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- EMDB-48543: Electron-bifurcating Tungstopyranopterin-containing aldehyde oxid... -
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Open data
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Basic information
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Title | Electron-bifurcating Tungstopyranopterin-containing aldehyde oxidoreductase with NADH | ||||||||||||
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![]() | electron bifurcation / OXIDOREDUCTASE | ||||||||||||
Function / homology | ![]() oxidoreductase activity, acting on the aldehyde or oxo group of donors, iron-sulfur protein as acceptor / NADH dehydrogenase (ubiquinone) activity / 2 iron, 2 sulfur cluster binding / FMN binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / metal ion binding Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | ||||||||||||
![]() | Feng X / Li H | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: An electron-bifurcating "plug" to a protein nanowire in tungsten-dependent aldehyde detoxification. Authors: Xiang Feng / Gerrit J Schut / Saisuki Putumbaka / Huilin Li / Michael W W Adams / ![]() Abstract: Members of the tungsten-containing oxidoreductase (WOR) family, which contain a tungstopyranopterin (Tuco) cofactor, are typically either monomeric (WorL) or heterodimeric (WorLS). These enzymes ...Members of the tungsten-containing oxidoreductase (WOR) family, which contain a tungstopyranopterin (Tuco) cofactor, are typically either monomeric (WorL) or heterodimeric (WorLS). These enzymes oxidize aldehydes to the corresponding acids while reducing the redox protein ferredoxin. They have been structurally characterized mainly using WORs from hyperthermophilic archaea. The WORs of some bacteria contain three additional subunits of the BfuABC family and these chimeric WorABCSL enzymes catalyze an electron-bifurcating reaction in which aldehyde oxidation is coupled to the simultaneous reduction of ferredoxin and nicotinamide adenine dinucleotide. In human gut microbes, electron bifurcation by WorABSL is proposed to enable the detoxification of aldehydes generated from cooked foods and in the tungstocentric production of beneficial short chain fatty acids from lactate, potentially impacting health. Herein we present the high-resolution cryogenic electron microscopy (cryo-EM) structure of the WorABCSL purified from the bacterium The structure reveals a surprising 1:3 stoichiometry between WorABC and WorSL, with the WorSL units forming a nanowire-like architecture leading from three Tuco-containing catalytic sites in WorL via strings of multiple iron-sulfur clusters in WorS to a single bifurcating WorABC core. Our structure uncovers a distinct domain arrangement that links three Tuco-dependent aldehyde oxidation sites with the bifurcation process and potentially facilitates environmental aldehyde oxidation. | ||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 164.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 22.7 KB 22.7 KB | Display Display | ![]() |
Images | ![]() | 94.2 KB | ||
Filedesc metadata | ![]() | 7.7 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 525.1 KB | Display | ![]() |
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Full document | ![]() | 524.6 KB | Display | |
Data in XML | ![]() | 7.2 KB | Display | |
Data in CIF | ![]() | 8.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9mqxMC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.828 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
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Sample components
+Entire : electron-bifurcating tungstopyranopterin-containing aldehyde oxid...
+Supramolecule #1: electron-bifurcating tungstopyranopterin-containing aldehyde oxid...
+Macromolecule #1: NADH:ubiquinone oxidoreductase chain G-like protein
+Macromolecule #2: NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit
+Macromolecule #3: NADH:ubiquinone oxidoreductase 24 kD subunit
+Macromolecule #4: Aldehyde:ferredoxin oxidoreductase
+Macromolecule #5: Fe-S-cluster-containing hydrogenase subunit
+Macromolecule #6: IRON/SULFUR CLUSTER
+Macromolecule #7: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #8: ZINC ION
+Macromolecule #9: FLAVIN MONONUCLEOTIDE
+Macromolecule #10: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
+Macromolecule #11: TUNGSTOPTERIN COFACTOR
+Macromolecule #12: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 | |||||||||
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 59.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |