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- EMDB-17785: Cryo-EM structure of styrene oxide isomerase bound to benzylamine... -

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Basic information

Entry
Database: EMDB / ID: EMD-17785
TitleCryo-EM structure of styrene oxide isomerase bound to benzylamine inhibitor
Map datafull map
Sample
  • Complex: Styrene oxide isomerase-Nanobody-Benzylamine complex
    • Protein or peptide: Styrene oxide isomerase
    • Protein or peptide: Nanobody
  • Ligand: BENZYLAMINE
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: water
KeywordsHeme binding protein / Enzyme / Isomerase / MEMBRANE PROTEIN
Function / homology: / isomerase activity / membrane / Styrene oxide isomerase
Function and homology information
Biological speciesPseudomonas sp. VLB120 (bacteria) / Vicugna pacos (alpaca)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.12 Å
AuthorsKhanppnavar B / Korkhov V / Li X
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Not funded Switzerland
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, 2023-
Header (metadata) releaseApr 3, 2024-
Map releaseApr 3, 2024-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17785.png

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Map

FileDownload / File: emd_17785.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationfull map
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.66 Å/pix.
x 450 pix.
= 297. Å		0.66 Å/pix.
x 450 pix.
= 297. Å		0.66 Å/pix.
x 450 pix.
= 297. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.66 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.05528641 - 0.18291268
Average (Standard dev.)0.000048395876 (±0.0018522408)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 297.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_17785_msk_1.map
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Half map: half1

Fileemd_17785_half_map_1.map
Annotationhalf1
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Half map: half2

Fileemd_17785_half_map_2.map
Annotationhalf2
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Sample components

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Entire : Styrene oxide isomerase-Nanobody-Benzylamine complex

EntireName: Styrene oxide isomerase-Nanobody-Benzylamine complex
Components
  • Complex: Styrene oxide isomerase-Nanobody-Benzylamine complex
    • Protein or peptide: Styrene oxide isomerase
    • Protein or peptide: Nanobody
  • Ligand: BENZYLAMINE
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: water

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Supramolecule #1: Styrene oxide isomerase-Nanobody-Benzylamine complex

SupramoleculeName: 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
Source (natural)Organism: Pseudomonas sp. VLB120 (bacteria)
Molecular weightTheoretical: 201.7 kDa/nm

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Macromolecule #1: Styrene oxide isomerase

MacromoleculeName: Styrene oxide isomerase / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas sp. VLB120 (bacteria) / Strain: Pseudomonas sp. VLB120 / Cell: bacteria
Molecular weightTheoretical: 19.680867 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MGSSHHHHHH SQDPMLHAFE RKMAGHGILM IFCTLLFGVG LWMNLVGGFE IIPGYIIEFH VPGSPEGWAR AHSGPALNGM MVIAVAFVL PSLGFADKTA RLLGSIIVLD GWSNVGFYLF SNFSPNRGLT FGPNQFGPGD IFSFLALAPA YLFGVLAMGA L AVIGYQAL KSTRSRKAVP HAAAE

UniProtKB: Styrene oxide isomerase

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Macromolecule #2: Nanobody

MacromoleculeName: Nanobody / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Vicugna pacos (alpaca)
Molecular weightTheoretical: 14.055473 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
AQGQLVESGG GLVQAGGSLR LSCTGSGRAF VTPAVGWFRQ APGKEREFVG TINWSGSHTS YADPVKGRFT ISRDNAKETV YLQMNNLKP EDADVYYCAS RGVSGRYEYW GKGTPVTVSS HHHHHHEPEA

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Macromolecule #3: BENZYLAMINE

MacromoleculeName: BENZYLAMINE / type: ligand / ID: 3 / Number of copies: 6 / Formula: ABN
Molecular weightTheoretical: 107.153 Da
Chemical component information

ChemComp-ABN:
BENZYLAMINE

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Macromolecule #4: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 4 / Number of copies: 6 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 264 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 65.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf (ver. 1.06) / Type: NONE
Startup modelType of model: INSILICO MODEL / In silico model: Alphafold 2.0
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.12 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.3) / Number images used: 61171
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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