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- PDB-9jdb: Structure of chanoclavine synthase from Claviceps fusiformis -

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Basic information

Entry
Database: PDB / ID: 9jdb
TitleStructure of chanoclavine synthase from Claviceps fusiformis
ComponentsCatalase easC
KeywordsOXIDOREDUCTASE / Alkaloid metabolism / Heme / Metal-binding / Peroxidase
Function / homology
Function and homology information


Oxidoreductases; Acting on a peroxide as acceptor / indole alkaloid biosynthetic process / catalase activity / hydrogen peroxide catabolic process / response to hydrogen peroxide / peroxisome / heme binding / mitochondrion / metal ion binding
Similarity search - Function
Catalase, mono-functional, haem-containing, clades 1 and 3 / Catalase haem-binding site / Catalase proximal heme-ligand signature. / Catalase / Catalase active site / Catalase proximal active site signature. / Catalase core domain / Catalase, mono-functional, haem-containing / Catalase / catalase family profile. / Catalase superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Catalase easC
Similarity search - Component
Biological speciesClaviceps fusiformis (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.64 Å
AuthorsLiu, Z.W. / Wang, T. / Li, X. / Shen, P.P. / Huang, J.-W. / Chen, C.-C. / Guo, R.-T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nature / Year: 2025
Title: Chanoclavine synthase operates by an NADPH-independent superoxide mechanism.
Authors: Chun-Chi Chen / Zhi-Pu Yu / Ziwei Liu / Yongpeng Yao / Peter-Leon Hagedoorn / Rob Alexander Schmitz / Lujia Yang / Lu Yu / Aokun Liu / Xiang Sheng / Hao Su / Yaqing Ma / Te Wang / Jian-Wen ...Authors: Chun-Chi Chen / Zhi-Pu Yu / Ziwei Liu / Yongpeng Yao / Peter-Leon Hagedoorn / Rob Alexander Schmitz / Lujia Yang / Lu Yu / Aokun Liu / Xiang Sheng / Hao Su / Yaqing Ma / Te Wang / Jian-Wen Huang / Lilan Zhang / Juzhang Yan / Jinping Bao / Chengsen Cui / Xian Li / Panpan Shen / Wuyuan Zhang / Jian Min / Chang-Yun Wang / Rey-Ting Guo / Shu-Shan Gao /
Abstract: More than ten ergot alkaloids comprising both natural and semi-synthetic products are used to treat various diseases. The central C ring forms the core pharmacophore for ergot alkaloids, giving them ...More than ten ergot alkaloids comprising both natural and semi-synthetic products are used to treat various diseases. The central C ring forms the core pharmacophore for ergot alkaloids, giving them structural similarity to neurotransmitters, thus enabling their modulation of neurotransmitter receptors. The haem catalase chanoclavine synthase (EasC) catalyses the construction of this ring through complex radical oxidative cyclization. Unlike canonical catalases, which catalyse HO disproportionation, EasC and its homologues represent a broader class of catalases that catalyse O-dependent radical reactions. We have elucidated the structure of EasC by cryo-electron microscopy, revealing a nicotinamide adenine dinucleotide phosphate (reduced) (NADPH)-binding pocket and a haem pocket common to all haem catalases, with a unique homodimeric architecture that is, to our knowledge, previously unobserved. The substrate prechanoclavine unprecedentedly binds in the NADPH-binding pocket, instead of the previously suspected haem-binding pocket, and two pockets were connected by a slender tunnel. Contrary to the established mechanisms, EasC uses superoxide rather than the more generally used transient haem iron-oxygen complexes (such as compounds I, II and III), to mediate substrate transformation through superoxide-mediated cooperative catalysis of the two distant pockets. We propose that this reactive oxygen species mechanism could be widespread in metalloenzyme-catalysed reactions.
History
DepositionAug 31, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 1, 2025Provider: repository / Type: Initial release
Revision 1.0Jan 1, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _em_admin.last_update
Revision 1.2Mar 19, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _em_admin.last_update
Revision 1.3Apr 30, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Catalase easC
B: Catalase easC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,3244
Polymers108,0912
Non-polymers1,2332
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Catalase easC / Ergot alkaloid synthesis protein C


Mass: 54045.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Claviceps fusiformis (fungus) / Gene: easC / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A8C7R6, Oxidoreductases; Acting on a peroxide as acceptor
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: Ergot alkaloid synthesis protein C / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Claviceps fusiformis (fungus)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5 / Details: 20 mM Tris-HCL, 150 mM NaCl,pH 7.5
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 52 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.64 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 590067 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0076792
ELECTRON MICROSCOPYf_angle_d1.0949264
ELECTRON MICROSCOPYf_dihedral_angle_d6.852888
ELECTRON MICROSCOPYf_chiral_restr0.044960
ELECTRON MICROSCOPYf_plane_restr0.0051204

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