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- EMDB-17785: Cryo-EM structure of styrene oxide isomerase bound to benzylamine... -
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Open data
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Basic information
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Title | Cryo-EM structure of styrene oxide isomerase bound to benzylamine inhibitor | |||||||||
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![]() | Heme binding protein / ![]() ![]() ![]() | |||||||||
Function / homology | ![]() ![]() ![]() | |||||||||
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![]() | Khanppnavar B / Korkhov V / Li X | |||||||||
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![]() | ![]() Title: Structural basis of the Meinwald rearrangement catalysed by styrene oxide isomerase. Authors: Basavraj Khanppnavar / Joel P S Choo / Peter-Leon Hagedoorn / Grigory Smolentsev / Saša Štefanić / Selvapravin Kumaran / Dirk Tischler / Fritz K Winkler / Volodymyr M Korkhov / Zhi Li / ...Authors: Basavraj Khanppnavar / Joel P S Choo / Peter-Leon Hagedoorn / Grigory Smolentsev / Saša Štefanić / Selvapravin Kumaran / Dirk Tischler / Fritz K Winkler / Volodymyr M Korkhov / Zhi Li / Richard A Kammerer / Xiaodan Li / ![]() ![]() ![]() ![]() Abstract: Membrane-bound styrene oxide isomerase (SOI) catalyses the Meinwald rearrangement-a Lewis-acid-catalysed isomerization of an epoxide to a carbonyl compound-and has been used in single and cascade ...Membrane-bound styrene oxide isomerase (SOI) catalyses the Meinwald rearrangement-a Lewis-acid-catalysed isomerization of an epoxide to a carbonyl compound-and has been used in single and cascade reactions. However, the structural information that explains its reaction mechanism has remained elusive. Here we determine cryo-electron microscopy (cryo-EM) structures of SOI bound to a single-domain antibody with and without the competitive inhibitor benzylamine, and elucidate the catalytic mechanism using electron paramagnetic resonance spectroscopy, functional assays, biophysical methods and docking experiments. We find ferric haem b bound at the subunit interface of the trimeric enzyme through H58, where Fe(III) acts as the Lewis acid by binding to the epoxide oxygen. Y103 and N64 and a hydrophobic pocket binding the oxygen of the epoxide and the aryl group, respectively, position substrates in a manner that explains the high regio-selectivity and stereo-specificity of SOI. Our findings can support extending the range of epoxide substrates and be used to potentially repurpose SOI for the catalysis of new-to-nature Fe-based chemical reactions. | |||||||||
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 21.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 16.4 KB 16.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 15.9 KB | Display | ![]() |
Images | ![]() | 38.3 KB | ||
Masks | ![]() | 347.6 MB | ![]() | |
Filedesc metadata | ![]() | 5.8 KB | ||
Others | ![]() ![]() | 277.8 MB 277.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8pnuMC ![]() 8pnvC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | full map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.66 Å | ||||||||||||||||||||
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Sample components
-Entire : Styrene oxide isomerase-Nanobody-Benzylamine complex
Entire | Name: Styrene oxide isomerase-Nanobody-Benzylamine complex |
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Components |
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-Supramolecule #1: Styrene oxide isomerase-Nanobody-Benzylamine complex
Supramolecule | Name: Styrene oxide isomerase-Nanobody-Benzylamine complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 Details: Styrene oxide isomerase bound to nanobody complex and benzylamine inhibitor |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 201.7 kDa/nm |
-Macromolecule #1: Styrene oxide isomerase
Macromolecule | Name: Styrene oxide isomerase / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 19.680867 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: MGSSHHHHHH SQDPMLHAFE RKMAGHGILM IFCTLLFGVG LWMNLVGGFE IIPGYIIEFH VPGSPEGWAR AHSGPALNGM MVIAVAFVL PSLGFADKTA RLLGSIIVLD GWSNVGFYLF SNFSPNRGLT FGPNQFGPGD IFSFLALAPA YLFGVLAMGA L AVIGYQAL KSTRSRKAVP HAAAE UniProtKB: Styrene oxide isomerase |
-Macromolecule #2: Nanobody
Macromolecule | Name: Nanobody / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 14.055473 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: AQGQLVESGG GLVQAGGSLR LSCTGSGRAF VTPAVGWFRQ APGKEREFVG TINWSGSHTS YADPVKGRFT ISRDNAKETV YLQMNNLKP EDADVYYCAS RGVSGRYEYW GKGTPVTVSS HHHHHHEPEA |
-Macromolecule #3: BENZYLAMINE
Macromolecule | Name: BENZYLAMINE / type: ligand / ID: 3 / Number of copies: 6 / Formula: ABN |
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Molecular weight | Theoretical: 107.153 Da |
Chemical component information | ![]() ChemComp-ABN: |
-Macromolecule #4: PROTOPORPHYRIN IX CONTAINING FE
Macromolecule | Name: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 4 / Number of copies: 6 / Formula: HEM |
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Molecular weight | Theoretical: 616.487 Da |
Chemical component information | ![]() ChemComp-HEM: |
-Macromolecule #5: water
Macromolecule | Name: water / type: ligand / ID: 5 / Number of copies: 264 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ![]() ChemComp-HOH: |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 65.0 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |