+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34443 | |||||||||
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Title | cryo-EM structure of a bacterial dioxygenase | |||||||||
Map data | Cryo-EM structure of a bacterial dioxygenase | |||||||||
Sample |
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Keywords | heterohexamer / dioxygenase / FLAVOPROTEIN | |||||||||
Function / homology | Function and homology information 3-phenylpropionate catabolic process / dioxygenase activity / 2 iron, 2 sulfur cluster binding / oxidoreductase activity / iron ion binding Similarity search - Function | |||||||||
Biological species | Variovorax paradoxus (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.59 Å | |||||||||
Authors | Yu G / Li Z / Zhang H | |||||||||
Funding support | China, 2 items
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Citation | Journal: PLoS Biol / Year: 2023 Title: Structural and biochemical characterization of the key components of an auxin degradation operon from the rhizosphere bacterium Variovorax. Authors: Yongjian Ma / Xuzichao Li / Feng Wang / Lingling Zhang / Shengmin Zhou / Xing Che / Dehao Yu / Xiang Liu / Zhuang Li / Huabing Sun / Guimei Yu / Heng Zhang / Abstract: Plant-associated bacteria play important regulatory roles in modulating plant hormone auxin levels, affecting the growth and yields of crops. A conserved auxin degradation (iad) operon was recently ...Plant-associated bacteria play important regulatory roles in modulating plant hormone auxin levels, affecting the growth and yields of crops. A conserved auxin degradation (iad) operon was recently identified in the Variovorax genomes, which is responsible for root growth inhibition (RGI) reversion, promoting rhizosphere colonization and root growth. However, the molecular mechanism underlying auxin degradation by Variovorax remains unclear. Here, we systematically screened Variovorax iad operon products and identified 2 proteins, IadK2 and IadD, that directly associate with auxin indole-3-acetic acid (IAA). Further biochemical and structural studies revealed that IadK2 is a highly IAA-specific ATP-binding cassette (ABC) transporter solute-binding protein (SBP), likely involved in IAA uptake. IadD interacts with IadE to form a functional Rieske non-heme dioxygenase, which works in concert with a FMN-type reductase encoded by gene iadC to transform IAA into the biologically inactive 2-oxindole-3-acetic acid (oxIAA), representing a new bacterial pathway for IAA inactivation/degradation. Importantly, incorporation of a minimum set of iadC/D/E genes could enable IAA transformation by Escherichia coli, suggesting a promising strategy for repurposing the iad operon for IAA regulation. Together, our study identifies the key components and underlying mechanisms involved in IAA transformation by Variovorax and brings new insights into the bacterial turnover of plant hormones, which would provide the basis for potential applications in rhizosphere optimization and ecological agriculture. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34443.map.gz | 36.3 MB | EMDB map data format | |
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Header (meta data) | emd-34443-v30.xml emd-34443.xml | 16.5 KB 16.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_34443_fsc.xml | 7.2 KB | Display | FSC data file |
Images | emd_34443.png | 103.8 KB | ||
Filedesc metadata | emd-34443.cif.gz | 5.8 KB | ||
Others | emd_34443_half_map_1.map.gz emd_34443_half_map_2.map.gz | 37.7 MB 37.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34443 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34443 | HTTPS FTP |
-Validation report
Summary document | emd_34443_validation.pdf.gz | 852.5 KB | Display | EMDB validaton report |
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Full document | emd_34443_full_validation.pdf.gz | 852.1 KB | Display | |
Data in XML | emd_34443_validation.xml.gz | 15.1 KB | Display | |
Data in CIF | emd_34443_validation.cif.gz | 19.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34443 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34443 | HTTPS FTP |
-Related structure data
Related structure data | 8h2tMC 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_34443.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM structure of a bacterial dioxygenase | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.85 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half Map 1
File | emd_34443_half_map_1.map | ||||||||||||
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Annotation | Half Map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half Map 2
File | emd_34443_half_map_2.map | ||||||||||||
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Annotation | Half Map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : enzyme complex
Entire | Name: enzyme complex |
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Components |
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-Supramolecule #1: enzyme complex
Supramolecule | Name: enzyme complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Variovorax paradoxus (bacteria) |
-Macromolecule #1: Rieske (2Fe-2S) domain protein
Macromolecule | Name: Rieske (2Fe-2S) domain protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Variovorax paradoxus (bacteria) / Strain: S110 |
Molecular weight | Theoretical: 49.656898 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MTSYRDNPDA IRALVQDDRV HRDLYTSQEL FELEQEHFFA NTWNYVGHES QLPKPGDWIS NEIAGRPLIV ARHSDGSVRA MMNRCAHKG SRLVNGPCGN TGKFFRCPYH AWTFKTDGSL LAIPLKTGYE NTALHECESA KGLTTLRYVR SHRGFIFVKI S DAGPDFDD ...String: MTSYRDNPDA IRALVQDDRV HRDLYTSQEL FELEQEHFFA NTWNYVGHES QLPKPGDWIS NEIAGRPLIV ARHSDGSVRA MMNRCAHKG SRLVNGPCGN TGKFFRCPYH AWTFKTDGSL LAIPLKTGYE NTALHECESA KGLTTLRYVR SHRGFIFVKI S DAGPDFDD YFGDSLSSID NMADRSPEGE LEIAGGCLRF MHQCNWKMFV ENLNDTMHPM VAHESSAGTA KRMWADKPED EP KPMAVEQ FAPFMSDYKF FEDMGIRTYD NGHSFTGVHF SIHSKYKAIP AYDDAMKARY GEAKTAQILG MARHNTVYYP NLT IKGAIQ AIRVVKPISA DRTLIESWTF RLKGAPPELL QRTTMYNRLI NSPFSVVGHD DLQAYRGMQA GLHASGNEWV SLHR NYDPS ELKGGEITTG GTNELPMRNQ YRAWVQRMTE TM UniProtKB: Rieske (2Fe-2S) domain protein |
-Macromolecule #2: Aromatic-ring-hydroxylating dioxygenase beta subunit
Macromolecule | Name: Aromatic-ring-hydroxylating dioxygenase beta subunit / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Variovorax paradoxus (bacteria) |
Molecular weight | Theoretical: 18.952352 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MAGTEVTRQD LIDFVVNEAH LLDTRRYEEW NALFTDDAFY WVPLVPDQED GLNHTSHLYE DKLLRELRIE RLKSPRAFSQ QPPSRCHHL LQVPVVEQFD AEGNRFVLRT GFHYTESQGD ELQFYVGTFF HHLTVRDGAL RMTLKRVNLL NCDAALPAVQ L FI UniProtKB: Aromatic-ring-hydroxylating dioxygenase beta subunit |
-Macromolecule #3: FE2/S2 (INORGANIC) CLUSTER
Macromolecule | Name: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 3 / Number of copies: 3 / Formula: FES |
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Molecular weight | Theoretical: 175.82 Da |
Chemical component information | ChemComp-FES: |
-Macromolecule #4: 1H-INDOL-3-YLACETIC ACID
Macromolecule | Name: 1H-INDOL-3-YLACETIC ACID / type: ligand / ID: 4 / Number of copies: 3 / Formula: IAC |
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Molecular weight | Theoretical: 175.184 Da |
Chemical component information | ChemComp-IAC: |
-Macromolecule #5: FE (III) ION
Macromolecule | Name: FE (III) ION / type: ligand / ID: 5 / Number of copies: 3 / Formula: FE |
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Molecular weight | Theoretical: 55.845 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.6 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
Details | No further treatment. |
-Electron microscopy
Microscope | JEOL CRYO ARM 300 |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm |