7RMW

Crystal structure of B. subtilis PurR bound to ppGpp


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

The nucleotide messenger (p)ppGpp is an anti-inducer of the purine synthesis transcription regulator PurR in Bacillus.

Anderson, B.W.Schumacher, M.A.Yang, J.Turdiev, A.Turdiev, H.Schroeder, J.W.He, Q.Lee, V.T.Brennan, R.G.Wang, J.D.

(2022) Nucleic Acids Res 50: 847-866

  • DOI: https://doi.org/10.1093/nar/gkab1281
  • Primary Citation of Related Structures:  
    7RMW

  • PubMed Abstract: 

    The nucleotide messenger (p)ppGpp allows bacteria to adapt to fluctuating environments by reprogramming the transcriptome. Despite its well-recognized role in gene regulation, (p)ppGpp is only known to directly affect transcription in Proteobacteria by binding to the RNA polymerase. Here, we reveal a different mechanism of gene regulation by (p)ppGpp in Firmicutes: (p)ppGpp directly binds to the transcription factor PurR to downregulate purine biosynthesis gene expression upon amino acid starvation. We first identified PurR as a receptor of (p)ppGpp in Bacillus anthracis. A co-structure with Bacillus subtilis PurR reveals that (p)ppGpp binds to a PurR pocket reminiscent of the active site of phosphoribosyltransferase enzymes that has been repurposed to serve a purely regulatory role, where the effectors (p)ppGpp and PRPP compete to allosterically control transcription. PRPP inhibits PurR DNA binding to induce transcription of purine synthesis genes, whereas (p)ppGpp antagonizes PRPP to enhance PurR DNA binding and repress transcription. A (p)ppGpp-refractory purR mutant in B. subtilis fails to downregulate purine synthesis genes upon amino acid starvation. Our work establishes the precedent of (p)ppGpp as an effector of a classical transcription repressor and reveals the key function of (p)ppGpp in regulating nucleotide synthesis through gene regulation, from soil bacteria to pathogens.


  • Organizational Affiliation

    Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pur operon repressor
A, B, C, D, E
A, B, C, D, E, F
285Bacillus subtilisMutation(s): 0 
Gene Names: purRB4122_4510B4417_1788BS16045_00058CFD21_22225ETA10_00295ETL41_13190FAL52_19670FIU26_15290SC09_Contig28orf00392
UniProt
Find proteins for P37551 (Bacillus subtilis (strain 168))
Explore P37551 
Go to UniProtKB:  P37551
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37551
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.264α = 62.75
b = 90.969β = 75.36
c = 98.708γ = 78.53
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM130290

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-22
    Type: Initial release
  • Version 1.1: 2022-01-12
    Changes: Database references
  • Version 1.2: 2022-02-02
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Refinement description