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PDBsum entry 1izc
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Insight into a natural diels-Alder reaction from the structure of macrophomate synthase.
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Authors
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T.Ose,
K.Watanabe,
T.Mie,
M.Honma,
H.Watanabe,
M.Yao,
H.Oikawa,
I.Tanaka.
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Ref.
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Nature, 2003,
422,
185-189.
[DOI no: ]
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PubMed id
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Abstract
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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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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.
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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.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nature
(2003,
422,
185-189)
copyright 2003.
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Added reference #1*
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Title
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Structure of macrophomate synthase.
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Authors
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T.Ose,
K.Watanabe,
M.Yao,
M.Honma,
H.Oikawa,
I.Tanaka.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 2004,
60,
1187-1197.
[DOI no: ]
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PubMed id
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Figure 3.
Figure 3 Active-site comparison of MPS (a, c) and DDG aldolase
(b, d). Both enzymes are viewed from almost the same direction.
Octahedrally coordinated magnesium ions and their ligands are
shown. The ligands are the carboxyl O atoms of Glu and Asp, the
C2 carbonyl and C1 carboxyl O atoms of pyruvate (magenta) and
two water molecules, W1 and W2. The dotted lines indicate
interactions via hydrogen bonding. The atoms are coloured as
follows: red, oxygen, blue, nitrogen, yellow, carbon and green,
magnesium.
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Figure 6.
Figure 6 Proposed reaction mechanism of oxalacetate
decarboxylation, Diels-Alder reaction and concomitant
reorganization. Charged and hydrogen-bonding interactions are
shown as dotted lines and the residues involved in the
hydrophobic interactions are indicated with arcs. The carbon
skeleton of the oxalacetate is shown in purple. The green lines
represent the carbon-carbon bonds formed by the Diels-Alder
reaction. The bulkiest substituants permitted at the R[1] and
R[2] positions of substrates are 2-hydroxylpropyl and phenyl
groups, respectively, as shown in the figure.
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The above figures are
reproduced from the cited reference
with permission from the IUCr
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*Note, "added" references are those not in the PDB file but
which have either been obtained from the journal or suggested by the
author(s).
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