5DCU | pdb_00005dcu

Iridoid synthase from Catharanthus roseus - ternary complex with NADP+ and triethylene glycol carboxylic acid

PDB DOI: https://doi.org/10.2210/pdb5DCU/pdb

Classification: OXIDOREDUCTASE
Organism(s): Catharanthus roseus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.179 (Depositor), 0.185 (DCC)
R-Value Work:
0.155 (Depositor)
R-Value Observed:
0.156 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

PubMed: 26551396 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/nchembio.1955
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 85.61 kDa
Atom Count: 7,111
Modeled Residue Count: 728
Deposited Residue Count: 742
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Iridoid synthase	A, B	371	Catharanthus roseus	Mutation(s): 1 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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	K7WDL7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain C [auth A] MOL2 format, chain G [auth B] MOL2 format, chain C [auth A] mmCIF format, chain G [auth B] mmCIF format, chain C [auth A]	C [auth A], G [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
TEG Query on TEG Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain E [auth A]	E [auth A], I [auth B]	[2-(2-hydroxyethoxy)ethoxy]acetic acid C₆ H₁₂ O₅ PRBXPAHXMGDVNQ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain H [auth B] SDF format, chain F [auth A] SDF format, chain D [auth A] MOL2 format, chain J [auth B] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] MOL2 format, chain D [auth A] mmCIF format, chain J [auth B] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A] mmCIF format, chain D [auth A]	D [auth A], F [auth A], H [auth B], J [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.179 (Depositor), 0.185 (DCC)
R-Value Work: 0.155 (Depositor)
R-Value Observed: 0.156 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.03	α = 90
b = 96.11	β = 90
c = 172.63	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2015-10-28

Deposition Author(s):

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 (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, Derived calculations, Refinement description