5UV0

Crystal Structure of (+)-Limonene Synthase from Citrus sinensis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

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This is version 1.1 of the entry. See complete history


Literature

Functional and Structural Characterization of a (+)-Limonene Synthase from Citrus sinensis.

Morehouse, B.R.Kumar, R.P.Matos, J.O.Olsen, S.N.Entova, S.Oprian, D.D.

(2017) Biochemistry 56: 1706-1715

  • DOI: 10.1021/acs.biochem.7b00143
  • Primary Citation of Related Structures:  
    5UV0

  • PubMed Abstract: 
  • Terpenes make up the largest and most diverse class of natural compounds and have important commercial and medical applications. Limonene is a cyclic monoterpene (C 10 ) present in nature as two enantiomers, (+) and (-), which are produced by different enzymes ...

    Terpenes make up the largest and most diverse class of natural compounds and have important commercial and medical applications. Limonene is a cyclic monoterpene (C 10 ) present in nature as two enantiomers, (+) and (-), which are produced by different enzymes. The mechanism of production of the (-)-enantiomer has been studied in great detail, but to understand how enantiomeric selectivity is achieved in this class of enzymes, it is important to develop a thorough biochemical description of enzymes that generate (+)-limonene, as well. Here we report the first cloning and biochemical characterization of a (+)-limonene synthase from navel orange (Citrus sinensis). The enzyme obeys classical Michaelis-Menten kinetics and produces exclusively the (+)-enantiomer. We have determined the crystal structure of the apoprotein in an "open" conformation at 2.3 Å resolution. Comparison with the structure of (-)-limonene synthase (Mentha spicata), which is representative of a fully closed conformation (Protein Data Bank entry 2ONG ), reveals that the short H-α1 helix moves nearly 5 Å inward upon substrate binding, and a conserved Tyr flips to point its hydroxyl group into the active site.


    Organizational Affiliation

    Department of Biochemistry, Brandeis University , Waltham, Massachusetts 02454, United States.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
(+)-limonene synthaseA607Citrus sinensisMutation(s): 0 
EC: 4.2.3.20
UniProt
Find proteins for A0A1C9J6A7 (Citrus sinensis)
Explore A0A1C9J6A7 
Go to UniProtKB:  A0A1C9J6A7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1C9J6A7
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.79α = 90
b = 85.79β = 90
c = 216.35γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-22
    Type: Initial release
  • Version 1.1: 2017-04-05
    Changes: Database references