Information on EC 2.3.1.179 - beta-ketoacyl-[acyl-carrier-protein] synthase II

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The expected taxonomic range for this enzyme is: Eukaryota, Bacteria

EC NUMBER
COMMENTARY hide
2.3.1.179
-
RECOMMENDED NAME
GeneOntology No.
beta-ketoacyl-[acyl-carrier-protein] synthase II
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
a (Z)-hexadec-11-enoyl-[acyl-carrier protein] + a malonyl-[acyl-carrier protein] = a (Z)-3-oxooctadec-13-enoyl-[acyl-carrier protein] + CO2 + an [acyl-carrier protein]
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Claisen condensation
-
-
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
Biotin metabolism
-
-
cis-vaccenate biosynthesis
Fatty acid biosynthesis
-
-
Metabolic pathways
-
-
petroselinate biosynthesis
-
-
SYSTEMATIC NAME
IUBMB Comments
(Z)-hexadec-11-enoyl-[acyl-carrier protein]:malonyl-[acyl-carrier protein] C-acyltransferase (decarboxylating)
Involved in the dissociated (or type II) fatty acid biosynthesis system that occurs in plants and bacteria. While the substrate specificity of this enzyme is very similar to that of EC 2.3.1.41, beta-ketoacyl-ACP synthase I, it differs in that palmitoleoyl-ACP is not a good substrate of EC 2.3.1.41 but is an excellent substrate of this enzyme [1,2]. The fatty-acid composition of Escherichia coli changes as a function of growth temperature, with the proportion of unsaturated fatty acids increasing with lower growth temperature. This enzyme controls the temperature-dependent regulation of fatty-acid composition, with mutants lacking this acivity being deficient in the elongation of palmitoleate to cis-vaccenate at low temperatures [3,4].
CAS REGISTRY NUMBER
COMMENTARY hide
9077-10-5
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
-
-
Manually annotated by BRENDA team
Northern ecotype
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-
Manually annotated by BRENDA team
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-
-
Manually annotated by BRENDA team
gene fabF homologues designated as CAC3573, CAC2008 and CAA0093
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
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-
-
Manually annotated by BRENDA team
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UniProt
Manually annotated by BRENDA team
subspecies lactis IL1403
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-
Manually annotated by BRENDA team
strain H37Rv, gene mtkasB, i.e. Rv2246
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-
Manually annotated by BRENDA team
strain H37Rv, gene mtkasB, i.e. Rv2246
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-
Manually annotated by BRENDA team
syn. Jessenia bataua
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-
Manually annotated by BRENDA team
gene PffabB/F
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-
Manually annotated by BRENDA team
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-
-
Manually annotated by BRENDA team
PCC 6803
Uniprot
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
malfunction
-
endogenous H2O2 (mainly produced by pyruvate oxidase) inhibits FabF activity by specifically oxidizing its active site cysteine-thiol residue
physiological function
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
(Z)-hexadec-11-enoyl-[acyl-carrier protein] + malonyl-[acyl-carrier protein]
(Z)-3-oxooctadec-13-enoyl-[acyl-carrier protein] + CO2 + [acyl-carrier protein]
show the reaction diagram
-
-
-
-
-
(Z)-hexadec-11-enoyl-[acyl-carrier protein] + malonyl-[acyl-carrier protein]
(Z)-3-oxooctadeca-13-enoyl-[acyl-carrier protein] + CO2 + [acyl-carrier protein]
show the reaction diagram
-
-
-
-
?
acetyl-[acyl-carrier protein] + malonyl-[acyl-carrier protein]
acetoacetyl-[acyl-carrier protein] + CO2 + [acyl-carrier protein]
show the reaction diagram
-
-
-
-
?
cis-3-decenoyl-[acyl-carrier protein] + malonyl-[acyl-carrier protein]
? + CO2 + [acyl-carrier protein]
show the reaction diagram
-
-
-
-
?
decanoyl-[acyl-carrier protein] + malonyl-[acyl-carrier protein]
? + CO2 + [acyl-carrier protein]
show the reaction diagram
-
-
-
-
?
dodec-5-enoyl-[acyl-carrier protein] + malonyl-[acyl-carrier protein]
? + CO2 + [acyl-carrier protein]
show the reaction diagram
-
-
-
?
malonyl-ACP + lauroyl-ACP
?
show the reaction diagram
-
-
-
-
?
malonyl-CoA + lauroyl-CoA
?
show the reaction diagram
-
-
-
-
?
malonyl-phosphopantetheine + lauroyl-CoA
?
show the reaction diagram
-
-
-
-
?
malonyl-phosphopantetheine-14-mer + lauroyl-CoA
?
show the reaction diagram
-
-
-
-
?
malonyl-phosphopantetheine-16-mer + lauroyl-CoA
?
show the reaction diagram
-
-
-
-
?
malonyl-phosphopantetheine-8-mer + lauroyl-CoA
?
show the reaction diagram
-
-
-
-
?
myristoyl-[acyl-carrier protein] + malonyl-[acyl-carrier protein]
? + CO2 + [acyl-carrier protein]
show the reaction diagram
-
-
-
-
?
palmitoleoyl-[acyl-carrier protein] + malonyl-[acyl-carrier protein]
cis-vaccenoyl-[acyl-carrier protein] + CO2 + [acyl-carrier protein]
show the reaction diagram
palmitoyl-[acyl-carrier protein] + malonyl-[acyl-carrier protein]
? + CO2 + [acyl-carrier protein]
show the reaction diagram
-
-
-
-
?
tetradec-7-enoyl-[acyl-carrier protein] + malonyl-[acyl-carrier protein]
? + CO2 + [acyl-carrier protein]
show the reaction diagram
-
-
-
?
tetradecanoyl-[acyl-carrier protein] + malonyl-[acyl-carrier protein]
? + CO2 + [acyl-carrier protein]
show the reaction diagram
-
-
-
?
additional information
?
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
(Z)-hexadec-11-enoyl-[acyl-carrier protein] + malonyl-[acyl-carrier protein]
(Z)-3-oxooctadec-13-enoyl-[acyl-carrier protein] + CO2 + [acyl-carrier protein]
show the reaction diagram
-
-
-
-
-
additional information
?
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Mn2+
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divatent cations such Mn neutralize inhibition by EDTA
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
Acyl carrier protein
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0.0017 mM, 50% inhibition of myristic acid transfer from myristoyl-[acyl-carrier protein] to wild-type enzyme
arsenite
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1 mM, 42% inhibition
cerulenin
dihydroplatensimycin
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IC50: 97 nM
fasamycin A
fasamycin B
iodoacetamide
-
prior incubation of the enzymes with fatty acyl thioesters prevents inhibition
NEM
-
5 mM, complete inhibition
PCMB
-
1 mM, complete inhibition
platencin
-
; exhibits a broad-spectrum Gram-positive antibacterial activity through inhibition of fatty acid biosynthesis, targets the two essential proteins, beta-ketoacyl-[acyl carrier protein] synthase II and III, i.e. FabF and FabH, FabF IC50: 113 nM, overview
platensimycin
thiolactomycin
additional information
-
in vivo inhibition assays
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.014
acetyl-[acyl-carrier protein]
-
pH 7.2
0.017
cis-3-decenoyl-[acyl-carrier protein]
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pH 7.2
0.0133
decanoyl-[acyl-carrier protein]
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-
0.024
dodec-5-enoyl-[acyl-carrier protein]
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27C; 37C
0.0537
Lauroyl-CoA
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wild type protein, acceptor malonyl-CoA, 0.5 mM malonyl-CoA, pH 6.5, 25C
0.0082
malonyl-ACP
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wild type protein, donor lauroyl-ACP, 0.01 mM lauroyl-ACP, pH 6.5, 25C
0.0055 - 0.51
malonyl-CoA
0.59
malonyl-phosphopantetheine
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wild type protein, donor lauroyl-CoA, 0.075 mM lauroyl-CoA, pH 6.5, 25C
0.0061
malonyl-phosphopantetheine-14-mer
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wild type protein, donor lauroyl-CoA, 0.075 mM lauroyl-CoA, pH 6.5, 25C
0.0062
malonyl-phosphopantetheine-16-mer
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wild type protein, donor lauroyl-CoA, 0.075 mM lauroyl-CoA, pH 6.5, 25C
0.0237
malonyl-phosphopantetheine-8-mer
-
wild type protein, donor lauroyl-CoA, 0.075 mM lauroyl-CoA, pH 6.5, 25C
0.0139
myristoyl-[acyl-carrier protein]
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-
0.04 - 0.216
palmitoleoyl-[acyl-carrier protein]
0.0036
palmitoyl-[acyl-carrier protein]
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-
0.043 - 0.06
tetradec-7-enoyl-[acyl-carrier protein]
0.047 - 0.068
tetradecanoyl-[acyl-carrier protein]
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.047
Lauroyl-CoA
Escherichia coli
-
wild type protein, acceptor malonyl-CoA, 0.5 mM malonyl-CoA, pH 6.5, 25C
0.029
malonyl-ACP
Escherichia coli
-
wild type protein, donor lauroyl-ACP, 0.01 mM lauroyl-ACP, pH 6.5, 25C
0.022 - 0.042
malonyl-CoA
0.023
malonyl-phosphopantetheine-14-mer
Escherichia coli
-
wild type protein, donor lauroyl-CoA, 0.075 mM lauroyl-CoA, pH 6.5, 25C
0.022
malonyl-phosphopantetheine-16-mer
Escherichia coli
-
wild type protein, donor lauroyl-CoA, 0.075 mM lauroyl-CoA, pH 6.5, 25C
0.018
malonyl-phosphopantetheine-8-mer
Escherichia coli
-
wild type protein, donor lauroyl-CoA, 0.075 mM lauroyl-CoA, pH 6.5, 25C
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1
Lauroyl-CoA
Escherichia coli
-
wild type protein, acceptor malonyl-CoA, 0.5 mM malonyl-CoA, pH 6.5, 25C
718
3.8
malonyl-ACP
Escherichia coli
-
wild type protein, donor lauroyl-ACP, 0.01 mM lauroyl-ACP, pH 6.5, 25C
4300
0.083 - 0.83
malonyl-CoA
0.037
malonyl-phosphopantetheine
Escherichia coli
-
wild type protein, donor lauroyl-CoA, 0.075 mM lauroyl-CoA, pH 6.5, 25C
42170
4.2
malonyl-phosphopantetheine-14-mer
Escherichia coli
-
wild type protein, donor lauroyl-CoA, 0.075 mM lauroyl-CoA, pH 6.5, 25C
8946
3.8
malonyl-phosphopantetheine-16-mer
Escherichia coli
-
wild type protein, donor lauroyl-CoA, 0.075 mM lauroyl-CoA, pH 6.5, 25C
8947
0.083
malonyl-phosphopantetheine-8-mer
Escherichia coli
-
wild type protein, donor lauroyl-CoA, 0.075 mM lauroyl-CoA, pH 6.5, 25C
8945
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.000097
dihydroplatensimycin
Escherichia coli
-
IC50: 97 nM
0.000113
platencin
Staphylococcus aureus
-
exhibits a broad-spectrum Gram-positive antibacterial activity through inhibition of fatty acid biosynthesis, targets the two essential proteins, beta-ketoacyl-[acyl carrier protein] synthase II and III, i.e. FabF and FabH, FabF IC50: 113 nM, overview
0.000048 - 0.00029
platensimycin
1.1
thiolactomycin
Escherichia coli
-
binding structure with mutant C163Q, IC50: 1.1 mM
additional information
additional information
Staphylococcus aureus
-
IC50 for platencin is 0.00195 ng/ml, IC50 for platensimycin is 0.00013 ng/ml
-
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
-
development of an elongation assay with FabF and FabH, EC 2.3.1.41
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5.5 - 6.1
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6.8 - 7
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assay at
7.5
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assay at
8.1 - 8.5
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pI VALUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
8.1
KAS2, sequence calculation
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
high KAS2 expression level, especially in cotyledonary stage embryos
Manually annotated by BRENDA team
additional information
KAS2 is expressed in all plant organs, except for roots and hypocotyls
Manually annotated by BRENDA team
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
PDB
SCOP
CATH
ORGANISM
UNIPROT
Bacillus subtilis (strain 168)
Bacillus subtilis (strain 168)
Bacillus subtilis (strain 168)
Bacillus subtilis (strain 168)
Burkholderia vietnamiensis (strain G4 / LMG 22486)
Burkholderia vietnamiensis (strain G4 / LMG 22486)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Neisseria meningitidis (strain alpha14)
Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)
Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)
Rickettsia rickettsii (strain Sheila Smith)
Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
56000
-
gel filtration
76000
-
gel filtration
84000
-
nondenaturing PAGE
85000
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equilibrium sedimentation
87800
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gel filtration
88000
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recombinant enzyme, gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
?
x * 57600, KAS2, sequence calculation
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
crystal structure determination and analysis at 2.6 A resolution
-
hanging drop vapour diffusion method at room temperature, using 27% PEG 8000 as precipitant and buffered at pH 7.5 with 0.1 M HEPES. Crystal structure is determined with the multiple isomorphous replacement method and refined at 2.4 A resolution, space group P3(1)21
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purified recombinant enzyme, sitting drop vapour diffusion method, from 100 mM Caps, pH 10.5, 20% w/v PEG 8000, 200 mM NaCl, and 5 mM C16-CoA, with spermidine-HCl and Foscholine-9 detergent added, X-ray diffraction crystal structure determination and analysis at 2.4-3.0 A resolution, molecular replacement, structure modeling
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hanging drop vapor diffusion method. 1.3 A resolution crystal structure
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hanging-drop vapour-diffusion method
purified recombinant mutant H303A from 20% polyethylene glycol 3350, 0.2 M potassium acetate, X-ray diffraction structure determination and analysis
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purified recombinant wild-type and mutant E383A enzymes, hanging-drop vapour-diffusion method at room temperature, 0.001 ml of protein solution, containing 10 mg/mlprotein in 20 mM Tris-HCl, pH 8.0, 50 mM NaCl, and 10% glycerol, is mixed with 0.001 ml of precipitating solution, containing 0.2 M sodium acetate, 0.1 M Tris-HCl, pH 8.5, and 30% PEG 4000, formation of different crystal forms, X-ray diffraction structure determinations and analysis at 1.3-2.1 A resolution
rod-shaped crystals of the purified enzyme are grown in two weeks by the hanging-drop vapor-diffusion method, 1.54 A resolution, space group P3(1)21, cells dimensions: a = b = 100.8 A, c = 74.7 A
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
43
-
t1/2: 81 min
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
immobilized metal ion affinity chromatography (Ni2+)
recombinant His-tagged enzyme from Escherichia coli by nickel affinity chromatography and gel filtration to near homogeneity
-
recombinant wild-type and mutant His-tagged FabF from Escherichia coli strain BL21(DE3) by nickel affinity chromatography
-
to homogeneity (>9000-fold purification), ion exchange chromatography (CM-Sepharose, HR-DEAE), hydroxyapatite and affinity chromatography (ACP-Sepharose)
-
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
AtKAS2, DNA and amino acid sequence determination and analysis, sequence comparisons, expression pattern, the promoter is active in various tissues, also in the embryo
construction of plasmids pXspFabF(M1) and pXspFabF(M2). The resulting plasmids are transformed into Escherichia coli XL1-Blue competent cells. Subsequently, pXSpFabF(M1) and pXspFabF(M2) isolated from Escherichia coli XL1-Blue cells are transformed into the expression strain Escherichia coli BL21 (DE3)
determined with the multiple isomorphous replacement method and refined at 2.4 A resolution. Hanging drop vapor diffusion method at room temperature, using 27% PEG 8000 as precipitant, buffered at pH 7.5 with 0.1 M HEPES. The crystals grow to a size of 0.5 * 0.3 * 0.2 mm3 within 3 days. The lifetime of these crystals is very limited, they will dissolve within 10 days of their appearance. Addition of 0.1% mercaptoethanol to the reservoir solution significantly increases the life time of the crystals. Space group: P3(1)21 with cell dimensions a = 76.4 A, c = 146.8 A, gamma = 120
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expressed in Arabidopsis thaliana
expressed in Escherichia coli BL21(DE3)
-
expression in Escherichia coli
expression of wild-type and mutant His-tagged FabF in Escherichia coli strain BL21(DE3)
-
gene fabF, subcloning in Escherichia coli strain XL1-Blue, expression in Escherichia coli strain BL21(DE3)
gene fabF1, expression in Escherichia coli strain BL21(DE3), and in strain K1060, a strain that carries an unconditional fabB allele, and in Escherichia coli strain CY242, which carries the same fabB(Ts) allele as strain CY244, but fabF1 fails to complement growth of the temperature sensitive fabB mutant strain CY242 at 42C
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gene mtkasB, expression of His-tagged enzyme in Escherichia coli
-
gene PffabB/Fm, FabB/F is encoded at locus MAL6P1.165, cloning and expression, expression in and complementation of Escherichia coli strain CY244, which is deficient in FabB and FabF, the latter by mutations S220N and G262M
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His-tagged protein expressed in Escherichia coli BL21(DE3)
-
His-tagged protein expressed in Escherichia coli is insoluble and not functional, GFP fusion protein expressed in Arabidopsis thaliana, Arabidopsis plants expressing GFP fusions have elevated levels of arachidic acid (C20:0) and erucic acid (C22:1) at the expense of stearic acid (C18:0) and oleic acid (C18:1)
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His-tagged protein expressed in Escherichia coli pLysS
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Lactococcus lactis FabF can functionally replace both the FabB (EC 2.3.1.41) and FabF (2.3.1.179) proteins of Escherichia coli and the FabH protein of Lactococcus lactis
-
overexpressed in Enterococcus faecalis
-
EXPRESSION
ORGANISM
UNIPROT
LITERATURE
during seed maturation
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
L337F
the point mutation, mutant fab1-1, causes a partially deficient KAS2 activity
C163Q
-
site-directed mutagenesis, interaction with platensimycin compared to the interaction with the wild-type enzyme
R206G
-
R206 impairs the binding of CoA
C164A
-
site-directed mutagenesis, inactive mutant
C164A/H337A
-
site-directed mutagenesis, inactive mutant
C164A/K332A
-
site-directed mutagenesis, inactive mutant
E346A
-
site-directed mutagenesis, the mutant shows similar activity compared to the wild-type enzyme
E383A
crystal structure determination and comparison to the wild-type enzyme, the mutation E383A appears to play a key role in disfavouring the less desirable triclinic crystal form and in generating a new surface for a packing interaction that stabilizes the new crystal form
E396A
-
site-directed mutagenesis, the mutant shows no condensation activity but retains about 50% of wild-type transacylation activity with acyl-ACP and ACP, and 40% of wild-type decarboxylation activity
H303A
-
site-directed mutagenesis, the mutant shows 74% reduced condensation activity, 40% reduced transacylation activity, and 5fold increased decarboxylation activity, compared to the wild-type enzyme
H337A
-
site-directed mutagenesis, inactive mutant
K332A
-
site-directed mutagenesis, the mutant shows no condensation activity but retains about 30% of wild-type transacylation activity with acyl-ACP and ACP, and 10% of wild-type decarboxylation activity
F107I
-
less efficient than wild type protein
F107L
-
less efficient than wild type protein
F107S
-
suggested that the Ser residue has less significant effects than the Ile and Leu mutations
additional information
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
biotechnology
-
modulating KASII activity is sufficient to convert the composition of a temperate seed oil into that of a palm-like tropical oil, overview
drug development
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