Architectures of Mammalian and
Fungal Fatty Acid Synthases
Presentation based on:
T. Maier, S. Jenni, N. Ban, Science 311, 1258 (2006).
-- Mammalian fatty acid at 4.5 Å resolution
S. Jenni, M. Leibundgut, T. Maier, N. Ban, Science 311, 1263 (2006).
-- Fungal fatty acid at 5 Å resolution
Agenda
1. fatty acid quick peak
2. catalytic cycle of fatty acid synthesis
3. mammalian fatty acid synthase structure
4. fungal fatty acid synthase structure
1. Fatty acid quick peak
Common fatty acids are carboxylic acids with long hydrocarbon tails:
comes with a COOH head and a tail of many CH2.
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2. Fatty acid catalytic cycle
2.1 Common elongation scheme
starter substrates Acetyl coenzyme A (Acetyl-CoA) and
Malonyl-CoA transfer the active functionals to acyl carrier
protein (ACP).
ACP transports substrate to different reaction sites,
catalyzed by different enzyme. A complete cycle gives the
acyl group an additional two carbon units.
This step-wise elongation repeats until a substrate length
of C16 to C18 is achieved.
Another enzyme then release the substrate from ACP,
completing the synthesis process.
2.2 Step-by-step details of catalytic cycle
:
A
catalysts for different
individual reactions
F
B
protein that releases the
completed product from ACP.
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C
E
D
2.3 Different fatty acid synthase (FAS) systems
Type II FAS (bacteria) -- all reactions carried out by individual,
monofunctional proteins.
Type I FAS (eukaryote) -- large, multifuctional polypeptides contains
all necessary enzymes for the enlongation
cycle.
Fungal FAS: 2.6-MD 66 dodecamer, catalytic domains
distributed over two distinct subunits.
Vertebrates and Mammal FAS: 270-kD 2 homodimer, contains
all catalytic activities.
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3. Mammalian fatty acid synthase
3.1 Functional proteins
ACP: acyl protein carrier
MAT: malonyl-CoA-/acetylCoA-ACP-transacylase
KS: -ketoacyl synthase
KR: -ketoacyl reductase
DH: dehydratase
ER: -enoyl reductase
TE: thioesterase
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3.2 overall structure and domain assignment
210Å  180Å  90Å
Blue bubble:
Electron density
cloud via
X-ray
crystallography
Colored proteins:
Identified as
specific domain
via mapping
homologous
protein structures
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3.2.1 KS domain
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Mammalian KS closely resembles the Escherichia coli KS I (FabB).
So KS domain was fitted with E. coli FabB.
3.2.2 MAT domain
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Mammalian MAT is homologous to bacterial malonyl transferase (FabD).
So we fit the MAT domain with Streptomyces coelicolor FabD.
3.2.3 DH domain
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Mammalian DH adopts a “double hot dog” fold that’s closely related
to the fold of the dimeric bacterial dehydratases FabA and FabZ. So
we fit DH with two monomers of dimeric E. coli FabA.
3.2.4 ER domain
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The best structural match for ER was obtained with a zinc-free bacterial
quinone reductase. Here the particular model is quinone reductase of T.
thermophilus.
3.2.5 KR domain
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KR belongs to the short-chain dehydrogenase family, and was modeled
with E. coli FabG.
ssor
.
3.2.6 ACP and TE domain
* ACP and TE domains could not be placed with confidence, likely due to their
inherent flexibility.
* However…
This blurred volume of
electron density, which
was observed only on
one side, might be
interpreted as arising
from the C-terminal ACP
and TE domains.
3.2.7 Table of structural and functional analogs
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3.3 intersubunit and interdomain connections
FAS is an intertwined dimer with a large dimerization interface.
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KS domain dimerize in the
same way as homologous
homodimeric FabB.
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The interaction between
ER monomers are guided
by the formation of a
continuous 12-stranded
-sheet. The same way
as the homologous
bacterial enzyme.
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COLORED: identified domains
GREY: unassigned region.
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There are other substantial
intersubunit contacts in the
unassigned region of electron
density map.
3.4 active sites and the two reaction chambers
Solid spheres: active sites
Hollow spheres: radii = length of the phosphopantheteine arm of ACP
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4. Fungal fatty acid synthase
4.1 Functional proteins
ACP: acyl protein carrier
MPT: malonyl/palmitoyl transferase
KS: ketoacyl synthase
KR: ketoacyl reductase
DH: dehydratase
ER: enoyl reductase
AT: acetyl transferase
PT: phosphopantetheine transferase
(for ACP activation)
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4.2 overall structure and domain assignment
230Å  230Å  260Å
MPT: malonyl/palmitoyl
transferase
KS: ketoacyl synthase
KR: ketoacyl reductase
DH: dehydratase
ER: enoyl reductase
AT: acetyl transferase
ACP and PT structures could
not be identified.
White regions denote
unidentified electron density.
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4.2.1 KS domain
KS dimer domain was identified by finding
the thiolase fold in the FAS electron density
map (bacterial KS is known to adopt a
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Bacterial KS homolog fits almost perfectly
into the density map.
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4.2.2 KR domain
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The 4-helix bundle is a characteristic trait
of one of the dimerization interface in type-II
tetrameric KR homolog of Brassica napus.
It also contains a Rossmann fold.
The Brassica napus KR homolog fits FAS
electron density remarkably well.
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4.2.3 DH domain
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The closest sequence homolog with known
structure of fungal DH is the human
Peroxisomal 2-enoyl-CoA hydratase 2
involved in  oxidation of fatty acids.
It is a pseudo-dimer, has two “hot dog”
folds, and forms a large  sheet.
DH structures of bacterial FAS fits less
well, since they are true homodimers.
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4.2.4 ER domain
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The fungal ER, unlike other FAS systems,
is a FMN-containing oxidoreductase, and
no homology has been observed.
Since a TIM-barrel fold was discovered near
the FMN-binding pocket, the 21 known TIMbarrel superfamilies were examined, and a
good fit was obtained with spinach glycolate
oxidase.
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4.2.5 AT and MPT
AT
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MPT
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AT and MPT are homologous in sequence,
catalyze similar reactions, and have same
protein fold. Therefore they are both fitted
with malonyl transferase from Streptomyces
coelicolor.
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In order to unambiguously assign AT and
MPT domain, the locations of their N
termini relative to the C terminus of DH
were observed.
4.3 The reaction chambers
COLORED: fitted domains
GREY: unassigned region.
** Two identical reaction chambers separated
by central wheel.
** Each contains three copies of a full set of
catalytic domains.
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** All active sites are oriented towards interior.
Red cones indicate entrances to active
sites.
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4.3 The reaction chambers
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Green sphere:
reaction chamber center.
A set of active sites in the reaction chamber with all
enzymatic
activities required for the synthesis cycle.
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4.3 The reaction chambers
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Schematic path of ACP, shuttling
substrate between the active
sites.