5YO8 | pdb_00005yo8

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 (Depositor), 0.236 (DCC) 
  • R-Value Work: 
    0.204 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.205 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5YO8

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 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.

Macromolecule Content 

  • Total Structure Weight: 83.76 kDa 
  • Atom Count: 6,573 
  • Modeled Residue Count: 695 
  • Deposited Residue Count: 708 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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 (Depositor), 0.236 (DCC) 
  • R-Value Work:  0.204 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.205 (Depositor) 
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