7TFC

B. subtilis GS(14)-Q-GlnR peptide

  • Classification: BIOSYNTHETIC PROTEIN, LIGASE
  • Organism(s): Bacillus subtilis
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2022-01-06 Released: 2022-06-29 
  • Deposition Author(s): Travis, B.A., Peck, J., Schumacher, M.A.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.96 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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
A, B, C, F, G
A, B, C, F, G, H, I, N, O, P, Q, R, S, T
464Bacillus subtilisMutation(s): 0 
Gene Names: B4122_0040B4417_0281
EC: 6.3.1.2
UniProt
Find proteins for A0A085CCI2 (Bacillus subtilis)
Explore A0A085CCI2 
Go to UniProtKB:  A0A085CCI2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A085CCI2
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
GlnR C-tail peptide10Bacillus subtilisMutation(s): 0 
UniProt
Find proteins for P37582 (Bacillus subtilis (strain 168))
Explore P37582 
Go to UniProtKB:  P37582
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37582
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GLN
Query on GLN

Download Ideal Coordinates CCD File 
CB [auth O]
EA [auth A]
FB [auth P]
HA [auth B]
IB [auth Q]
CB [auth O],
EA [auth A],
FB [auth P],
HA [auth B],
IB [auth Q],
KA [auth C],
LB [auth R],
NA [auth F],
OB [auth S],
QA [auth G],
RB [auth T],
TA [auth H],
WA [auth I],
ZA [auth N]
GLUTAMINE
C5 H10 N2 O3
ZDXPYRJPNDTMRX-VKHMYHEASA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth O]
BB [auth O]
CA [auth A]
DA [auth A]
DB [auth P]
AB [auth O],
BB [auth O],
CA [auth A],
DA [auth A],
DB [auth P],
EB [auth P],
FA [auth B],
GA [auth B],
GB [auth Q],
HB [auth Q],
IA [auth C],
JA [auth C],
JB [auth R],
KB [auth R],
LA [auth F],
MA [auth F],
MB [auth S],
NB [auth S],
OA [auth G],
PA [auth G],
PB [auth T],
QB [auth T],
RA [auth H],
SA [auth H],
UA [auth I],
VA [auth I],
XA [auth N],
YA [auth N]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.96 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19
RECONSTRUCTIONcryoSPARC3.2

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
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesF31-AI150138
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United StatesZIC-ES103326

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: 2024-02-28
    Changes: Data collection