7BZB | pdb_00007bzb

Crystal structure of plant sesterterpene synthase AtTPS18

• PDB DOI: https://doi.org/10.2210/pdb7BZB/pdb

• Classification: LYASE
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-04-27 Released: 2020-09-23 
• Deposition Author(s): Li, J.X., Wang, G.D., Zhang, P.
• Funding Organization(s): National Natural Science Foundation of China (NSFC), Chinese Academy of Sciences

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.254 (Depositor), 0.253 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: experimental

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

• PubMed: 33367256 
• DOI: https://doi.org/10.1016/j.xplc.2020.100051
• Primary Citation 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.

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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.
National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.
University of Chinese Academy of Sciences, Beijing 100039, China.
Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
Graduate School of Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi, Osaka 558-8585, Japan.
Department of Applied Biological Chemistry, Faculty of Agriculture, Graduate School of Science and Technology, Niigata University, 8050 Ikarashi-2, Niigata 950-2181, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 69.73 kDa 
• Atom Count: 4,566 
• Modeled Residue Count: 534 
• Deposited Residue Count: 605 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Terpenoid synthase 18	A	605	Arabidopsis thaliana	Mutation(s): 0  Gene Names: TPS18, At3g14520, MIE1.2 EC: 4.2.3
UniProt
Find proteins for Q9LUE2 (Arabidopsis thaliana) Explore Q9LUE2  Go to UniProtKB:  Q9LUE2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PPV (Subject of Investigation/LOI)	D [auth A]	PYROPHOSPHATE H4 O7 P2 XPPKVPWEQAFLFU-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)	B [auth A], C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.254 (Depositor), 0.253 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.562	α = 90
b = 80.925	β = 90
c = 125.776	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-09-23 
Deposition Author(s): Li, J.X., Wang, G.D., Zhang, P.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	2018YFA0900600
National Natural Science Foundation of China (NSFC)	China	31970315
National Natural Science Foundation of China (NSFC)	China	31700263
Chinese Academy of Sciences	China	ZDRW-ZS-2019-2
Chinese Academy of Sciences	China	XDB27020103

Revision History  

• 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