9JDB | pdb_00009jdb

Structure of chanoclavine synthase from Claviceps fusiformis


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.64 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Chanoclavine synthase operates by an NADPH-independent superoxide mechanism.

Chen, C.C.Yu, Z.P.Liu, Z.Yao, Y.Hagedoorn, P.L.Schmitz, R.A.Yang, L.Yu, L.Liu, A.Sheng, X.Su, H.Ma, Y.Wang, T.Huang, J.W.Zhang, L.Yan, J.Bao, J.Cui, C.Li, X.Shen, P.Zhang, W.Min, J.Wang, C.Y.Guo, R.T.Gao, S.S.

(2025) Nature 640: 840-846

  • DOI: https://doi.org/10.1038/s41586-025-08670-3
  • Primary Citation of Related Structures:  
    9JDB, 9JDC

  • PubMed Abstract: 

    More than ten ergot alkaloids comprising both natural and semi-synthetic products are used to treat various diseases 1,2 . The central C ring forms the core pharmacophore for ergot alkaloids, giving them structural similarity to neurotransmitters, thus enabling their modulation of neurotransmitter receptors 3 . The haem catalase chanoclavine synthase (EasC) catalyses the construction of this ring through complex radical oxidative cyclization 4 . Unlike canonical catalases, which catalyse H 2 O 2 disproportionation 5,6 , EasC and its homologues represent a broader class of catalases that catalyse O 2 -dependent radical reactions 4,7 . 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) 8,9 , 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.


  • Organizational Affiliation
    • Zhejiang Key Laboratory of Medical Epigenetics, Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, People's Republic of China.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Catalase easC
A, B
479Claviceps fusiformisMutation(s): 0 
Gene Names: easC
EC: 1.11
UniProt
Find proteins for A8C7R6 (Claviceps fusiformis)
Explore A8C7R6 
Go to UniProtKB:  A8C7R6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8C7R6
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.64 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-01
    Type: Initial release
  • Version 1.1: 2025-03-12
    Changes: Data collection, Database references
  • Version 1.2: 2025-03-19
    Changes: Data collection, Database references
  • Version 1.3: 2025-04-30
    Changes: Data collection, Database references