Crystal structure of the Listeria monocytogenes GS-Met-Sox-P- ADP complex to 3.5 Angstrom

Experimental Data Snapshot

  • Resolution: 3.50 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

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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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamine synthetase447Listeria monocytogenesMutation(s): 0 
Gene Names: glnABW273_06565CW834_10155E3W32_09805E5H26_02065FL871_07615GF092_00575GIG92_01785GIH49_01255HF764_002412
Find proteins for A0A5D5GA79 (Listeria monocytogenes)
Explore A0A5D5GA79 
Go to UniProtKB:  A0A5D5GA79
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A5D5GA79
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
AA [auth O]
CA [auth Q]
EA [auth S]
GA [auth U]
IA [auth W]
AA [auth O],
CA [auth Q],
EA [auth S],
GA [auth U],
IA [auth W],
M [auth A],
O [auth E],
Q [auth B],
S [auth D],
U [auth H],
W [auth J],
Y [auth M]
C10 H15 N5 O10 P2
P3S (Subject of Investigation/LOI)
Query on P3S

Download Ideal Coordinates CCD File 
BA [auth O]
DA [auth Q]
FA [auth S]
HA [auth U]
JA [auth W]
BA [auth O],
DA [auth Q],
FA [auth S],
HA [auth U],
JA [auth W],
N [auth A],
P [auth E],
R [auth B],
T [auth D],
V [auth H],
X [auth J],
Z [auth M]
C5 H13 N2 O6 P S
Experimental Data & Validation

Experimental Data

  • Resolution: 3.50 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.608α = 60.75
b = 137.613β = 87.16
c = 138.023γ = 68.4
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
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 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