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Yorodumi- PDB-7mft: Glutamate synthase, glutamate dehydrogenase counter-enzyme comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7mft | |||||||||
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Title | Glutamate synthase, glutamate dehydrogenase counter-enzyme complex (GudB6-GltA6-GltB6) | |||||||||
Components |
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Keywords | CYTOSOLIC PROTEIN / Counter-enzyme complex / glutamate synthase / glutamate dehydrogenae | |||||||||
Function / homology | Function and homology information glutamate synthase activity / oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor / glutamate biosynthetic process / glutamate dehydrogenase (NAD+) activity / glutamate catabolic process / 3 iron, 4 sulfur cluster binding / glutamine metabolic process / iron-sulfur cluster binding / nucleotide binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Bacillus subtilis subsp. subtilis NCIB 3610 = ATCC 6051 = DSM 10 (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Jayaraman, V. / Lee, D.J. / Elad, N. / Fraser, J.S. / Tawfik, D.S. | |||||||||
Funding support | Israel, United States, 2items
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Citation | Journal: Nat Chem Biol / Year: 2022 Title: A counter-enzyme complex regulates glutamate metabolism in Bacillus subtilis. Authors: Vijay Jayaraman / D John Lee / Nadav Elad / Shay Vimer / Michal Sharon / James S Fraser / Dan S Tawfik / Abstract: Multi-enzyme assemblies composed of metabolic enzymes catalyzing sequential reactions are being increasingly studied. Here, we report the discovery of a 1.6 megadalton multi-enzyme complex from ...Multi-enzyme assemblies composed of metabolic enzymes catalyzing sequential reactions are being increasingly studied. Here, we report the discovery of a 1.6 megadalton multi-enzyme complex from Bacillus subtilis composed of two enzymes catalyzing opposite ('counter-enzymes') rather than sequential reactions: glutamate synthase (GltAB) and glutamate dehydrogenase (GudB), which make and break glutamate, respectively. In vivo and in vitro studies show that the primary role of complex formation is to inhibit the activity of GudB. Using cryo-electron microscopy, we elucidated the structure of the complex and the molecular basis of inhibition of GudB by GltAB. The complex exhibits unusual oscillatory progress curves and is necessary for both planktonic growth, in glutamate-limiting conditions, and for biofilm growth, in glutamate-rich media. The regulation of a key metabolic enzyme by complexing with its counter enzyme may thus enable cell growth under fluctuating glutamate concentrations. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7mft.cif.gz | 786.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7mft.ent.gz | 646.4 KB | Display | PDB format |
PDBx/mmJSON format | 7mft.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7mft_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 7mft_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 7mft_validation.xml.gz | 77.3 KB | Display | |
Data in CIF | 7mft_validation.cif.gz | 116.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mf/7mft ftp://data.pdbj.org/pub/pdb/validation_reports/mf/7mft | HTTPS FTP |
-Related structure data
Related structure data | 23825MC 7mfmC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Symmetry | Point symmetry: (Schoenflies symbol: D3 (2x3 fold dihedral)) |
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 47100.715 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. subtilis NCIB 3610 = ATCC 6051 = DSM 10 (bacteria) Gene: gudB, B4122_2172, ETA10_11605, ETK61_12750, GII81_12565, SC09_Contig24orf00413 Production host: Bacillus subtilis (bacteria) / References: UniProt: A0A0C3GZC9 |
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-Glutamate synthase (NADPH) ... , 2 types, 2 molecules GI
#2: Protein | Mass: 169006.375 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. subtilis NCIB 3610 = ATCC 6051 = DSM 10 (bacteria) Gene: B4417_0011 / Production host: Bacillus subtilis (bacteria) / References: UniProt: A0A164XVV7 |
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#3: Protein | Mass: 58010.598 Da / Num. of mol.: 1 / Mutation: D78G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. subtilis NCIB 3610 = ATCC 6051 = DSM 10 (bacteria) Gene: B4417_0010 / Production host: Bacillus subtilis (bacteria) / References: UniProt: A0A164XVU4 |
-Non-polymers , 4 types, 5 molecules
#4: Chemical | ChemComp-FMN / |
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#5: Chemical | ChemComp-F3S / |
#6: Chemical | ChemComp-FAD / |
#7: Chemical |
-Details
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: GudB-GltA-GltB / Type: COMPLEX Details: Asymmetric unit (GudB-GltA-GltB) from a full GudB6-GltA6-GltB6 complex. Entity ID: #1-#3 / Source: RECOMBINANT |
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Molecular weight | Value: 1.62 MDa / Experimental value: YES |
Source (natural) | Organism: Bacillus subtilis (bacteria) |
Source (recombinant) | Organism: Bacillus subtilis (bacteria) |
Buffer solution | pH: 7.9 |
Specimen | Conc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 47.7 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.1_4122: / Classification: refinement | |||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||
Particle selection | Num. of particles selected: 60487 | |||||||||||||||||||||||||
3D reconstruction | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 11878 / Symmetry type: POINT | |||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL Details: Real-space refinement involved iterative rounds of ISOLDE, Coot and PHENIX refinement. 1OFD and 6S6T were used as templates for homology modeling in SWISS-MODEL. | |||||||||||||||||||||||||
Atomic model building | 3D fitting-ID: 1 / Source name: PDB / Type: experimental model
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Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 97.66 Å2 | |||||||||||||||||||||||||
Refine LS restraints |
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