8I6U

The cryo-EM structure of OsCyc1 dimer state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Structural and functional investigations of syn-copalyl diphosphate synthase from Oryza sativa.

Ma, X.Xu, H.Tong, Y.Luo, Y.Dong, Q.Jiang, T.

(2023) Commun Chem 6: 240-240

  • DOI: https://doi.org/10.1038/s42004-023-01042-w
  • Primary Citation of Related Structures:  
    8I6P, 8I6T, 8I6U, 8IH5, 8KBW

  • PubMed Abstract: 

    The large superfamily of labdane-related diterpenoids is defined by the cyclization of linear geranylgeranyl pyrophosphate (GGPP), catalyzed by copalyl diphosphate synthases (CPSs) to form the basic decalin core, the copalyl diphosphates (CPPs). Three stereochemically distinct CPPs have been found in plants, namely (+)-CPP, ent-CPP and syn-CPP. Here, we used X-ray crystallography and cryo-EM methods to describe different oligomeric structures of a syn-copalyl diphosphate synthase from Oryza sativa (OsCyc1), and provided a cryo-EM structure of OsCyc1 D367A mutant in complex with the substrate GGPP. Further analysis showed that tetramers are the dominant form of OsCyc1 in solution and are not necessary for enzyme activity in vitro. Through rational design, we identified an OsCyc1 mutant that can generate ent-CPP in addition to syn-CPP. Our work provides a structural and mechanistic basis for comparing different CPSs and paves the way for further enzyme design to obtain diterpene derivatives with specific chirality.


  • Organizational Affiliation

    National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China. maxiaoli@ibp.ac.cn.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Syn-copalyl diphosphate synthase, chloroplasticA [auth B],
B [auth A]
775Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: CPS4CYC1Os04g0178300LOC_Os04g09900OSJNBa0096F01.12
EC: 5.5.1.14
UniProt
Find proteins for Q0JF02 (Oryza sativa subsp. japonica)
Explore Q0JF02 
Go to UniProtKB:  Q0JF02
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ0JF02
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-06
    Type: Initial release