5DEC

Crystal structure of the small alarmone synthetase 1 from Bacillus subtilis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 

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This is version 1.1 of the entry. See complete history


Literature

Catalytic mechanism and allosteric regulation of an oligomeric (p)ppGpp synthetase by an alarmone.

Steinchen, W.Schuhmacher, J.S.Altegoer, F.Fage, C.D.Srinivasan, V.Linne, U.Marahiel, M.A.Bange, G.

(2015) Proc Natl Acad Sci U S A 112: 13348-13353

  • DOI: 10.1073/pnas.1505271112
  • Primary Citation of Related Structures:  
    5DEC, 5DED, 5F2V

  • PubMed Abstract: 
  • Nucleotide-based second messengers serve in the response of living organisms to environmental changes. In bacteria and plant chloroplasts, guanosine tetraphosphate (ppGpp) and guanosine pentaphosphate (pppGpp) [collectively named "(p)ppGpp"] act as alarmones that globally reprogram cellular physiology during various stress conditions ...

    Nucleotide-based second messengers serve in the response of living organisms to environmental changes. In bacteria and plant chloroplasts, guanosine tetraphosphate (ppGpp) and guanosine pentaphosphate (pppGpp) [collectively named "(p)ppGpp"] act as alarmones that globally reprogram cellular physiology during various stress conditions. Enzymes of the RelA/SpoT homology (RSH) family synthesize (p)ppGpp by transferring pyrophosphate from ATP to GDP or GTP. Little is known about the catalytic mechanism and regulation of alarmone synthesis. It also is unclear whether ppGpp and pppGpp execute different functions. Here, we unravel the mechanism and allosteric regulation of the highly cooperative alarmone synthetase small alarmone synthetase 1 (SAS1) from Bacillus subtilis. We determine that the catalytic pathway of (p)ppGpp synthesis involves a sequentially ordered substrate binding, activation of ATP in a strained conformation, and transfer of pyrophosphate through a nucleophilic substitution (SN2) reaction. We show that pppGpp-but not ppGpp-positively regulates SAS1 at an allosteric site. Although the physiological significance remains to be elucidated, we establish the structural and mechanistic basis for a biological activity in which ppGpp and pppGpp execute different functional roles.


    Organizational Affiliation

    LOEWE Center for Synthetic Microbiology, Philipps University Marburg, 35043 Marburg, Germany; Department of Chemistry, Philipps University Marburg, 35043 Marburg, Germany gert.bange@synmikro.uni-marburg.de.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GTP pyrophosphokinase YjbMA, B, C, D218Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: yjbMBSU11600
EC: 2.7.6.5
UniProt
Find proteins for O31611 (Bacillus subtilis (strain 168))
Explore O31611 
Go to UniProtKB:  O31611
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO31611
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.13α = 90
b = 77.69β = 90.4
c = 81.61γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
PHENIXrefinement
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-10-28
    Type: Initial release
  • Version 1.1: 2018-06-13
    Changes: Data collection