7TEA

Crystal structure of S. aureus GlnR-DNA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Molecular dissection of the glutamine synthetase-GlnR nitrogen regulatory circuitry in Gram-positive bacteria.

Travis, B.A.Peck, J.V.Salinas, R.Dopkins, B.Lent, N.Nguyen, V.D.Borgnia, M.J.Brennan, R.G.Schumacher, M.A.

(2022) Nat Commun 13: 3793-3793

  • DOI: https://doi.org/10.1038/s41467-022-31573-0
  • Primary Citation of Related Structures:  
    7TDP, 7TDV, 7TEA, 7TEC, 7TEN, 7TF6, 7TF7, 7TF9, 7TFA, 7TFB, 7TFC, 7TFD, 7TFE

  • PubMed Abstract: 

    How bacteria sense and respond to nitrogen levels are central questions in microbial physiology. In Gram-positive bacteria, nitrogen homeostasis is controlled by an operon encoding glutamine synthetase (GS), a dodecameric machine that assimilates ammonium into glutamine, and the GlnR repressor. GlnR detects nitrogen excess indirectly by binding glutamine-feedback-inhibited-GS (FBI-GS), which activates its transcription-repression function. The molecular mechanisms behind this regulatory circuitry, however, are unknown. Here we describe biochemical and structural analyses of GS and FBI-GS-GlnR complexes from pathogenic and non-pathogenic Gram-positive bacteria. The structures show FBI-GS binds the GlnR C-terminal domain within its active-site cavity, juxtaposing two GlnR monomers to form a DNA-binding-competent GlnR dimer. The FBI-GS-GlnR interaction stabilizes the inactive GS conformation. Strikingly, this interaction also favors a remarkable dodecamer to tetradecamer transition in some GS, breaking the paradigm that all bacterial GS are dodecamers. These data thus unveil unique structural mechanisms of transcription and enzymatic regulation.


  • Organizational Affiliation

    Department of Biochemistry, 307 Research Dr., Box 3711, Duke University Medical Center, Durham, NC, 27710, USA.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamine synthetase repressorA [auth B],
B [auth E],
E [auth A],
F [auth C]
86Staphylococcus aureusMutation(s): 0 
Gene Names: 
UniProt
Find proteins for Q2FYY7 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2FYY7 
Go to UniProtKB:  Q2FYY7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2FYY7
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*CP*GP*TP*GP*TP*CP*AP*GP*AP*TP*AP*AP*TP*CP*TP*GP*AP*CP*AP*CP*G)-3')C [auth G],
G [auth D]
21Staphylococcus aureus
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(*CP*GP*TP*GP*TP*CP*AP*GP*AP*TP*TP*AP*TP*CP*TP*GP*AP*CP*AP*CP*G)-3')D [auth F],
H
21Staphylococcus aureus
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 
  • Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.502α = 90
b = 99.265β = 90
c = 238.922γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35-GM130290

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-29
    Type: Initial release
  • Version 1.1: 2022-08-10
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description