1IZC

Crystal Structure Analysis of Macrophomate synthase


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 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


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

  • 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 ...

    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.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
macrophomate synthase intermolecular Diels-AlderaseA339Macrophoma commelinaeMutation(s): 1 
Find proteins for Q9UVD4 (Macrophoma commelinae)
Explore Q9UVD4 
Go to UniProtKB:  Q9UVD4
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PYR
Query on PYR

Download CCD File 
A
PYRUVIC ACID
C3 H4 O3
LCTONWCANYUPML-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
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 = 106.678α = 90
b = 106.678β = 90
c = 120.755γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
CNSrefinement
CCP4data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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