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- PDB-8pnv: Cryo-EM structure of styrene oxide isomerase -

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Basic information

Entry
Database: PDB / ID: 8pnv
TitleCryo-EM structure of styrene oxide isomerase
Components
  • Nanobody
  • Styrene oxide isomerase
KeywordsMEMBRANE PROTEIN / Heme binding protein / Isomerase / Enzyme
Function / homology: / isomerase activity / membrane / PROTOPORPHYRIN IX CONTAINING FE / Styrene oxide isomerase
Function and homology information
Biological speciesPseudomonas sp. VLB120 (bacteria)
Vicugna pacos (alpaca)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.048 Å
AuthorsKhanppnavar, B. / Korkhov, B. / Li, X.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: 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
DepositionJul 2, 2023Deposition site: PDBE / Processing site: PDBE
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Styrene oxide isomerase
B: Styrene oxide isomerase
C: Styrene oxide isomerase
D: Nanobody
E: Nanobody
F: Nanobody
G: Styrene oxide isomerase
H: Styrene oxide isomerase
I: Styrene oxide isomerase
J: Nanobody
K: Nanobody
L: Nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,11718
Polymers202,41812
Non-polymers3,6996
Water9,404522
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization, size-exclusion chromatography
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area34770 Å2
ΔGint-391 kcal/mol
Surface area63090 Å2

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Components

#1: Protein
Styrene oxide isomerase


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 line: Pseudomonas sp. VLB120 / Gene: stdC / Variant: Pseudomonas sp. VLB120 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: O50216
#2: Antibody
Nanobody


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-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 522 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Styrene oxide isomerase-nanobody complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Pseudomonas sp. VLB120 (bacteria)
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 65 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELION3.1.3particle selection
4Gctf1.06CTF correction
8PHENIXmodel refinement
13RELION3.1.33D reconstruction
CTF correctionType: NONE
SymmetryPoint symmetry: D3 (2x3 fold dihedral)
3D reconstructionResolution: 2.048 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 137013 / Symmetry type: POINT

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