5YO8

Crystal structure of beta-C25/C30/C35-prene synthase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure and functional analysis of large-terpene synthases belonging to a newly found subclass.

Fujihashi, M.Sato, T.Tanaka, Y.Yamamoto, D.Nishi, T.Ueda, D.Murakami, M.Yasuno, Y.Sekihara, A.Fuku, K.Shinada, T.Miki, K.

(2018) Chem Sci 9: 3754-3758

  • DOI: https://doi.org/10.1039/c8sc00289d
  • Primary Citation of Related Structures:  
    5YO8

  • PubMed Abstract: 

    Thousands of terpenes have been identified to date. However, only two classes of enzymes are known to be involved in their biosynthesis, and each class has characteristic amino-acid motifs. We recently identified a novel large-terpene (C 25 /C 30 /C 35 ) synthase, which shares no motifs with known enzymes. To elucidate the molecular mechanism of this enzyme, we determined the crystal structure of a large-β-prene synthase from B. alcalophilus (BalTS). Surprisingly, the overall structure of BalTS is similar to that of the α-domain of class I terpene synthases although their primary structures are totally different from each other. Two novel aspartate-rich motifs, DYLDNLxD and DY(F,L,W)IDxxED, are identified, and mutations of any one of the aspartates eliminate its enzymatic activity. The present work leads us to propose a new subclass of terpene synthases, class IB, which is probably responsible for large-terpene biosynthesis.


  • Organizational Affiliation

    Department of Chemistry , Graduate School of Science , Kyoto University , Sakyo-ku , Kyoto 606-8502 , Japan . Email: mfuji@kuchem.kyoto-u.ac.jp ; Email: miki@kuchem.kyoto-u.ac.jp.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tetraprenyl-beta-curcumene synthase
A, B
354Alkalihalobacillus alcalophilus ATCC 27647 = CGMCC 1.3604Mutation(s): 0 
Gene Names: BALCAV_0202405
UniProt
Find proteins for A0A094YZ24 (Alkalihalobacillus alcalophilus ATCC 27647 = CGMCC 1.3604)
Explore A0A094YZ24 
Go to UniProtKB:  A0A094YZ24
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A094YZ24
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.205 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.35α = 90
b = 151.67β = 110.03
c = 53.84γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan--

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-09
    Type: Initial release
  • Version 1.1: 2018-05-16
    Changes: Data collection
  • Version 1.2: 2019-12-25
    Changes: Database references
  • Version 1.3: 2024-03-27
    Changes: Data collection, Database references