6FGX

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.223 

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 aureusMutation(s): 0 
Gene Names: ywaC_3 (ywaC, ywaC_1)
EC: 2.7.6.5
Find proteins for W8U368 (Staphylococcus aureus)
Go to UniProtKB:  W8U368
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
APC
Query on APC

Download SDF File 
Download CCD File 
A, B
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE
C11 H18 N5 O12 P3
CAWZRIXWFRFUQB-IOSLPCCCSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 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 = 90.00
b = 125.862β = 90.00
c = 217.879γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction

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