+Open data
-Basic information
Entry | Database: PDB / ID: 7tfc | ||||||||||||
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Title | B. subtilis GS(14)-Q-GlnR peptide | ||||||||||||
Components |
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Keywords | BIOSYNTHETIC PROTEIN / LIGASE / glutamine synthetase repressor tetradecamer | ||||||||||||
Function / homology | Function and homology information glutamine synthetase / glutamine biosynthetic process / glutamine synthetase activity / DNA-binding transcription factor activity / DNA binding / ATP binding / identical protein binding / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Bacillus subtilis (bacteria) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.96 Å | ||||||||||||
Authors | Travis, B.A. / Peck, J. / Schumacher, M.A. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7tfc.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7tfc.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7tfc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tf/7tfc ftp://data.pdbj.org/pub/pdb/validation_reports/tf/7tfc | HTTPS FTP |
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-Related structure data
Related structure data | 25869MC 7tdpC 7tdvC 7teaC 7tecC 7tenC 7tf6C 7tf7C 7tf9C 7tfaC 7tfbC 7tfdC 7tfeC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 52509.449 Da / Num. of mol.: 14 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: B4122_0040, B4417_0281 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A085CCI2, glutamine synthetase #2: Protein/peptide | Mass: 1246.396 Da / Num. of mol.: 14 / Fragment: Residues 124-133 / Source method: obtained synthetically / Source: (synth.) Bacillus subtilis (bacteria) / References: UniProt: P37582 #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-GLN / Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Tetradecameric B. subtilis GS complex with glutamine and GlnR C-tail peptides Type: COMPLEX / Entity ID: #1-#2 / Source: MULTIPLE SOURCES |
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Molecular weight | Experimental value: NO |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2200 nm / Nominal defocus min: 400 nm |
Image recording | Electron dose: 43.74 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: D7 (2x7 fold dihedral) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 1.96 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1376404 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Space: REAL | ||||||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 75.17 Å2 | ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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