Rep 8: 2195-2195

  • DOI: 10.1038/s41598-018-20634-4
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The nutritional alarmones ppGpp and pppGpp (collectively: (p)ppGpp) are nucleotide-based second messengers enabling bacteria to respond to environmental and stress conditions. Several bacterial species contain two highly homologous (p)ppGpp synthetas ...

    The nutritional alarmones ppGpp and pppGpp (collectively: (p)ppGpp) are nucleotide-based second messengers enabling bacteria to respond to environmental and stress conditions. Several bacterial species contain two highly homologous (p)ppGpp synthetases named RelP (SAS2, YwaC) and RelQ (SAS1, YjbM). It is established that RelQ forms homotetramers that are subject to positive allosteric regulation by pppGpp, but structural and mechanistic insights into RelP lack behind. Here we present a structural and mechanistic characterization of RelP. In stark contrast to RelQ, RelP is not allosterically regulated by pppGpp and displays a different enzyme kinetic behavior. This discrepancy is evoked by different conformational properties of the guanosine-substrate binding site (G-Loop) of both proteins. Our study shows how minor structural divergences between close homologues result in new functional features during the course of molecular evolution.


    Organizational Affiliation

    Philipps-University Marburg, LOEWE Center for Synthetic Microbiology & Department of Chemistry, Hans-Meerwein-Stra├če, 35043 Marburg, Germany. wieland.steinchen@synmikro.uni-marburg.de.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GTP pyrophosphokinase
A, B
237Staphylococcus aureusGene Names: ywaC
Find proteins for W8U368 (Staphylococcus aureus)
Go to UniProtKB:  W8U368
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PGE
Query on PGE

Download SDF File 
Download CCD File 
A, B
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.251 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.200 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 71.802α = 90.00
b = 71.802β = 90.00
c = 190.828γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-02-07
    Type: Initial release
  • Version 1.1: 2018-02-14
    Type: Database references