5DF1

Iridoid synthase from Catharanthus roseus - ternary complex with NADP+ and geranic acid

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 


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

  • 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.

    • Organizational Affiliation: 

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


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Iridoid synthase
A, B
368Catharanthus roseusMutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupK7WDL7
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP
Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]		NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
58X
Query on 58X
Download Ideal Coordinates CCD File 
D [auth A],
H [auth B]		(2E)-3,7-dimethylocta-2,6-dienoic acid
C10 H16 O2
ZHYZQXUYZJNEHD-VQHVLOKHSA-N
IMD
Query on IMD
Download Ideal Coordinates CCD File 
F [auth A]IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
EDO
Query on EDO
Download Ideal Coordinates CCD File 
E [auth A],
I [auth B],
J [auth B],
K [auth B],
L [auth B]		1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.94α = 90
b = 95.47β = 90
c = 172.21γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
European Research CouncilUnited Kingdom311363
Swiss National Science FoundationSwitzerland155581
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/J004561/1

Revision History  (Full details and data files)

  • 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