5DCW

Iridoid synthase from Catharanthus roseus - ligand free structure

• PDB DOI: https://doi.org/10.2210/pdb5DCW/pdb

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


• Deposited: 2015-08-24 Released: 2015-10-28 
• Deposition Author(s): Caputi, L., Kries, H., Stevenson, C.E.M., Kamileen, M.O., Sherden, N.H., Geu-Flores, F., Lawson, D.M., O'Connor, S.E.
• Funding Organization(s): European Research Council, Swiss National Science Foundation, Biotechnology and Biological Sciences Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.209 
• R-Value Work: 0.176 
• R-Value Observed: 0.178 

Starting Model: experimental

Literature

Structural determinants of reductive terpene cyclization in iridoid biosynthesis.

Kries, H., Caputi, L., Stevenson, C.E., Kamileen, M.O., Sherden, N.H., Geu-Flores, F., Lawson, D.M., O'Connor, S.E.

(2016) Nat Chem Biol 12: 6-8

• PubMed: 26551396 
• DOI: https://doi.org/10.1038/nchembio.1955
• Primary Citation of Related Structures:  
  5DCU, 5DCW, 5DCY, 5DF1


• PubMed Abstract: 
  

  The carbon skeleton of ecologically and pharmacologically important iridoid monoterpenes is formed in a reductive cyclization reaction unrelated to canonical terpene cyclization. Here we report the crystal structure of the recently discovered iridoid cyclase (from Catharanthus roseus) bound to a mechanism-inspired inhibitor that illuminates substrate binding and catalytic function of the enzyme. Key features that distinguish iridoid synthase from its close homolog progesterone 5β-reductase are highlighted.

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Organizational Affiliation: 

The John Innes Centre, Department of Biological Chemistry, Norwich Research Park, Norwich NR4 7UH, UK.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 42.02 kDa 
• Atom Count: 3,190 
• Modelled Residue Count: 358 
• Deposited Residue Count: 371 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Iridoid synthase	A	371	Catharanthus roseus	Mutation(s): 0  EC: 1.3.1.99 (PDB Primary Data), 1.3.1.122 (UniProt)
UniProt
Find proteins for K7WDL7 (Catharanthus roseus) Explore K7WDL7  Go to UniProtKB:  K7WDL7

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.209 
• R-Value Work: 0.176 
• R-Value Observed: 0.178 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.2	α = 90
b = 141.2	β = 90
c = 106.05	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-10-28 
Deposition Author(s): Caputi, L., Kries, H., Stevenson, C.E.M., Kamileen, M.O., Sherden, N.H., Geu-Flores, F., Lawson, D.M., O'Connor, S.E.

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Funding Organization	Location	Grant Number
European Research Council	United Kingdom	311363
Swiss National Science Foundation	Switzerland	155581
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/J004561/1

Revision History  

• Version 1.0: 2015-10-28
  Type: Initial release
  
• Version 1.1: 2015-11-18
  Changes: Database references
• Version 1.2: 2015-12-30
  Changes: Database references
• Version 1.3: 2024-01-10
  Changes: Data collection, Database references, Refinement description