4R24

Complete dissection of B. subtilis nitrogen homeostatic circuitry


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.217 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structures of regulatory machinery reveal novel molecular mechanisms controlling B. subtilis nitrogen homeostasis.

Schumacher, M.A.Chinnam, N.B.Cuthbert, B.Tonthat, N.K.Whitfill, T.

(2015) Genes Dev 29: 451-464

  • DOI: 10.1101/gad.254714.114
  • Primary Citation of Related Structures:  
    4R22, 4R24, 4R25, 4R4E, 4RX6, 4S0R

  • PubMed Abstract: 
  • All cells must sense and adapt to changing nutrient availability. However, detailed molecular mechanisms coordinating such regulatory pathways remain poorly understood. In Bacillus subtilis, nitrogen homeostasis is controlled by a unique circuitry composed of the regulator TnrA, which is deactivated by feedback-inhibited glutamine synthetase (GS) during nitrogen excess and stabilized by GlnK upon nitrogen depletion, and the repressor GlnR ...

    All cells must sense and adapt to changing nutrient availability. However, detailed molecular mechanisms coordinating such regulatory pathways remain poorly understood. In Bacillus subtilis, nitrogen homeostasis is controlled by a unique circuitry composed of the regulator TnrA, which is deactivated by feedback-inhibited glutamine synthetase (GS) during nitrogen excess and stabilized by GlnK upon nitrogen depletion, and the repressor GlnR. Here we describe a complete molecular dissection of this network. TnrA and GlnR, the global nitrogen homeostatic transcription regulators, are revealed as founders of a new structural family of dimeric DNA-binding proteins with C-terminal, flexible, effector-binding sensors that modulate their dimerization. Remarkably, the TnrA sensor domains insert into GS intersubunit catalytic pores, destabilizing the TnrA dimer and causing an unprecedented GS dodecamer-to-tetradecamer conversion, which concomitantly deactivates GS. In contrast, each subunit of the GlnK trimer "templates" active TnrA dimers. Unlike TnrA, GlnR sensors mediate an autoinhibitory dimer-destabilizing interaction alleviated by GS, which acts as a GlnR chaperone. Thus, these studies unveil heretofore unseen mechanisms by which inducible sensor domains drive metabolic reprograming in the model Gram-positive bacterium B. subtilis.


    Organizational Affiliation

    Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HTH-type transcriptional regulator TnrAA [auth B]85Priestia megaterium WSH-002Mutation(s): 0 
Gene Names: tnrABMWSH_3277
UniProt
Find proteins for G2RUZ1 (Priestia megaterium (strain WSH-002))
Explore G2RUZ1 
Go to UniProtKB:  G2RUZ1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG2RUZ1
Protein Feature View
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(*CP*GP*TP*GP*TP*AP*AP*GP*GP*AP*AP*TP*TP*CP*TP*GP*AP*CP*AP*CP*G)-3')B [auth G]21synthetic construct
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.217 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.36α = 90
b = 100.21β = 90
c = 46.76γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACTdata extraction
ADSCdata collection

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2014-08-08 
  • Released Date: 2015-03-04 
  • Deposition Author(s): Schumacher, M.A.

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-04
    Type: Initial release
  • Version 1.1: 2015-03-11
    Changes: Derived calculations