PDBsum entry 1izc

Lyase

PDB id: 1izc

Contents

Protein chain

299 a.a. *

Ligands

PYR

Metals

_MG

Waters ×360

* Residue conservation analysis

PDB id:

1izc

Name:

Lyase

Title:

Crystal structure analysis of macrophomate synthase

Structure:

Macrophomate synthase intermolecular diels-alderase. Chain: a. Synonym: macrophomate synthase. Engineered: yes. Mutation: yes

Source:

Macrophoma commelinae. Organism_taxid: 108330. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Hexamer (from PDB file)

Resolution:

1.70Å R-factor: 0.176 R-free: 0.203

Authors:

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

Key ref:

T.Ose et al. (2003). Insight into a natural Diels-Alder reaction from the structure of macrophomate synthase. Nature, 422, 185-189. PubMed id: 12634789 DOI: 10.1038/nature01454

Date:

01-Oct-02 Release date: 01-Apr-03

Protein chain

Q9UVD4  (Q9UVD4_9PEZI) -  Macrophomate synthase from Macrophoma commelinae

Seq: 339 a.a.

Struc: 299 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DOI no: 10.1038/nature01454

Nature 422:185-189 (2003)

PubMed id: 12634789

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

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

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.

Selected figure(s)

Figure 1.
Figure 1: Details of individual reaction steps with macrophomate synthase. Step 1 is decarboxylation of oxalacetate. Step 2 are Diels -Alder reactions of the enolate and 2-pyrones 2 and 4 to form higher energy adducts 3 and 5, respectively. Step 3 is degradation of 3 in which abstraction of hydrogen triggers C -O bond cleavage followed by decarboxylation and elimination of hydroxy group. The steric energies (SE) of each compound were determined by molecular mechanics calculations using the MM2 force field.

Figure 4.
Figure 4: Comparison of Diels -Alderases. a, Solanapyrone synthase (SPS) catalyses oxidation of alcohol 7 to the reactive formyl derivative which readily promotes [4 + 2] cycloaddition to give solanapyrone A 8. b, Lovastatin nonaketide synthase (LNKS) catalyses intramolecular [4 + 2] cycloaddition from 9 to 10. LNKS also catalyses condensation of acetyl CoA and malonyl CoA to form an enzyme bound analogue of 9. SNAC is N-acetylcysteamine thioester. c, Diels -Alderase antibody 1E9 transforms thiophene dioxide 11 and maleimide 12 to intermediate 13 via [4 + 2] cycloaddition, which is then converted into aromatic product 14 with elimination of sulphur dioxide and the subsequent oxidation. Non-catalysed degradation from 13 to 14 allows this catalytic antibody to escape the product inhibition. This leads 1E9 to be the most efficient Diels -Alderase antibody.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2003, 422, 185-189) copyright 2003.

Figures were selected by an automated process.