7BUV

Eucommia ulmoides TPT3, crystal form 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.282 
  • R-Value Observed: 0.283 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


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

  • DOI: https://doi.org/10.1038/s42003-021-01739-5
  • Primary Citation of 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.


  • Organizational Affiliation

    International Center for Biotechnology, Osaka University, 2-1 Yamada-oka, Suita, Osaka, 565-0871, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
FPS3
A, B, C, D, E
A, B, C, D, E, F, G
364Eucommia ulmoidesMutation(s): 0 
Gene Names: FPS3
UniProt
Find proteins for A0A1L3KPU1 (Eucommia ulmoides)
Explore A0A1L3KPU1 
Go to UniProtKB:  A0A1L3KPU1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1L3KPU1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.282 
  • R-Value Observed: 0.283 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 234.386α = 90
b = 131.06β = 111.98
c = 103.924γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan17H05732
Japan Society for the Promotion of Science (JSPS)Japan18K06094
Japan Society for the Promotion of Science (JSPS)Japan19H04735
Japan Society for the Promotion of Science (JSPS)Japan19K16060

Revision History  (Full details and data files)

  • 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