6RJ8 | pdb_00006rj8

Structure of the alpha-beta hydrolase CorS from Tabernathe iboga

• PDB DOI: https://doi.org/10.2210/pdb6RJ8/pdb

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


• Deposited: 2019-04-26 Released: 2020-03-04 
• Deposition Author(s): Farrow, S.C., Caputi, L., Kamileen, M.O., Bussey, K., Stevenson, C.E.M., Mundy, J., 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: 1.42 Å
• R-Value Free: 
  0.182 (Depositor), 0.187 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.161 (DCC) 
• R-Value Observed: 
  0.156 (Depositor) 

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 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.
Leibniz University Hannover, Centre for Biomolecular Drug Research, Hannover, Germany.
John Innes Centre, Department of Biological Chemistry, Norwich Research Park, Norwich, UK.
Laboratorio de Ciencias Quimicas-UENF-Campos dos Goytacazes-RJ, Campos dos Goytacazes, Brazil.
John Innes Centre, Department of Biological Chemistry, Norwich Research Park, Norwich, UK. [e-mail].
Max Planck Institute of Chemical Ecology, Department of Natural Product Biosynthesis, Jena, Germany. [e-mail].

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 37.28 kDa 
• Atom Count: 2,944 
• Modeled Residue Count: 316 
• Deposited Residue Count: 326 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
alpha-beta hydrolase CorS	A	326	Tabernanthe iboga	Mutation(s): 0  Gene Names: corS EC: 4.2.1.105 (PDB Primary Data), 5.5.1 (UniProt)
UniProt
Find proteins for A0A5B8X6B5 (Tabernanthe iboga) Explore A0A5B8X6B5  Go to UniProtKB:  A0A5B8X6B5

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	B [auth A], C [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PEG	D [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.42 Å
• R-Value Free:  0.182 (Depositor), 0.187 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.161 (DCC) 
• R-Value Observed: 0.156 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.838	α = 90
b = 82.838	β = 90
c = 247.556	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	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): Farrow, S.C., Caputi, L., Kamileen, M.O., Bussey, K., Stevenson, C.E.M., Mundy, J., 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