5C05

Crystal Structure of Gamma-terpinene Synthase from Thymus vulgaris

• PDB DOI: https://doi.org/10.2210/pdb5C05/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Thymus vulgaris
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-06-12 Released: 2016-01-13 
• Deposition Author(s): Parthier, C.P., Rudolph, K., Muller, Y.A., Mueller-Uri, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.186 
• R-Value Work: 0.164 
• R-Value Observed: 0.164 

Literature

Expression, crystallization and structure elucidation of gamma-terpinene synthase from Thymus vulgaris.

Rudolph, K., Parthier, C., Egerer-Sieber, C., Geiger, D., Muller, Y.A., Kreis, W., Muller-Uri, F.

(2016) Acta Crystallogr F Struct Biol Commun 72: 16-23

• PubMed: 26750479 
• DOI: https://doi.org/10.1107/S2053230X15023043
• Primary Citation of Related Structures:  
  5C05


• PubMed Abstract: 
  

  The biosynthesis of γ-terpinene, a precursor of the phenolic isomers thymol and carvacrol found in the essential oil from Thymus sp., is attributed to the activitiy of γ-terpinene synthase (TPS). Purified γ-terpinene synthase from T. vulgaris (TvTPS), the Thymus species that is the most widely spread and of the greatest economical importance, is able to catalyze the enzymatic conversion of geranyl diphosphate (GPP) to γ-terpinene. The crystal structure of recombinantly expressed and purified TvTPS is reported at 1.65 Å resolution, confirming the dimeric structure of the enzyme. The putative active site of TvTPS is deduced from its pronounced structural similarity to enzymes from other species of the Lamiaceae family involved in terpenoid biosynthesis: to (+)-bornyl diphosphate synthase and 1,8-cineole synthase from Salvia sp. and to (4S)-limonene synthase from Mentha spicata.

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Organizational Affiliation: 

Lehrstuhl für Pharmazeutische Biologie, Department für Biologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstrasse 5, D-91058 Erlangen, Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 131.2 kDa 
• Atom Count: 9,638 
• Modelled Residue Count: 1,036 
• Deposited Residue Count: 1,118 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative gamma-terpinene synthase	A, B	559	Thymus vulgaris	Mutation(s): 0
UniProt
Find proteins for A0A0M3Q1Q3 (Thymus vulgaris) Explore A0A0M3Q1Q3  Go to UniProtKB:  A0A0M3Q1Q3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A], D [auth A], E [auth A], F [auth A], G [auth B], H [auth B], I [auth B], J [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.186 
• R-Value Work: 0.164 
• R-Value Observed: 0.164 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.2	α = 94.79
b = 79.61	β = 103.31
c = 93.32	γ = 105.56

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-01-13 
Deposition Author(s): Parthier, C.P., Rudolph, K., Muller, Y.A., Mueller-Uri, F.

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Funding Organization	Location	Grant Number
	Germany	--

Revision History  

• Version 1.0: 2016-01-13
  Type: Initial release
  
• Version 1.1: 2016-01-20
  Changes: Database references
• Version 1.2: 2018-03-07
  Changes: Data collection
• Version 1.3: 2024-01-10
  Changes: Data collection, Database references, Refinement description