6FGK | pdb_00006fgk

Crystal structure of the small alarmone synthethase 2 from Bacillus subtilis

• PDB DOI: https://doi.org/10.2210/pdb6FGK/pdb

• Classification: TRANSFERASE
• Organism(s): Bacillus subtilis subsp. subtilis str. 168
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-01-11 Released: 2018-02-07 
• Deposition Author(s): Bange, G., Vogt, M., Steinchen, W., Altegoer, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 
  0.319 (Depositor), 0.314 (DCC) 
• R-Value Work: 
  0.257 (Depositor), 0.258 (DCC) 
• R-Value Observed: 
  0.260 (Depositor) 

Starting Model: experimental

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

• PubMed: 29391580 
• DOI: https://doi.org/10.1038/s41598-018-20634-4
• Primary Citation 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.

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Organizational Affiliation: 
• Philipps-University Marburg, LOEWE Center for Synthetic Microbiology & Department of Chemistry, Hans-Meerwein-Straße, 35043 Marburg, Germany. [e-mail].
Philipps-University Marburg, LOEWE Center for Synthetic Microbiology & Department of Chemistry, Hans-Meerwein-Straße, 35043 Marburg, Germany.
University of Tübingen, Interfaculty Institute of Microbiology and Infection Medicine, Elfriede-Aulhorn-Straße 6, 72076 Tübingen, Germany.
Philipps-University Marburg, LOEWE Center for Synthetic Microbiology & Department of Chemistry, Hans-Meerwein-Straße, 35043 Marburg, Germany. [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration, homology

Macromolecule Content 

• Total Structure Weight: 98.55 kDa 
• Atom Count: 6,058 
• Modeled Residue Count: 734 
• Deposited Residue Count: 840 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTP pyrophosphokinase YwaC	A, B, C, D	210	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0  Gene Names: ywaC, BSU38480, ipa-7d EC: 2.7.6.5
UniProt
Find proteins for P39583 (Bacillus subtilis (strain 168)) Explore P39583  Go to UniProtKB:  P39583

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free:  0.319 (Depositor), 0.314 (DCC) 
• R-Value Work:  0.257 (Depositor), 0.258 (DCC) 
• R-Value Observed: 0.260 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.67	α = 90
b = 99.92	β = 90
c = 122.884	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-02-07 
Deposition Author(s): Bange, G., Vogt, M., Steinchen, W., Altegoer, F.

Revision History  

• 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, Refinement description