7TEA | pdb_00007tea

Crystal structure of S. aureus GlnR-DNA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 
    0.264 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.213 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 
    0.216 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7TEA

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 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.

Macromolecule Content 

  • Total Structure Weight: 66.42 kDa 
  • Atom Count: 4,368 
  • Modeled Residue Count: 392 
  • Deposited Residue Count: 428 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 2

Macromolecules


Find similar proteins by:|  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
Expand
Reference Sequence
Find similar nucleic acids by:  Sequence
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
Expand
Reference Sequence
Find similar nucleic acids by:  Sequence
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 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.213 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 0.216 (Depositor) 
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

View Full Validation Report



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