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Yorodumi- PDB-8umc: Deinococcus aerius TR0125 C-glucosyl deglycosidase (CGD), cryo-EM -
+Open data
-Basic information
Entry | Database: PDB / ID: 8umc | ||||||||||||||||||
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Title | Deinococcus aerius TR0125 C-glucosyl deglycosidase (CGD), cryo-EM | ||||||||||||||||||
Components |
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Keywords | LYASE / bacterial C-glucosyl deglycosidase / C-C bond cleavage / C-glucosyl aromatic polyketides / C-glucosyl flavonoids / Deinococcus aerius / soil bacterium / N-terminal DUF6379 beta-sandwich domain / C-terminal TIM-barrel domain / alpha2beta2 heterotetramer | ||||||||||||||||||
Function / homology | Domain of unknown function DUF6379 / Domain of unknown function (DUF6379) / : / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily / : / Xylose isomerase-like TIM barrel domain-containing protein / DUF6379 domain-containing protein Function and homology information | ||||||||||||||||||
Biological species | Deinococcus aerius (bacteria) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å | ||||||||||||||||||
Authors | Furlanetto, V. / Kalyani, D.C. / Kostelac, A. / Haltrich, D. / Hallberg, B.M. / Divne, C. | ||||||||||||||||||
Funding support | Sweden, Austria, 5items
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Citation | Journal: J Mol Biol / Year: 2024 Title: Structural and Functional Characterization of a Gene Cluster Responsible for Deglycosylation of C-glucosyl Flavonoids and Xanthonoids by Deinococcus aerius. Authors: Valentina Furlanetto / Dayanand C Kalyani / Anja Kostelac / Jolanta Puc / Dietmar Haltrich / B Martin Hällberg / Christina Divne / Abstract: Plant C-glycosylated aromatic polyketides are important for plant and animal health. These are specialized metabolites that perform functions both within the plant, and in interaction with soil or ...Plant C-glycosylated aromatic polyketides are important for plant and animal health. These are specialized metabolites that perform functions both within the plant, and in interaction with soil or intestinal microbes. Despite the importance of these plant compounds, there is still limited knowledge of how they are metabolized. The Gram-positive aerobic soil bacterium Deinococcus aerius strain TR0125 and other Deinococcus species thrive in a wide range of harsh environments. In this work, we identified a C-glycoside deglycosylation gene cluster in the genome of D. aerius. The cluster includes three genes coding for a GMC-type oxidoreductase (DaCGO1) that oxidizes the glucosyl C3 position in aromatic C-glucosyl compounds, which in turn provides the substrate for the C-glycoside deglycosidase (DaCGD; composed of α+β subunits) that cleaves the glucosyl-aglycone C-C bond. Our results from size-exclusion chromatography, single particle cryo-electron microscopy and X-ray crystallography show that DaCGD is an αβ heterotetramer, which represents a novel oligomeric state among bacterial CGDs. Importantly, the high-resolution X-ray structure of DaCGD provides valuable insights into the activation of the catalytic hydroxide ion by Lys261. DaCGO1 is specific for the 6-C-glucosyl flavones isovitexin, isoorientin and the 2-C-glucosyl xanthonoid mangiferin, and the subsequent C-C-bond cleavage by DaCGD generated apigenin, luteolin and norathyriol, respectively. Of the substrates tested, isovitexin was the preferred substrate (DaCGO1, K 0.047 mM, k 51 min; DaCGO1/DaCGD, K 0.083 mM, k 0.42 min). | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8umc.cif.gz | 182.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8umc.ent.gz | 145 KB | Display | PDB format |
PDBx/mmJSON format | 8umc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8umc_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8umc_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8umc_validation.xml.gz | 39.6 KB | Display | |
Data in CIF | 8umc_validation.cif.gz | 58.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/um/8umc ftp://data.pdbj.org/pub/pdb/validation_reports/um/8umc | HTTPS FTP |
-Related structure data
Related structure data | 42375MC 8qvcC 8qvdC 8qveC 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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1 |
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-Components
#1: Protein | Mass: 40554.328 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Deinococcus aerius (bacteria) / Strain: TR0125 / Gene: DAERI_200053 / Plasmid: pNIC-CTHO / Production host: Escherichia coli B (bacteria) / Strain (production host): (DE3)-T1 / References: UniProt: A0A2I9DAN1 #2: Protein | Mass: 13755.647 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Deinococcus aerius (bacteria) / Strain: TR0125 / Gene: DAERI_200052 / Plasmid: 2A-T / Production host: Escherichia coli B (bacteria) / Strain (production host): (DE3)-T1 / References: UniProt: A0A2I9E2I0 #3: Chemical | 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: C-glucosyl deglycosidase, alpha subunit / Type: COMPLEX Details: The complex contains two alpha subunits and two beta subunits that form an alpha2beta2 heteroteramer Entity ID: #1-#2 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Deinococcus aerius (bacteria) / Strain: TR0125 |
Source (recombinant) | Organism: Escherichia coli B (bacteria) / Strain: (DE3)-T1 / Plasmid: pNIC-CTHO (alpha subunit), 2A-T (beta subunit) |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS Details: Data collected at the Karolinska Institutet 3D-EM facility |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 200 nm / Cs: 2.7 mm / C2 aperture diameter: 20 µm / Alignment procedure: ZEMLIN TABLEAU |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 1.5 sec. / Electron dose: 56 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2153 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 10 eV |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 335185 | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 101068 / Algorithm: BACK PROJECTION / Symmetry type: POINT |