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- EMDB-25869: B. subtilis GS(14)-Q-GlnR peptide -

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Basic information

Entry
Database: EMDB / ID: EMD-25869
TitleB. subtilis GS(14)-Q-GlnR peptide
Map dataSharpened (B factor 74.9 A^2)
Sample
  • Complex: Tetradecameric B. subtilis GS complex with glutamine and GlnR C-tail peptides
    • Protein or peptide: Glutamine synthetase
    • Protein or peptide: GlnR C-tail peptide
  • Ligand: MAGNESIUM ION
  • Ligand: GLUTAMINE
Keywordsglutamine synthetase repressor tetradecamer / BIOSYNTHETIC PROTEIN / LIGASE
Function / homology
Function and homology information


glutamine synthetase / glutamine biosynthetic process / glutamine synthetase activity / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA binding / ATP binding / metal ion binding / identical protein binding / cytoplasm
Similarity search - Function
Glutamine synthetase class-I, adenylation site / Glutamine synthetase class-I adenylation site. / MerR-type HTH domain signature. / Glutamine synthetase type I / : / MerR HTH family regulatory protein / helix_turn_helix, mercury resistance / MerR-type HTH domain profile. / MerR-type HTH domain / Glutamine synthetase, N-terminal conserved site ...Glutamine synthetase class-I, adenylation site / Glutamine synthetase class-I adenylation site. / MerR-type HTH domain signature. / Glutamine synthetase type I / : / MerR HTH family regulatory protein / helix_turn_helix, mercury resistance / MerR-type HTH domain profile. / MerR-type HTH domain / Glutamine synthetase, N-terminal conserved site / Glutamine synthetase signature 1. / Glutamine synthetase, beta-Grasp domain / Glutamine synthetase, glycine-rich site / Glutamine synthetase putative ATP-binding region signature. / Glutamine synthetase (GS) beta-grasp domain profile. / Glutamine synthetase, N-terminal domain superfamily / Glutamine synthetase, catalytic domain / Glutamine synthetase, N-terminal domain / Glutamine synthetase, catalytic domain / Glutamine synthetase (GS) catalytic domain profile. / Glutamine synthetase, catalytic domain / Glutamine synthetase/guanido kinase, catalytic domain / Putative DNA-binding domain superfamily
Similarity search - Domain/homology
Glutamine synthetase / HTH-type transcriptional regulator GlnR
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.96 Å
AuthorsTravis BA / Peck J
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM130290 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)F31-AI150138 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ZIC-ES103326 United States
CitationJournal: Nat Commun / Year: 2022
Title: Molecular dissection of the glutamine synthetase-GlnR nitrogen regulatory circuitry in Gram-positive bacteria.
Authors: Brady A Travis / Jared V Peck / Raul Salinas / Brandon Dopkins / Nicholas Lent / Viet D Nguyen / Mario J Borgnia / Richard G Brennan / Maria A Schumacher /
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 ...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.
History
DepositionJan 6, 2022-
Header (metadata) releaseJun 29, 2022-
Map releaseJun 29, 2022-
UpdateFeb 28, 2024-
Current statusFeb 28, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_25869.png

Downloads & links

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Map

FileDownload / File: emd_25869.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened (B factor 74.9 A^2)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 400 pix.
= 352. Å		0.88 Å/pix.
x 400 pix.
= 352. Å		0.88 Å/pix.
x 400 pix.
= 352. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.88 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.7
Minimum - Maximum-3.1154788 - 5.137776
Average (Standard dev.)-0.00020775707 (±0.12016226)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 352.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened

Fileemd_25869_additional_1.map
AnnotationUnsharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Tetradecameric B. subtilis GS complex with glutamine and GlnR C-t...

EntireName: Tetradecameric B. subtilis GS complex with glutamine and GlnR C-tail peptides
Components
  • Complex: Tetradecameric B. subtilis GS complex with glutamine and GlnR C-tail peptides
    • Protein or peptide: Glutamine synthetase
    • Protein or peptide: GlnR C-tail peptide
  • Ligand: MAGNESIUM ION
  • Ligand: GLUTAMINE

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Supramolecule #1: Tetradecameric B. subtilis GS complex with glutamine and GlnR C-t...

SupramoleculeName: Tetradecameric B. subtilis GS complex with glutamine and GlnR C-tail peptides
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2

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Macromolecule #1: Glutamine synthetase

MacromoleculeName: Glutamine synthetase / type: protein_or_peptide / ID: 1 / Number of copies: 14 / Enantiomer: LEVO / EC number: glutamine synthetase
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 52.509449 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SSGLVPRGSH MAKYTREDIE KLVKEENVKY IRLQFTDILG TIKNVEIPVS QLGKALDNKV MFDGSSIEGF VRIEESDMY LYPDLNTFVI FPWTAEKGKV ARFICDIYNP DGTPFEGDPR NNLKRILKEM EDLGFSDFNL GPEPEFFLFK L DEKGEPTL ...String:
MGSSHHHHHH SSGLVPRGSH MAKYTREDIE KLVKEENVKY IRLQFTDILG TIKNVEIPVS QLGKALDNKV MFDGSSIEGF VRIEESDMY LYPDLNTFVI FPWTAEKGKV ARFICDIYNP DGTPFEGDPR NNLKRILKEM EDLGFSDFNL GPEPEFFLFK L DEKGEPTL ELNDKGGYFD LAPTDLGENC RRDIVLELEE MGFEIEASHH EVAPGQHEID FKYAGAVRSC DDIQTFKLVV KT IARKHGL HATFMPKPLF GVNGSGMHCN LSLFKNGVNA FFDENADLQL SETAKHFIAG IVKHATSFTA VTNPTVNSYK RLV PGYEAP CYVAWSAQNR SPLIRIPASR GISTRVEVRS VDPAANPYLA LSVLLAAGLD GIKNKLEAPA PIDRNIYVMS KEER MENGI VDLPATLAEA LEEFKSNEVM VKALGEHLFE HFIEAKEIEW DMFRTQVHPW EREQYMSQY

UniProtKB: Glutamine synthetase

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Macromolecule #2: GlnR C-tail peptide

MacromoleculeName: GlnR C-tail peptide / type: protein_or_peptide / ID: 2 / Number of copies: 14 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 1.246396 KDa
SequenceString:
TFRQGDMSRF

UniProtKB: HTH-type transcriptional regulator GlnR

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 28 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #4: GLUTAMINE

MacromoleculeName: GLUTAMINE / type: ligand / ID: 4 / Number of copies: 14 / Formula: GLN
Molecular weightTheoretical: 146.144 Da
Chemical component information

ChemComp-GLN:
GLUTAMINE

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.0 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 43.74 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.4 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: D7 (2x7 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 1.96 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2) / Number images used: 1376404
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2)

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Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-7tfc:
B. subtilis GS(14)-Q-GlnR peptide

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