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- PDB-8p5s: Crystal structure of the homohexameric 2-oxoglutarate dehydrogena... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8p5s | |||||||||
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Title | Crystal structure of the homohexameric 2-oxoglutarate dehydrogenase OdhA from Corynebacterium glutamicum | |||||||||
![]() | 2-oxoglutarate dehydrogenase E1/E2 component | |||||||||
![]() | OXIDOREDUCTASE / 2-oxoglutarate dehydrogenase / ODH | |||||||||
Function / homology | ![]() 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 | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Yang, L. / Boyko, A. / Bellinzoni, M. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 452.7 KB | Display | ![]() |
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PDB format | ![]() | 363.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 41 KB | Display | |
Data in CIF | ![]() | 60.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8p5rSC ![]() 8p5tC ![]() 8p5uC ![]() 8p5vC ![]() 8p5wC ![]() 8p5xC S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 124510.570 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: odhA, Cgl1129, cg1280 / Production host: ![]() ![]() References: UniProt: Q8NRC3, oxoglutarate dehydrogenase (succinyl-transferring), dihydrolipoyllysine-residue succinyltransferase |
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-Non-polymers , 6 types, 402 molecules ![](data/chem/img/EPE.gif)
![](data/chem/img/COA.gif)
![](data/chem/img/ACO.gif)
![](data/chem/img/TPP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/COA.gif)
![](data/chem/img/ACO.gif)
![](data/chem/img/TPP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-EPE / |
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#3: Chemical | ChemComp-COA / |
#4: Chemical | ChemComp-ACO / |
#5: Chemical | ChemComp-TPP / |
#6: Chemical | ChemComp-MG / |
#7: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.58 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.1 M Hepes-NaOH pH 7.5, 5% (w/v) PEG 4000, 30% (v/v) methylpentanediol (MPD) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Aug 26, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 2.46→100.52 Å / Num. obs: 38261 / % possible obs: 94.4 % / Redundancy: 10.4 % / CC1/2: 0.998 / Rpim(I) all: 0.047 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 2.46→2.7 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1913 / CC1/2: 0.658 / Rpim(I) all: 0.466 / % possible all: 63.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 8P5R Resolution: 2.459→27.53 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.905 / SU R Cruickshank DPI: 0.987 / Cross valid method: THROUGHOUT / SU R Blow DPI: 1.167 / SU Rfree Blow DPI: 0.323 / SU Rfree Cruickshank DPI: 0.325
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Displacement parameters | Biso mean: 59.01 Å2
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Refine analyze | Luzzati coordinate error obs: 0.34 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.459→27.53 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.46→2.6 Å
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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