7TFB

P. polymyxa GS(14)-Q-GlnR peptide

  • Classification: BIOSYNTHETIC PROTEIN, LIGASE
  • Organism(s): Paenibacillus polymyxa
  • 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: 2.28 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:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GlnR C-tail peptide
A,
AA [auth a],
C,
E,
G,
H,
I,
M,
O,
P,
Q,
R,
W,
X
10Paenibacillus polymyxaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamine synthetase
B,
BA [auth b],
D,
F,
J,
K,
L,
N,
S,
T,
U,
V,
Y,
Z
462Paenibacillus polymyxaMutation(s): 0 
Gene Names: glnA2LK13_01575NCTC10343_02989
EC: 6.3.1.2
UniProt
Find proteins for A0A0F0G8G2 (Paenibacillus polymyxa)
Explore A0A0F0G8G2 
Go to UniProtKB:  A0A0F0G8G2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0F0G8G2
Sequence Annotations
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  • 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 T]
EA [auth B]
FB [auth U]
HA [auth D]
IB [auth V]
CB [auth T],
EA [auth B],
FB [auth U],
HA [auth D],
IB [auth V],
KA [auth F],
LB [auth Y],
NA [auth J],
OB [auth Z],
QA [auth K],
RB [auth b],
TA [auth L],
WA [auth N],
ZA [auth S]
GLUTAMINE
C5 H10 N2 O3
ZDXPYRJPNDTMRX-VKHMYHEASA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth T]
BB [auth T]
CA [auth B]
DA [auth B]
DB [auth U]
AB [auth T],
BB [auth T],
CA [auth B],
DA [auth B],
DB [auth U],
EB [auth U],
FA [auth D],
GA [auth D],
GB [auth V],
HB [auth V],
IA [auth F],
JA [auth F],
JB [auth Y],
KB [auth Y],
LA [auth J],
MA [auth J],
MB [auth Z],
NB [auth Z],
OA [auth K],
PA [auth K],
PB [auth b],
QB [auth b],
RA [auth L],
SA [auth L],
UA [auth N],
VA [auth N],
XA [auth S],
YA [auth S]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.28 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