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- EMDB-25863: S. aureus GS(12)-Q-GlnR peptide -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-25863
TitleS. aureus GS(12)-Q-GlnR peptide
Map dataSharpened (B factor 62A^2)
Sample
  • Complex: Dodecameric GS complex with glutamine and GlnR C-tail peptides
    • Protein or peptide: Glutamine synthetase
    • Protein or peptide: Peptide from Glutamine synthetase repressor
  • Ligand: MAGNESIUM ION
  • Ligand: GLUTAMINE
Keywordsglutamine synthetase repressor dodecamer / BIOSYNTHETIC PROTEIN / LIGASE
Function / homology
Function and homology information


glutamine synthetase / glutamine biosynthetic process / glutamine synthetase activity / DNA-binding transcription factor activity / DNA binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Glutamine synthetase type I / : / Glutamine synthetase (GS) beta-grasp domain profile. / Glutamine synthetase (GS) catalytic domain profile. / Glutamine synthetase, N-terminal conserved site / Glutamine synthetase signature 1. / Glutamine synthetase, beta-Grasp domain / MerR HTH family regulatory protein / MerR-type HTH domain profile. / helix_turn_helix, mercury resistance ...Glutamine synthetase type I / : / Glutamine synthetase (GS) beta-grasp domain profile. / Glutamine synthetase (GS) catalytic domain profile. / Glutamine synthetase, N-terminal conserved site / Glutamine synthetase signature 1. / Glutamine synthetase, beta-Grasp domain / MerR HTH family regulatory protein / MerR-type HTH domain profile. / helix_turn_helix, mercury resistance / Glutamine synthetase, glycine-rich site / Glutamine synthetase putative ATP-binding region signature. / MerR-type HTH domain / Glutamine synthetase, N-terminal domain / Glutamine synthetase, N-terminal domain superfamily / Glutamine synthetase, catalytic domain / Glutamine synthetase, catalytic domain / Glutamine synthetase, catalytic domain / Glutamine synthetase/guanido kinase, catalytic domain / Putative DNA-binding domain superfamily
Similarity search - Domain/homology
Glutamine synthetase / Glutamine synthetase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.15 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_25863.png

Downloads & links

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Map

FileDownload / File: emd_25863.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened (B factor 62A^2)
Voxel sizeX=Y=Z: 0.88 Å
Density
Contour LevelBy AUTHOR: 0.7
Minimum - Maximum-1.8618367 - 3.0327888
Average (Standard dev.)0.00042683075 (±0.1122966)
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: #1

Fileemd_25863_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Dodecameric GS complex with glutamine and GlnR C-tail peptides

EntireName: Dodecameric GS complex with glutamine and GlnR C-tail peptides
Components
  • Complex: Dodecameric GS complex with glutamine and GlnR C-tail peptides
    • Protein or peptide: Glutamine synthetase
    • Protein or peptide: Peptide from Glutamine synthetase repressor
  • Ligand: MAGNESIUM ION
  • Ligand: GLUTAMINE

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Supramolecule #1: Dodecameric GS complex with glutamine and GlnR C-tail peptides

SupramoleculeName: Dodecameric 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: 12 / Enantiomer: LEVO / EC number: glutamine synthetase
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 51.19684 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GSHMPKRTFT KEDIRKFAEE ENVRYLRLQF TDILGTIKNV EVPVSQLEKV LDNEMMFDGS SIEGFVRIEE SDMYLHPDLD TWVIFPWTA GQGKVARLIC DVYKTDGTPF EGDPRANLKR VLKEMEDLGF TDFNLGPEPE FFLFKLDEKG EPTLELNDDG G YFDLAPTD ...String:
GSHMPKRTFT KEDIRKFAEE ENVRYLRLQF TDILGTIKNV EVPVSQLEKV LDNEMMFDGS SIEGFVRIEE SDMYLHPDLD TWVIFPWTA GQGKVARLIC DVYKTDGTPF EGDPRANLKR VLKEMEDLGF TDFNLGPEPE FFLFKLDEKG EPTLELNDDG G YFDLAPTD LGENCRRDIV LELEDMGFDI EASHHEVAPG QHEIDFKYAD AVTACDNIQT FKLVVKTIAR KHNLHATFMP KP LFGVNGS GMHFNVSLFK GKENAFFDPN TEMGLTETAY QFTAGVLKNA RGFTAVCNPL VNSYKRLVPG YEAPCYIAWS GKN RSPLIR VPSSRGLSTR IEVRSVDPAA NPYMALAAIL EAGLDGIKNK LKVPEPVNQN IYEMNREERE AVGIQDLPST LYTA LKAMR ENEVIKKALG NHIYNQFINS KSIEWDYYRT QVSEWERDQY MKQY

UniProtKB: Glutamine synthetase

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Macromolecule #2: Peptide from Glutamine synthetase repressor

MacromoleculeName: Peptide from Glutamine synthetase repressor / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 1.289485 KDa
SequenceString:
PINRGDLSRF I

UniProtKB: Glutamine synthetase

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 24 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #4: GLUTAMINE

MacromoleculeName: GLUTAMINE / type: ligand / ID: 4 / Number of copies: 12 / Formula: GLN
Molecular weightTheoretical: 146.144 Da
Chemical component information

ChemComp-GLN:
GLUTAMINE / 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

Concentration0.75 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.5 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.5 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2)
Final reconstructionApplied symmetry - Point group: D6 (2x6 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.15 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2) / Number images used: 222918

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Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-7tf6:
S. aureus GS(12)-Q-GlnR peptide

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