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Yorodumi- PDB-8pnu: Cryo-EM structure of styrene oxide isomerase bound to benzylamine... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8pnu | ||||||
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Title | Cryo-EM structure of styrene oxide isomerase bound to benzylamine inhibitor | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / Heme binding protein / Enzyme / Isomerase | ||||||
Function / homology | isomerase activity / membrane / BENZYLAMINE / PROTOPORPHYRIN IX CONTAINING FE / Styrene oxide isomerase Function and homology information | ||||||
Biological species | Pseudomonas sp. VLB120 (bacteria) Vicugna pacos (alpaca) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.12 Å | ||||||
Authors | Khanppnavar, B. / Korkhov, V. / Li, X. | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: Nat Chem / Year: 2024 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8pnu.cif.gz | 320.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8pnu.ent.gz | 260.6 KB | Display | PDB format |
PDBx/mmJSON format | 8pnu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pn/8pnu ftp://data.pdbj.org/pub/pdb/validation_reports/pn/8pnu | HTTPS FTP |
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-Related structure data
Related structure data | 17785MC 8pnvC 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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-Components
#1: Protein | Mass: 19680.867 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas sp. VLB120 (bacteria) / Strain: Pseudomonas sp. VLB120 / Cell: bacteria / Cell line: Pseudomonas sp. VLB120 / Gene: stdC / Variant: Pseudomonas sp. VLB120 / Plasmid: pRSFDuet_SOI / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: O50216 #2: Antibody | Mass: 14055.473 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vicugna pacos (alpaca) Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) #3: Chemical | ChemComp-ABN / #4: Chemical | ChemComp-HEM / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: Styrene oxide isomerase-Nanobody-Benzylamine complex / Type: COMPLEX Details: Styrene oxide isomerase bound to nanobody complex and benzylamine inhibitor Entity ID: #1-#2 / Source: RECOMBINANT |
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Molecular weight | Value: 201.7 kDa/nm / Experimental value: NO |
Source (natural) | Organism: Pseudomonas sp. VLB120 (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 65 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
EM software |
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CTF correction | Type: NONE | ||||||||||||||||
3D reconstruction | Resolution: 2.12 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 61171 / Symmetry type: POINT |