4R25

Structure of B. subtilis GlnK


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5193 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.0 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:  

  • 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 co ...

    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 maria.schumacher@duke.edu.,Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nitrogen regulatory PII-like protein
A
114Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: nrgB
Find proteins for Q07428 (Bacillus subtilis (strain 168))
Go to UniProtKB:  Q07428
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5193 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.213 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 66.600α = 90.00
b = 66.600β = 90.00
c = 189.300γ = 120.00
Software Package:
Software NamePurpose
ADSCdata collection
SCALAdata scaling
PHENIXrefinement
MOSFLMdata reduction
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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

Revision History 

  • Version 1.0: 2015-03-04
    Type: Initial release