6RS4

Structure of tabersonine synthase - an alpha-beta hydrolase from Catharanthus roseus

• PDB DOI: https://doi.org/10.2210/pdb6RS4/pdb

• Classification: HYDROLASE
• Organism(s): Catharanthus roseus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-05-21 Released: 2020-03-04 
• Deposition Author(s): Caputi, L., Franke, J., Bussey, K., Farrow, S.C., Curcino Vieira, I.J., Stevenson, C.E.M., Lawson, D.M., O'Connor, S.E.
• Funding Organization(s): European Research Council, Biotechnology and Biological Sciences Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.162 
• R-Value Work: 0.133 
• R-Value Observed: 0.134 

Starting Model: experimental

Literature

Structural basis of cycloaddition in biosynthesis of iboga and aspidosperma alkaloids.

Caputi, L., Franke, J., Bussey, K., Farrow, S.C., Vieira, I.J.C., Stevenson, C.E.M., Lawson, D.M., O'Connor, S.E.

(2020) Nat Chem Biol 16: 383-386

• PubMed: 32066966 
• DOI: https://doi.org/10.1038/s41589-019-0460-x
• Primary Citation of Related Structures:  
  6RJ8, 6RS4, 6RT8


• PubMed Abstract: 
  

  Cycloaddition reactions generate chemical complexity in a single step. Here we report the crystal structures of three homologous plant-derived cyclases involved in the biosynthesis of iboga and aspidosperma alkaloids. These enzymes act on the same substrate, named angryline, to generate three distinct scaffolds. Mutational analysis reveals how these highly similar enzymes control regio- and stereo-selectivity.

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Organizational Affiliation: 

Max Planck Institute of Chemical Ecology, Department of Natural Product Biosynthesis, Jena, Germany.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 73.19 kDa 
• Atom Count: 6,010 
• Modelled Residue Count: 630 
• Deposited Residue Count: 642 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tabersonine synthase	A, B	321	Catharanthus roseus	Mutation(s): 0  Gene Names: TS, HL2 EC: 4
UniProt
Find proteins for A0A2P1GIW3 (Catharanthus roseus) Explore A0A2P1GIW3  Go to UniProtKB:  A0A2P1GIW3

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 A], H [auth A], I [auth B], J [auth B], K [auth B], L [auth B], M [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.162 
• R-Value Work: 0.133 
• R-Value Observed: 0.134 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.485	α = 90
b = 108.962	β = 108.54
c = 63.235	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-03-04 
Deposition Author(s): Caputi, L., Franke, J., Bussey, K., Farrow, S.C., Curcino Vieira, I.J., Stevenson, C.E.M., Lawson, D.M., O'Connor, S.E.

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Funding Organization	Location	Grant Number
European Research Council	Belgium	788301
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/P012523/1

Revision History  

• Version 1.0: 2020-03-04
  Type: Initial release
  
• Version 1.1: 2020-04-01
  Changes: Database references
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Refinement description