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Yorodumi- EMDB-42375: Deinococcus aerius TR0125 C-glucosyl deglycosidase (CGD), cryo-EM -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-42375 | ||||||||||||||||||
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Title | Deinococcus aerius TR0125 C-glucosyl deglycosidase (CGD), cryo-EM | ||||||||||||||||||
Map data | Refinement map. | ||||||||||||||||||
Sample |
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Keywords | 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 / LYASE | ||||||||||||||||||
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 | single particle reconstruction / cryo EM / Resolution: 2.5 Å | ||||||||||||||||||
Authors | Furlanetto V / Kalyani DC / Kostelac A / Haltrich D / Hallberg BM / Divne C | ||||||||||||||||||
Funding support | Sweden, Austria, 5 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_42375.map.gz | 55.2 MB | EMDB map data format | |
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Header (meta data) | emd-42375-v30.xml emd-42375.xml | 19.3 KB 19.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_42375_fsc.xml | 8.4 KB | Display | FSC data file |
Images | emd_42375.png | 96.2 KB | ||
Masks | emd_42375_msk_1.map | 64 MB | Mask map | |
Filedesc metadata | emd-42375.cif.gz | 6.4 KB | ||
Others | emd_42375_half_map_1.map.gz emd_42375_half_map_2.map.gz | 59.3 MB 59.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-42375 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-42375 | HTTPS FTP |
-Validation report
Summary document | emd_42375_validation.pdf.gz | 760.1 KB | Display | EMDB validaton report |
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Full document | emd_42375_full_validation.pdf.gz | 759.7 KB | Display | |
Data in XML | emd_42375_validation.xml.gz | 16 KB | Display | |
Data in CIF | emd_42375_validation.cif.gz | 21.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42375 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42375 | HTTPS FTP |
-Related structure data
Related structure data | 8umcMC 8qvcC 8qvdC 8qveC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_42375.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Refinement map. | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.01 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_42375_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: halfmap B
File | emd_42375_half_map_1.map | ||||||||||||
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Annotation | halfmap B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: halfmap A
File | emd_42375_half_map_2.map | ||||||||||||
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Annotation | halfmap A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : C-glucosyl deglycosidase, alpha subunit
Entire | Name: C-glucosyl deglycosidase, alpha subunit |
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Components |
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-Supramolecule #1: C-glucosyl deglycosidase, alpha subunit
Supramolecule | Name: C-glucosyl deglycosidase, alpha subunit / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 Details: The complex contains two alpha subunits and two beta subunits that form an alpha2beta2 heteroteramer |
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Source (natural) | Organism: Deinococcus aerius (bacteria) / Strain: TR0125 |
-Macromolecule #1: Xylose isomerase-like TIM barrel domain-containing protein
Macromolecule | Name: Xylose isomerase-like TIM barrel domain-containing protein type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Deinococcus aerius (bacteria) / Strain: TR0125 |
Molecular weight | Theoretical: 40.554328 KDa |
Recombinant expression | Organism: Escherichia coli B (bacteria) |
Sequence | String: MTQPQIKRGV SLYSFQEEFF LRKMTLEDCV AACASMGAYG IESLAEQMMP GFPNLDDAFY DGWHAMMAKY GTVSVCHDMF LDTKKFRGR LMTLDEQVES FVRDIRHASR LGCTVIRVLN FVSPELMEKV LPHAEQSNMR LGLEIHAPMH FEHPWVLRHI E FMDRLGSP ...String: MTQPQIKRGV SLYSFQEEFF LRKMTLEDCV AACASMGAYG IESLAEQMMP GFPNLDDAFY DGWHAMMAKY GTVSVCHDMF LDTKKFRGR LMTLDEQVES FVRDIRHASR LGCTVIRVLN FVSPELMEKV LPHAEQSNMR LGLEIHAPMH FEHPWVLRHI E FMDRLGSP LLGFIPDMGI FTKHFPPVMA ERLIRQGATP HIIEYIREQY DRRVLAEYVV GDVRNMGGNP VDIRAAEMLR HN NWSNPRR LLEHMDRIFH VHAKFYEMDE QDRETSLGYE EVIPVLKEGG YSGYLASEYE GNRHIQDAFE VDSVEQVRRH QRM LARLIG EREVAHVAEN LYFQSHHHHH H UniProtKB: Xylose isomerase-like TIM barrel domain-containing protein |
-Macromolecule #2: DUF6379 domain-containing protein
Macromolecule | Name: DUF6379 domain-containing protein / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Deinococcus aerius (bacteria) / Strain: TR0125 |
Molecular weight | Theoretical: 13.755647 KDa |
Recombinant expression | Organism: Escherichia coli B (bacteria) |
Sequence | String: MFDKYIVVED SLKRVPGGVQ FGVRLPYYRG LGLSMVETMD VTVDGERVPE ENLTVTLGDR TVPFARRDDE TDTIWNFGEI ATVTARLPH ELGPGEHQVG VNFGLRISYF PVPMVGQDAK TLKL UniProtKB: DUF6379 domain-containing protein |
-Macromolecule #3: MANGANESE (II) ION
Macromolecule | Name: MANGANESE (II) ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: MN |
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Molecular weight | Theoretical: 54.938 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: UltrAuFoil / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 10 eV |
Details | Data collected at the Karolinska Institutet 3D-EM facility |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 2153 / Average exposure time: 1.5 sec. / Average electron dose: 56.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 20.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.2 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |