Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 70.44 kDa 
• Atom Count: 4489 
• Modelled Residue Count: 522 
• Deposited Residue Count: 607 
• Unique protein chains: 1

5UV0

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

• PDB DOI: 10.2210/pdb5UV0/pdb

• Classification: LYASE
• Organism(s): Citrus sinensis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-02-17 Released: 2017-03-22 
• Deposition Author(s): Prem Kumar, R., Oprian, D.D.

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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 

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

• PubMed: 28272875 
• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
(+)-limonene synthase	A	607	Citrus sinensis	Mutation(s): 0  EC: 4.2.3.20
UniProt
Find proteins for A0A1C9J6A7 (Citrus sinensis) Explore A0A1C9J6A7  Go to UniProtKB:  A0A1C9J6A7

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 = 85.79	α = 90
b = 85.79	β = 90
c = 216.35	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2017-02-17 
• Released Date: 2017-03-22 
Deposition Author(s): Prem Kumar, R., Oprian, D.D.

Revision History  

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