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Yorodumi- PDB-8p5w: Single particle cryo-EM structure of homohexameric 2-oxoglutarate... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8p5w | |||||||||
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Title | Single particle cryo-EM structure of homohexameric 2-oxoglutarate dehydrogenase OdhA from Corynebacterium glutamicum following reaction with the 2-oxoglutarate analogue succinyl phosphonate | |||||||||
Components | 2-oxoglutarate dehydrogenase E1/E2 component | |||||||||
Keywords | OXIDOREDUCTASE / 2-oxoglutarate dehydrogenase / ODH | |||||||||
Function / homology | Function and homology information oxoglutarate dehydrogenase (succinyl-transferring) / oxoglutarate dehydrogenase (succinyl-transferring) activity / dihydrolipoyllysine-residue succinyltransferase / dihydrolipoyllysine-residue succinyltransferase activity / oxoglutarate dehydrogenase complex / thiamine pyrophosphate binding / tricarboxylic acid cycle / magnesium ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Corynebacterium glutamicum ATCC 13032 (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.26 Å | |||||||||
Authors | Yang, L. / Mechaly, A.M. / Bellinzoni, M. | |||||||||
Funding support | France, 2items
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Citation | Journal: Nat Commun / Year: 2023 Title: High resolution cryo-EM and crystallographic snapshots of the actinobacterial two-in-one 2-oxoglutarate dehydrogenase. Authors: Lu Yang / Tristan Wagner / Ariel Mechaly / Alexandra Boyko / Eduardo M Bruch / Daniela Megrian / Francesca Gubellini / Pedro M Alzari / Marco Bellinzoni / Abstract: Actinobacteria possess unique ways to regulate the oxoglutarate metabolic node. Contrary to most organisms in which three enzymes compose the 2-oxoglutarate dehydrogenase complex (ODH), ...Actinobacteria possess unique ways to regulate the oxoglutarate metabolic node. Contrary to most organisms in which three enzymes compose the 2-oxoglutarate dehydrogenase complex (ODH), actinobacteria rely on a two-in-one protein (OdhA) in which both the oxidative decarboxylation and succinyl transferase steps are carried out by the same polypeptide. Here we describe high-resolution cryo-EM and crystallographic snapshots of representative enzymes from Mycobacterium smegmatis and Corynebacterium glutamicum, showing that OdhA is an 800-kDa homohexamer that assembles into a three-blade propeller shape. The obligate trimeric and dimeric states of the acyltransferase and dehydrogenase domains, respectively, are critical for maintaining the overall assembly, where both domains interact via subtle readjustments of their interfaces. Complexes obtained with substrate analogues, reaction products and allosteric regulators illustrate how these domains operate. Furthermore, we provide additional insights into the phosphorylation-dependent regulation of this enzymatic machinery by the signalling protein OdhI. #1: Journal: Biorxiv / Year: 2023 Title: High resolution cryo-EM and crystallographic snapshots of the large actinobacterial 2-oxoglutarate dehydrogenase: an all-in-one fusion with unique properties Authors: Yang, L. / Wagner, T. / Mechaly, A. / Boyko, A. / Bruch, E.M. / Megrian, D. / Gubellini, F. / Alzari, P.M. / Bellinzoni, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8p5w.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8p5w.ent.gz | 1 MB | Display | PDB format |
PDBx/mmJSON format | 8p5w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8p5w_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 8p5w_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 8p5w_validation.xml.gz | 163.4 KB | Display | |
Data in CIF | 8p5w_validation.cif.gz | 259.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p5/8p5w ftp://data.pdbj.org/pub/pdb/validation_reports/p5/8p5w | HTTPS FTP |
-Related structure data
Related structure data | 17455MC 8p5rC 8p5sC 8p5tC 8p5uC 8p5vC 8p5xC 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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-Components
#1: Protein | Mass: 134972.078 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corynebacterium glutamicum ATCC 13032 (bacteria) Gene: odhA, Cgl1129, cg1280 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q8NRC3, oxoglutarate dehydrogenase (succinyl-transferring), dihydrolipoyllysine-residue succinyltransferase #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-ACO / #4: Chemical | ChemComp-QSP / ( Has ligand of interest | Y | |
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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: Homohexameric 2-oxoglutarate dehydrogenase / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT | ||||||||||||
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Molecular weight | Value: 0.808 MDa / Experimental value: NO | ||||||||||||
Source (natural) | Organism: Corynebacterium glutamicum ATCC 13032 (bacteria) | ||||||||||||
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) | ||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||
Buffer component |
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Specimen | Conc.: 12 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: EMS Lacey Carbon | ||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-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 / Nominal magnification: 105000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 1.4 sec. / Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 16647 / Details: Each image was composed by 60 frames |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: D3 (2x3 fold dihedral) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.26 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 646352 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 8P5T Accession code: 8P5T / Source name: PDB / Type: experimental model | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Resolution: 2.26→2.26 Å / Cor.coef. Fo:Fc: 0.88 / SU B: 6.094 / SU ML: 0.129 / ESU R: 0.143 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Solvent model: PARAMETERS FOR MASK CACLULATION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.874 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Total: 52656 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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