7BZC

Crystal structure of plant sesterterpene synthase AtTPS18 complexed with farnesyl thiolodiphosphate (FSPP)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 

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This is version 1.2 of the entry. See complete history


Literature

Molecular Basis for Sesterterpene Diversity Produced by Plant Terpene Synthases.

Chen, Q.Li, J.Liu, Z.Mitsuhashi, T.Zhang, Y.Liu, H.Ma, Y.He, J.Shinada, T.Sato, T.Wang, Y.Liu, H.Abe, I.Zhang, P.Wang, G.

(2020) Plant Commun 1: 100051-100051

  • DOI: https://doi.org/10.1016/j.xplc.2020.100051
  • Primary Citation of Related Structures:  
    7BZB, 7BZC

  • PubMed Abstract: 

    Class I terpene synthase (TPS) generates bioactive terpenoids with diverse backbones. Sesterterpene synthase (sester-TPS, C25), a branch of class I TPSs, was recently identified in Brassicaceae. However, the catalytic mechanisms of sester-TPSs are not fully understood. Here, we first identified three nonclustered functional sester-TPSs (AtTPS06, AtTPS22, and AtTPS29) in Arabidopsis thaliana . AtTPS06 utilizes a type-B cyclization mechanism, whereas most other sester-TPSs produce various sesterterpene backbones via a type-A cyclization mechanism. We then determined the crystal structure of the AtTPS18-FSPP complex to explore the cyclization mechanism of plant sester-TPSs. We used structural comparisons and site-directed mutagenesis to further elucidate the mechanism: (1) mainly due to the outward shift of helix G, plant sester-TPSs have a larger catalytic pocket than do mono-, sesqui-, and di-TPSs to accommodate GFPP; (2) type-A sester-TPSs have more aromatic residues (five or six) in their catalytic pocket than classic TPSs (two or three), which also determines whether the type-A or type-B cyclization mechanism is active; and (3) the other residues responsible for product fidelity are determined by interconversion of AtTPS18 and its close homologs. Altogether, this study improves our understanding of the catalytic mechanism of plant sester-TPS, which ultimately enables the rational engineering of sesterterpenoids for future applications.


  • Organizational Affiliation

    State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Terpenoid synthase 18605Arabidopsis thalianaMutation(s): 0 
Gene Names: TPS18At3g14520MIE1.2
EC: 4.2.3
UniProt
Find proteins for Q9LUE2 (Arabidopsis thaliana)
Explore Q9LUE2 
Go to UniProtKB:  Q9LUE2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9LUE2
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 
  • Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.388α = 90
b = 81.537β = 90
c = 125.57γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China2018YFA0900600
National Natural Science Foundation of China (NSFC)China31970315
National Natural Science Foundation of China (NSFC)China31700263
Chinese Academy of SciencesChinaZDRW-ZS-2019-2
Chinese Academy of SciencesChinaXDB27020103

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-23
    Type: Initial release
  • Version 1.1: 2021-01-13
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Database references, Refinement description