7BUX | pdb_00007bux

Eucommia ulmoides FPS1

• PDB DOI: https://doi.org/10.2210/pdb7BUX/pdb

• Classification: PLANT PROTEIN
• Organism(s): Eucommia ulmoides
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-04-08 Released: 2021-02-17 
• Deposition Author(s): Kajiura, H., Yoshizawa, T., Tokumoto, Y., Suzuki, N., Takeno, S., Takeno, K.J., Yamashita, T., Tanaka, S., Kaneko, Y., Fujiyama, K., Matsumura, H., Nakazawa, Y.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.248 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.233 (Depositor), 0.235 (DCC) 
• R-Value Observed: 
  0.234 (Depositor) 

Starting Model: experimental

Literature

Structure-function studies of ultrahigh molecular weight isoprenes provide key insights into their biosynthesis.

Kajiura, H., Yoshizawa, T., Tokumoto, Y., Suzuki, N., Takeno, S., Takeno, K.J., Yamashita, T., Tanaka, S.I., Kaneko, Y., Fujiyama, K., Matsumura, H., Nakazawa, Y.

(2021) Commun Biol 4: 215-215

• PubMed: 33594248 
• DOI: https://doi.org/10.1038/s42003-021-01739-5
• Primary Citation Related Structures: 
  7BUU, 7BUV, 7BUW, 7BUX


• PubMed Abstract: 
  

  Some plant trans-1,4-prenyltransferases (TPTs) produce ultrahigh molecular weight trans-1,4-polyisoprene (TPI) with a molecular weight of over 1.0 million. Although plant-derived TPI has been utilized in various industries, its biosynthesis and physiological function(s) are unclear. Here, we identified three novel Eucommia ulmoides TPT isoforms-EuTPT1, 3, and 5, which synthesized TPI in vitro without other components. Crystal structure analysis of EuTPT3 revealed a dimeric architecture with a central hydrophobic tunnel. Mutation of Cys94 and Ala95 on the central hydrophobic tunnel no longer synthesizd TPI, indicating that Cys94 and Ala95 were essential for forming the dimeric architecture of ultralong-chain TPTs and TPI biosynthesis. A spatiotemporal analysis of the physiological function of TPI in E. ulmoides suggested that it is involved in seed development and maturation. Thus, our analysis provides functional and mechanistic insights into TPI biosynthesis and uncovers biological roles of TPI in plants.

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Organizational Affiliation: 
• International Center for Biotechnology, Osaka University, 2-1 Yamada-oka, Suita, Osaka, 565-0871, Japan.
Technical Research Institute, Hitachi Zosen Corporation, 2-2-11 Funamachi, Taisyo, Osaka, 551-0022, Japan.
Department of Biotechnology, College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga, 525-8577, Japan.
Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
Yeast Genetic Resources Lab, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka, 565-0871, Japan.
Department of Biotechnology, College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga, 525-8577, Japan. [e-mail].
Technical Research Institute, Hitachi Zosen Corporation, 2-2-11 Funamachi, Taisyo, Osaka, 551-0022, Japan. [e-mail].
Faculty of Bioscience and Bioindustry, Tokushima University, 2-1 Minami-josanjima, Tokushima, 770-8513, Japan. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 83.18 kDa 
• Atom Count: 5,540 
• Modeled Residue Count: 672 
• Deposited Residue Count: 716 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FPS2	A, B	358	Eucommia ulmoides	Mutation(s): 0  Gene Names: EUFPS2, FPS2
UniProt
Find proteins for Q94IE8 (Eucommia ulmoides) Explore Q94IE8  Go to UniProtKB:  Q94IE8

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.248 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.233 (Depositor), 0.235 (DCC) 
• R-Value Observed: 0.234 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54	α = 90
b = 71.27	β = 103.497
c = 103.38	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
PHENIX	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-02-17 
Deposition Author(s): Kajiura, H., Yoshizawa, T., Tokumoto, Y., Suzuki, N., Takeno, S., Takeno, K.J., Yamashita, T., Tanaka, S., Kaneko, Y., Fujiyama, K., Matsumura, H., Nakazawa, Y.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	17H05732
Japan Society for the Promotion of Science (JSPS)	Japan	18K06094
Japan Society for the Promotion of Science (JSPS)	Japan	19H04735
Japan Society for the Promotion of Science (JSPS)	Japan	19K16060

Revision History  

• Version 1.0: 2021-02-17
  Type: Initial release
  
• Version 1.1: 2021-03-10
  Changes: Database references
• Version 1.2: 2023-11-29
  Changes: Data collection, Database references, Refinement description