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PDBsum entry 1ps9
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Oxidoreductase
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PDB id
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1ps9
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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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The crystal structure and reaction mechanism of escherichia coli 2,4-Dienoyl-Coa reductase.
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Authors
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P.A.Hubbard,
X.Liang,
H.Schulz,
J.J.Kim.
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Ref.
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J Biol Chem, 2003,
278,
37553-37560.
[DOI no: ]
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PubMed id
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Abstract
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Escherichia coli 2,4-dienoyl-CoA reductase is an iron-sulfur flavoenzyme
required for the metabolism of unsaturated fatty acids with double bonds at even
carbon positions. The enzyme contains FMN, FAD, and a 4Fe-4S cluster and
exhibits sequence homology to another iron-sulfur flavoprotein, trimethylamine
dehydrogenase. It also requires NADPH as an electron source, resulting in
reduction of the C4-C5 double bond of the acyl chain of the CoA thioester
substrate. The structure presented here of a ternary complex of E. coli
2,4-dienoyl-CoA reductase with NADP+ and a fatty acyl-CoA substrate reveals a
possible mechanism for substrate reduction and provides details of a plausible
electron transfer mechanism involving both flavins and the iron-sulfur cluster.
The reaction is initiated by hydride transfer from NADPH to FAD, which in turn
transfers electrons, one at a time, to FMN via the 4Fe-4S cluster. In the final
stages of the reaction, the fully reduced FMN provides a hydride ion to the C5
atom of substrate, and Tyr-166 and His-252 are proposed to form a catalytic dyad
that protonates the C4 atom of the substrate and complete the reaction.
Inspection of the substrate binding pocket explains the relative promiscuity of
the enzyme, catalyzing reduction of both 2-trans,4-cis- and
2-trans,4-trans-dienoyl-CoA thioesters.
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Figure 1.
FIG. 1. Ribbon diagram outlining the overall fold of E.
coli DCR. The N-terminal TIM barrel is red, with the substrate
in yellow balls-and-sticks and FMN in pink balls-and-sticks. The
4Fe-4S cluster is in the center of the figure. The middle
flavodoxin-like domain is in green, with FAD drawn as green
balls-and-sticks. The C-terminal domain is in blue and includes
NADP(H) as blue balls-and-sticks. For clarity, the N and C
termini are denoted with the letters N and C, respectively.
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Figure 6.
FIG. 6. Proposed reaction mechanism of E. coli DCR. I, the
C5 atom of the acyl chain of substrate undergoes nucleophilic
attack by the hydride ion from the N5 atom of fully reduced FMN.
Glu-164 and a water molecule (WAT[2]) form hydrogen bonds to the
thioester carbonyl oxygen of substrate, stabilizing the enolate
form of substrate, and the C5 atom is primed for nucleophilic
attack. A water molecule (WAT[1]) acts as a general base to
deprotonate the N1 atom of FMN during flavin oxidation. II,
Tyr-166 provides a proton to the C4 carbanion of substrate,
completing reduction of the C4-C5 double bond. III, His-252 acts
to stabilize the phenolate intermediate by providing a hydrogen
bond to Tyr-166.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2003,
278,
37553-37560)
copyright 2003.
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Secondary reference #1
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Title
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Cloning and expression of the fadh gene and characterization of the gene product 2,4-Dienoyl coenzyme a reductase from escherichia coli.
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Authors
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X.Y.He,
S.Y.Yang,
H.Schulz.
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Ref.
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Eur J Biochem, 1997,
248,
516-520.
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PubMed id
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