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- PDB-9ofa: The structure of a Fungal Cyanide Hydratase from Gloeocercospora ... -

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Basic information

Entry
Database: PDB / ID: 9ofa
TitleThe structure of a Fungal Cyanide Hydratase from Gloeocercospora sorghi
ComponentsCyanide hydratase
KeywordsHYDROLASE / CynH / nitrilase / biorremediation / oligomer
Function / homology
Function and homology information


cyanide hydratase / cyanide catabolic process / cyanide hydratase activity / nitrilase activity
Similarity search - Function
Cyanide hydratase / Nitrilases / cyanide hydratase active site signature. / 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 speciesMicrodochium sorghi (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.04 Å
AuthorsJusto Arevalo, S. / Valle-Riestra F, V. / Balan, A. / Farah, C.S.
Funding support Brazil, 3items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2022/00943-1 Brazil
Sao Paulo Research Foundation (FAPESP)2021/10577-0 Brazil
Sao Paulo Research Foundation (FAPESP)2024/02456-6 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 29, 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
O: Cyanide hydratase
N: Cyanide hydratase
Q: Cyanide hydratase
P: Cyanide hydratase
S: Cyanide hydratase
R: Cyanide hydratase
T: Cyanide hydratase
M: Cyanide hydratase
L: Cyanide hydratase
E: Cyanide hydratase
D: Cyanide hydratase
G: Cyanide hydratase
F: Cyanide hydratase
I: Cyanide hydratase
H: Cyanide hydratase
K: Cyanide hydratase
J: Cyanide hydratase
A: Cyanide hydratase
C: Cyanide hydratase
B: Cyanide hydratase


Theoretical massNumber of molelcules
Total (without water)818,92320
Polymers818,92320
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, SEC-MALS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Cyanide hydratase / CHT / Cyanide-degrading nitrilase / Formamide hydrolyase


Mass: 40946.137 Da / Num. of mol.: 20
Source method: isolated from a genetically manipulated source
Details: Monomer of CynH / Source: (gene. exp.) Microdochium sorghi (fungus) / Gene: cht / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: P32964, cyanide hydratase
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 lef-handed helix of cyanide hydratase dimers
Type: COMPLEX / Details: wild type CynH from Gloeocercospora sorghi / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.981582 MDa / Experimental value: NO
Source (natural)Organism: Microdochium sorghi (fungus)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria) / 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: 5928
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
9cryoSPARC4.6.2initial Euler assignment
10cryoSPARC4.6.2final Euler assignment
11cryoSPARC4.6.2classification
12cryoSPARC4.6.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 742870
3D reconstructionResolution: 2.04 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 209895 / Symmetry type: POINT
Atomic model buildingSource name: AlphaFold / Type: in silico model

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