Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Dihedral - D3  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 36.38 kDa 
• Atom Count: 2637 
• Modelled Residue Count: 299 
• Deposited Residue Count: 339 
• Unique protein chains: 1

1IZC

Crystal Structure Analysis of Macrophomate synthase

• PDB DOI: 10.2210/pdb1IZC/pdb

• Classification: LYASE
• Organism(s): Macrophoma commelinae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2002-10-01 Released: 2003-04-01 
• Deposition Author(s): Ose, T., Watanabe, K., Mie, T., Honma, M., Watanabe, H., Yao, M., Oikawa, H., Tanaka, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.203 
• R-Value Work: 0.176 
• R-Value Observed: 0.178 

Literature

Insight into a natural Diels-Alder reaction from the structure of macrophomate synthase.

Ose, T., Watanabe, K., Mie, T., Honma, M., Watanabe, H., Yao, M., Oikawa, H., Tanaka, I.

(2003) Nature 422: 185-189

• PubMed: 12634789 
• DOI: 10.1038/nature01454
• Primary Citation of Related Structures:  
  1IZC


• PubMed Abstract: 
  

The Diels-Alder reaction, which forms a six-membered ring from an alkene (dienophile) and a 1,3-diene, is synthetically very useful for construction of cyclic products with high regio- and stereoselectivity under mild conditions. It has been applied to the synthesis of complex pharmaceutical and biologically active compounds. Although evidence on natural Diels-Alderases has been accumulated in the biosynthesis of secondary metabolites, there has been no report on the structural details of the natural Diels-Alderases. The function and catalytic mechanism of the natural Diels-Alderase are of great interest owing to the diversity of molecular skeletons in natural Diels-Alder adducts. Here we present the 1.70 A resolution crystal structure of the natural Diels-Alderase, fungal macrophomate synthase (MPS), in complex with pyruvate. The active site of the enzyme is large and hydrophobic, contributing amino acid residues that can hydrogen-bond to the substrate 2-pyrone. These data provide information on the catalytic mechanism of MPS, and suggest that the reaction proceeds via a large-scale structural reorganization of the product.

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Organizational Affiliation: 

Division of Biological Science, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
macrophomate synthase intermolecular Diels-Alderase	A	339	Macrophoma commelinae	Mutation(s): 1
UniProt
Find proteins for Q9UVD4 (Macrophoma commelinae) Explore Q9UVD4  Go to UniProtKB:  Q9UVD4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PYR	C [auth A]	PYRUVIC ACID C3 H4 O3 LCTONWCANYUPML-UHFFFAOYSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.203 
• R-Value Work: 0.176 
• R-Value Observed: 0.178 
• Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.678	α = 90
b = 106.678	β = 90
c = 120.755	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SHARP	phasing
CNS	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-10-01 
• Released Date: 2003-04-01 
Deposition Author(s): Ose, T., Watanabe, K., Mie, T., Honma, M., Watanabe, H., Yao, M., Oikawa, H., Tanaka, I.

Revision History  

• Version 1.0: 2003-04-01
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2021-11-10
  Changes: Database references, Derived calculations