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Yorodumi- PDB-7tdv: Crystal structure of S. aureus glutamine synthetase in Met-Sox-P/... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7tdv | ||||||
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Title | Crystal structure of S. aureus glutamine synthetase in Met-Sox-P/ADP transition state complex | ||||||
Components | Glutamine synthetase | ||||||
Keywords | LIGASE / Glutamine synthetase / glutamate-ammonium ligase / GlnR / S. aureus / femC | ||||||
Function / homology | Function and homology information glutamine synthetase / glutamine biosynthetic process / glutamine synthetase activity / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.92 Å | ||||||
Authors | Schumacher, M.A. | ||||||
Funding support | United States, 1items
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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 | 7tdv.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7tdv.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7tdv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/td/7tdv ftp://data.pdbj.org/pub/pdb/validation_reports/td/7tdv | HTTPS FTP |
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-Related structure data
Related structure data | 7tdpC 7teaC 7tecC 7tenC 7tf6C 7tf7C 7tf9C 7tfaC 7tfbC 7tfcC 7tfdC 7tfeC 4lniS S: Starting model for refinement 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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Unit cell |
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-Components
-Protein , 1 types, 6 molecules ACDEBH
#1: Protein | Mass: 51224.895 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) Gene: glnA, BSG37_06900, FAF32_003410, G6X35_05920, G6X37_15495, G6Y24_07770, SAMEA103891454_00902 Production host: Escherichia coli (E. coli) / References: UniProt: E3VXC2, glutamine synthetase |
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-Non-polymers , 5 types, 340 molecules
#2: Chemical | ChemComp-ADP / #3: Chemical | ChemComp-P3S / #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-SO4 / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.73 % |
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Crystal grow | Temperature: 273 K / Method: vapor diffusion, hanging drop Details: 28% Peg 400, 0.2 M calcium chloride, 0.1 M HEPES 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.09 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 13, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.09 Å / Relative weight: 1 |
Reflection | Resolution: 2.92→48.89 Å / Num. obs: 79309 / % possible obs: 99.9 % / Redundancy: 28 % / CC1/2: 0.999 / Rpim(I) all: 0.049 / Rsym value: 0.165 / Net I/σ(I): 19.1 |
Reflection shell | Resolution: 2.92→3.02 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 7783 / CC1/2: 0.744 / Rpim(I) all: 0.517 / Rsym value: 1.78 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4LNI Resolution: 2.92→48.89 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.58 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 190.94 Å2 / Biso mean: 69.5289 Å2 / Biso min: 30 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.92→48.89 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Origin x: -59.8408 Å / Origin y: 69.0059 Å / Origin z: 16.0161 Å
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Refinement TLS group |
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