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- PDB-9odt: The structure of a Bacterial Cyanide Dihydratase from Bacillus sa... -

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Basic information

Entry
Database: PDB / ID: 9odt
TitleThe structure of a Bacterial Cyanide Dihydratase from Bacillus safensis PER-URP-08
ComponentsCyanide dihydratase
KeywordsHYDROLASE / CynD / nitrilase / biorremediation / oligomer
Function / homology
Function and homology information


nitrilase / nitrilase activity / detoxification of nitrogen compound / nitrile hydratase activity
Similarity search - Function
Nitrilase/Cyanide hydratase / Nitrilases / cyanide hydratase signature 1. / Nitrilase/cyanide hydratase, conserved site / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase
Similarity search - Domain/homology
Biological speciesBacillus safensis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.04 Å
AuthorsJusto Arevalo, S. / Valle-Riestra F, V. / Balan, A. / Chuck, C.S.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2022/00943-1 Brazil
Sao Paulo Research Foundation (FAPESP)2021/10577-0 Brazil
CitationJournal: Structure / Year: 2026
Title: The single-particle cryo-EM structures of a bacterial cyanide dihydratase and a fungal cyanide hydratase.
Authors: Santiago Justo Arevalo / Valeria Valle-Riestra Felice / Mikaela Barahona Acuña / Katia Ordinola Flores / Mauro Quiñones Aguilar / Andrea Balan / Chuck Shaker Farah /
Abstract: Cyanide is widely used in industries due to its affinity for metals, a property that also underlies its toxicity. Industries, therefore, must reduce cyanide concentration before the final disposal of ...Cyanide is widely used in industries due to its affinity for metals, a property that also underlies its toxicity. Industries, therefore, must reduce cyanide concentration before the final disposal of wastewater. Physical, chemical, and biological methods have been developed for this; however, knowledge about the structure of enzymes involved in cyanide degradation remains limited. Structural characterization of these proteins could facilitate the development of enzymes with enhanced bioremediation potential. Here, we present the single-particle cryo-electron microscopy structures of a cyanide dihydratase from Bacillus safensis and a cyanide hydratase from Gloeocercospora sorghi at 2.2 Å and 2.0 Å resolution, respectively. We provide a comprehensive description and comparative analysis alongside all previously determined nitrilase structures. Importantly, our full-length structures reveal new features in the C-terminal as well as specific intermolecular interactions between protomer interfaces and within the helix lumen. Finally, our findings offer insights into the reaction mechanisms of these two enzymes.
History
DepositionApr 27, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Cyanide dihydratase
A: Cyanide dihydratase
R: Cyanide dihydratase
J: Cyanide dihydratase
I: Cyanide dihydratase
K: Cyanide dihydratase
L: Cyanide dihydratase
M: Cyanide dihydratase
N: Cyanide dihydratase
H: Cyanide dihydratase
G: Cyanide dihydratase
F: Cyanide dihydratase
O: Cyanide dihydratase
E: Cyanide dihydratase
P: Cyanide dihydratase
D: Cyanide dihydratase
Q: Cyanide dihydratase
C: Cyanide dihydratase


Theoretical massNumber of molelcules
Total (without water)675,47218
Polymers675,47218
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, SEC-MALS
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Cyanide dihydratase


Mass: 37526.223 Da / Num. of mol.: 18
Source method: isolated from a genetically manipulated source
Details: Monomer of CynD / Source: (gene. exp.) Bacillus safensis (bacteria) / Strain: PER-URP-08 / Gene: nit, FX981_03157 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: A0A5C0WLX0, nitrilase
Has protein modificationN

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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: Quaternary left-handed helix of cyanide dihydratase dimers
Type: COMPLEX / Details: wild type CynD from Bacillus safensis PER-URP-08 / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.677232 MDa / Experimental value: NO
Source (natural)Organism: Bacillus safensis (bacteria) / Strain: PER-URP-08
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21(DE3)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTrisC4H11NO31
2100 mMsodium chlorideNaCl1
SpecimenConc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm
Image recordingAverage exposure time: 4.39 sec. / Electron dose: 55.59 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3993
Details: Number of processing frames fractions collected were 30

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Processing

EM software
IDNameVersionCategory
1SPHIRE1.9.3particle selection
2EPUimage acquisition
4cisTEM1.0.0CTF correction
10cryoSPARC4.6.2initial Euler assignment
11cryoSPARC4.6.2final Euler assignment
12cryoSPARC4.6.2classification
13cryoSPARC4.6.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 822794
3D reconstructionResolution: 2.04 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 361080 / Symmetry type: POINT

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