Crystal structure of the small alarmone synthethase 2 from Staphylococcus aureus bound to AMPCPP

Experimental Data Snapshot

  • Resolution: 2.90 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.223 

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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: https://doi.org/10.1038/s41598-018-20634-4
  • Primary Citation of Related Structures:  
    6FGJ, 6FGK, 6FGX

  • 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 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-Straße, 35043 Marburg, Germany. wieland.steinchen@synmikro.uni-marburg.de.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GTP pyrophosphokinase
A, B
237Staphylococcus aureusMutation(s): 0 
Gene Names: 
Find proteins for W8U368 (Staphylococcus aureus)
Explore W8U368 
Go to UniProtKB:  W8U368
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupW8U368
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.90 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.223 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.862α = 90
b = 125.862β = 90
c = 217.879γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-07
    Type: Initial release
  • Version 1.1: 2018-02-14
    Changes: Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description