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Yorodumi- EMDB-27989: Octameric prenyltransferase domain of fusicoccadiene Synthase wit... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27989 | |||||||||
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Title | Octameric prenyltransferase domain of fusicoccadiene Synthase with C2 symmetry sans transiently associating cyclase domains | |||||||||
Map data | Structure of the octameric C-terminal prenyltransferase domain of fusicoccadiene synthase from Phomopsis amygdali (PaFS) at 3.73-angstrom resolution | |||||||||
Sample |
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Keywords | Terpene synthase / Prenyltransferase / TRANSFERASE | |||||||||
Function / homology | Function and homology information fusicocca-2,10(14)-diene synthase / alcohol biosynthetic process / mycotoxin biosynthetic process / geranylgeranyl diphosphate synthase / ketone biosynthetic process / farnesyltranstransferase activity / isoprenoid biosynthetic process / lyase activity / metal ion binding Similarity search - Function | |||||||||
Biological species | Diaporthe amygdali (fungus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.73 Å | |||||||||
Authors | Faylo JL / van Eeuwen T / Christianson DW | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Biochemistry / Year: 2022 Title: Transient Prenyltransferase-Cyclase Association in Fusicoccadiene Synthase, an Assembly-Line Terpene Synthase. Authors: Jacque L Faylo / Trevor van Eeuwen / Kushol Gupta / Kenji Murakami / David W Christianson / Abstract: Fusicoccadiene synthase from the fungus (PaFS) is an assembly-line terpene synthase that catalyzes the first two steps in the biosynthesis of Fusiccocin A, a diterpene glycoside. The C-terminal ...Fusicoccadiene synthase from the fungus (PaFS) is an assembly-line terpene synthase that catalyzes the first two steps in the biosynthesis of Fusiccocin A, a diterpene glycoside. The C-terminal prenyltransferase domain of PaFS catalyzes the condensation of one molecule of C dimethylallyl diphosphate and three molecules of C isopentenyl diphosphate to form C geranylgeranyl diphosphate, which then transits to the cyclase domain for cyclization to form fusicoccadiene. Previous structural studies of PaFS using electron microscopy (EM) revealed a central octameric prenyltransferase core with eight cyclase domains tethered in random distal positions through flexible 70-residue linkers. However, proximal prenyltransferase-cyclase configurations could be captured by covalent cross-linking and observed by cryo-EM and mass spectrometry. Here, we use cryo-EM to show that proximally configured prenyltransferase-cyclase complexes are observable even in the absence of covalent cross-linking; moreover, such complexes can involve multiple cyclase domains. A conserved basic patch on the prenyltransferase domain comprises the primary touchpoint with the cyclase domain. These results support a model for transient prenyltransferase-cyclase association in which the cyclase domains of PaFS are in facile equilibrium between proximal associated and random distal positions relative to the central prenyltransferase octamer. The results of biophysical measurements using small-angle X-ray scattering, analytical ultracentrifugation, dynamic light scattering, and size-exclusion chromatography in-line with multi-angle light scattering are consistent with this model. This model accordingly provides a framework for understanding substrate transit between the prenyltransferase and cyclase domains as well as the cooperativity observed for geranylgeranyl diphosphate cyclization. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_27989.map.gz | 189.8 MB | EMDB map data format | |
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Header (meta data) | emd-27989-v30.xml emd-27989.xml | 16.8 KB 16.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_27989_fsc.xml | 12.8 KB | Display | FSC data file |
Images | emd_27989.png | 204.8 KB | ||
Masks | emd_27989_msk_1.map | 216 MB | Mask map | |
Filedesc metadata | emd-27989.cif.gz | 5.8 KB | ||
Others | emd_27989_additional_1.map.gz emd_27989_half_map_1.map.gz emd_27989_half_map_2.map.gz | 106.4 MB 200.4 MB 200.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27989 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27989 | HTTPS FTP |
-Validation report
Summary document | emd_27989_validation.pdf.gz | 822.6 KB | Display | EMDB validaton report |
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Full document | emd_27989_full_validation.pdf.gz | 822.2 KB | Display | |
Data in XML | emd_27989_validation.xml.gz | 21.6 KB | Display | |
Data in CIF | emd_27989_validation.cif.gz | 28.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27989 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27989 | HTTPS FTP |
-Related structure data
Related structure data | 8eaxMC 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_27989.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Structure of the octameric C-terminal prenyltransferase domain of fusicoccadiene synthase from Phomopsis amygdali (PaFS) at 3.73-angstrom resolution | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_27989_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Unsharpened map generated in non-uniform refinement of the...
File | emd_27989_additional_1.map | ||||||||||||
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Annotation | Unsharpened map generated in non-uniform refinement of the PaFS prenyltransferase octamer | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-map 1 of the octameric C-terminal prenyltransferase domain...
File | emd_27989_half_map_1.map | ||||||||||||
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Annotation | Half-map 1 of the octameric C-terminal prenyltransferase domain of PaFS at 3.73-angstrom resolution | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-map 2 of the octameric C-terminal prenyltransferase domain...
File | emd_27989_half_map_2.map | ||||||||||||
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Annotation | Half-map 2 of the octameric C-terminal prenyltransferase domain of PaFS at 3.73-angstrom resolution | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Octamer of the prenylstransferase domain of fusicoccadiene syntha...
Entire | Name: Octamer of the prenylstransferase domain of fusicoccadiene synthase from Phomopsis amygdali (PaFS) |
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Components |
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-Supramolecule #1: Octamer of the prenylstransferase domain of fusicoccadiene syntha...
Supramolecule | Name: Octamer of the prenylstransferase domain of fusicoccadiene synthase from Phomopsis amygdali (PaFS) type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Diaporthe amygdali (fungus) |
Molecular weight | Theoretical: 392 KDa |
-Macromolecule #1: Fusicoccadiene synthase
Macromolecule | Name: Fusicoccadiene synthase / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO / EC number: fusicocca-2,10(14)-diene synthase |
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Source (natural) | Organism: Diaporthe amygdali (fungus) |
Molecular weight | Theoretical: 83.927977 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MGSSHHHHHH SSGLVPRGSH MEFKYSEVVE PSTYYTEGLC EGIDVRKSKF TTLEDRGAIR AHEDWNKHIG PCREYRGTLG PRFSFISVA VPECIPERLE VISYANEFAF LHDDVTDHVG HDTGEVENDE MMTVFLEAAH TGAIDTSNKV DIRRAGKKRI Q SQLFLEML ...String: MGSSHHHHHH SSGLVPRGSH MEFKYSEVVE PSTYYTEGLC EGIDVRKSKF TTLEDRGAIR AHEDWNKHIG PCREYRGTLG PRFSFISVA VPECIPERLE VISYANEFAF LHDDVTDHVG HDTGEVENDE MMTVFLEAAH TGAIDTSNKV DIRRAGKKRI Q SQLFLEML AIDPECAKTT MKSWARFVEV GSSRQHETRF VELAKYIPYR IMDVGEMFWF GLVTFGLGLH IPDHELELCR EL MANAWIA VGLQNDIWSW PKERDAATLH GKDHVVNAIW VLMQEHQTDV DGAMQICRKL IVEYVAKYLE VIEATKNDES ISL DLRKYL DAMLYSISGN VVWSLECPRY NPDVSFNKTQ LEWMRQGLPS LESCPVLARS PEIDSDESAV SPTADESDST EDSL GSGSR QDSSLSTGLS LSPVHSNEGK DLQRVDTDHI FFEKAVLEAP YDYIASMPSK GVRDQFIDAL NDWLRVPDVK VGKIK DAVR VLHNSSLLLD DFQDNSPLRR GKPSTHNIFG SAQTVNTATY SIIKAIGQIM EFSAGESVQE VMNSIMILFQ GQAMDL FWT YNGHVPSEEE YYRMIDQKTG QLFSIATSLL LNAADNEIPR TKIQSCLHRL TRLLGRCFQI CDDYQNLVSA DYTKQKG FC EDLDEGKWSL ALIHMIHKQR SHMALLNVLS TGRKHGGMTL EQKQFVLDII EEEKSLDYTR SVMMDLHVQL RAEIGRIE I LLDSPNPAMR LLLELLRV UniProtKB: Fusicoccadiene synthase |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 52.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |