Information on EC 2.3.1.47 - 8-amino-7-oxononanoate synthase

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

EC NUMBER
COMMENTARY hide
2.3.1.47
-
RECOMMENDED NAME
GeneOntology No.
8-amino-7-oxononanoate synthase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
pimeloyl-[acyl-carrier protein] + L-alanine = 8-amino-7-oxononanoate + CO2 + holo-[acyl-carrier protein]
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Acyl group transfer
-
-
-
-
Claisen condensation
-
-
condensation
decarboxylation
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
8-amino-7-oxononanoate biosynthesis I
-
-
8-amino-7-oxononanoate biosynthesis II
-
-
8-amino-7-oxononanoate biosynthesis III
-
-
biotin biosynthesis
-
-
Biotin metabolism
-
-
Metabolic pathways
-
-
Microbial metabolism in diverse environments
-
-
SYSTEMATIC NAME
IUBMB Comments
6-carboxyhexanoyl-[acyl-carrier protein]:L-alanine C-carboxyhexanoyltransferase (decarboxylating)
A pyridoxal-phosphate protein. The enzyme catalyses the decarboxylative condensation of L-alanine and pimeloyl-[acyl-carrier protein], a key step in the pathway for biotin biosynthesis. Pimeloyl-CoA can be used with lower efficiency [5].
CAS REGISTRY NUMBER
COMMENTARY hide
9075-61-0
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
Erwinia aroidea
-
-
-
Manually annotated by BRENDA team
C268
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
strain IFO 3525
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
Sporobolomyces coprophilus
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
(R)-8-amino-7-oxononanoic acid + S-adenosyl-L-methionine
(7R,8S)-diaminopelargonic acid + S-adenosyl-(4-methylthio-2-oxobutanoic acid)
show the reaction diagram
-
8.6% product is formed matching the portion of S-enantiomer substrate (9.3%),37C, direct assay with 100 mM N-(2-hydroxyethyl)piperazine-N'-(2-propanesulfonic acid) buffer (pH 8.6), 0.1 mM pyridoxal 5'-phosphate, 1 mM S-adenosyl-L-methionine, 10 microM (R)-8-amino-7-oxononanoic acid
-
-
?
(S)-8-amino-7-oxononanoic acid + (R)-8-amino-7-oxononanoic acid + S-adenosyl-L-methionine
(7R,8S)-diaminopelargonic acid + S-adenosyl-(4-methylthio-2-oxobutanoic acid)
show the reaction diagram
-
46.3% product is formed from the racemic substrate, 37C, direct assay with 100 mM N-(2-hydroxyethyl)piperazine-N'-(2-propanesulfonic acid) buffer (pH 8.6), 0.1 mM pyridoxal 5'-phosphate, 1 mM S-adenosyl-L-methionine, 2 microM racemic 8-amino-7-oxononanoic acid
-
-
?
(S)-8-amino-7-oxononanoic acid + S-adenosyl-L-methionine
(7R,8S)-diaminopelargonic acid + S-adenosyl-(4-methylthio-2-oxobutanoic acid)
show the reaction diagram
6-carboxyhexanoyl-CoA + D-alanine
8-amino-7-oxononanoate + CoA + CO2
show the reaction diagram
-
the L-isomer of the amino acid is preferred, D-alanine shows 5fold slower reaction, interaction analysis, overview
i.e. D-KAPA
-
?
6-carboxyhexanoyl-CoA + L-alanine
8-amino-7-oxononanoate + CoA + CO2
show the reaction diagram
6-carboxyhexanoyl-CoA + L-serine
9-hydroxy-8-amino-7-oxononanoate + CoA
show the reaction diagram
-
low activity
-
?
glycine + acetyl-CoA
?
show the reaction diagram
glycine + pimeloyl-CoA
?
show the reaction diagram
L-alanine + acetyl-CoA
?
show the reaction diagram
L-alanine + pimeloyl-CoA
8-amino-7-oxononanoate + CoA + CO2
show the reaction diagram
pimeloyl-CoA + D-alanine
?
show the reaction diagram
-
-
-
-
?
pimeloyl-CoA + L-alanine
8-amino-7-oxononanoate + CoA + CO2
show the reaction diagram
pimeloyl-CoA + L-alanine
?
show the reaction diagram
-
-
-
-
?
pimeloyl-CoA + L-alanine methyl ester
?
show the reaction diagram
-
trapping and determination of the reaction intermediate using the the more stable methyl ester of the substrate, overview
-
-
?
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
(S)-8-amino-7-oxononanoic acid + S-adenosyl-L-methionine
(7R,8S)-diaminopelargonic acid + S-adenosyl-(4-methylthio-2-oxobutanoic acid)
show the reaction diagram
6-carboxyhexanoyl-CoA + L-alanine
8-amino-7-oxononanoate + CoA + CO2
show the reaction diagram
pimeloyl-CoA + L-alanine
8-amino-7-oxononanoate + CoA + CO2
show the reaction diagram
Q8GW43
-
-
-
?
additional information
?
-
Q8GW43
the enzyme catalyzes the first committed enzyme of the biotin synthesis pathway
-
-
-
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
pyridoxal 5'-phosphate
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
(R)-8-amino-7-oxononanoic acid
1,10-phenanthroline
-
to some extent
2,3-dichloronaphthalene-1,4-dione
-
-
2-(furan-2-yl)-1H-benzimidazole
-
-
2-amino-3-hydroxy-2-methylnonadioic acid
-
competitive, transition state analogue
2-[(1,1,2,2-tetrachloroethyl)sulfanyl]-3a,4,7,7a-tetrahydro-1H-isoindole-1,3(2H)-dione
-
-
2-[(trichloromethyl)sulfanyl]-3a,4,7,7a-tetrahydro-1H-isoindole-1,3(2H)-dione
-
-
4-(1H-inden-3-yl)naphthalene-1,2-dione
-
-
4-carboxybutyl(1-amino-1-carboxyethyl)phosphonate
-
competitive, transition state analogue
5,10-dioxo-5,10-dihydronaphtho[2,3-b][1,4]dithiine-2,3-dicarbonitrile
-
-
5,8-dihydronaphthalene-1,4-dione
-
-
5,8-dihydroxynaphthalene-1,4-dione
-
-
5-hydroxy-2-methylnaphthalene-1,4-dione
-
-
5-hydroxynaphthalene-1,4-dione
-
-
8-amino-7-oxo-8-phosphonononanoic acid
-
strong inhibition
8-Amino-7-oxononanoate
-
product inhibition in vivo
8-amino-7-oxooctanoic acid
-
achiral analog of substrate, strong inhibitor of both enzyme forms, binding to active site
biotin
citrate
-
to some extent
D-alanine
D-cycloserine
-
-
D-KAPA
-
product inhibition
D-penicillamine
-
L-enantiomer not as effective
D/L-histidine
diisopropyl fluorophosphate
-
to some extent
glycine
hydroxylamine
-
-
isoniazide
-
to some extent
L-cysteine
L-serine
methyl 3-(5,6-dioxo-5,6-dihydronaphthalen-2-yl)propanoate
-
-
methyl 3-[8-(1H-inden-3-yl)-5,6-dioxo-5,6-dihydronaphthalen-2-yl]propanoate
-
-
methyl 3-[8-[(4-fluorophenyl)amino]-5,6-dioxo-5,6-dihydronaphthalen-2-yl]propanoate
-
-
methyl 3-[8-[(4-methylphenyl)amino]-5,6-dioxo-5,6-dihydronaphthalen-2-yl]propanoate
-
-
N-[dichloro(fluoro)-l4-sulfanyl]-N',N'-dimethyl-N-phenylsulfuric diamide
-
-
N-[dichloro(fluoromethyl)-lambda4-sulfanyl]-N',N'-dimethyl-N-(4-methylphenyl)sulfuric diamide
-
-
naphthalene-1,2-dione
-
-
phenylhydrazine
-
-
pyridoxal 5'-phosphate
-
high concentrations
Pyruvic acid
-
-
Semicarbazide
-
-
trifluoroalanine
-
binding structure, irreversible suicide inhibition of the enzyme, involves decarboxylative defluorination of the inhibitor-PLP aldimine followed by attack of the conjugated imine by the amino group of the active site lysine to afford a covalently bound difluorinated intermediate, which can subsequently undergo further HF losses and hydrolysis to afford a 2-(pyridoximine phosphate) acetoyl protein adduct
triphenyltin acetate
-
herbicidal activity (foliar treatment) under greenhouse conditions
additional information
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
biotin
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0013
(S)-8-amino-7-oxononanoic acid
-
calculated from the competitive and uncompetitive constants and the substrate concentration determined in inhibitor experiments, 37C, pH 8.6
0.2015
D-alanine
-
pH 7.7, 25C, recombinant enzyme, with pimeloyl-CoA
0.002 - 3
L-alanine
0.001 - 0.07
pimeloyl-CoA
0.0014
S-adenosyl-L-methionine
-
calculated from the competitive and uncompetitive constants and the substrate concentration determined in inhibitor experiments, 37C, pH 8.6
additional information
additional information
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0036
D-alanine
Mycobacterium tuberculosis
-
pH 7.7, 25C, recombinant enzyme, with pimeloyl-CoA
0.007 - 0.11
L-alanine
0.000833 - 0.5
pimeloyl-CoA
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.014 - 7.33
L-alanine
1.5 - 213
pimeloyl-CoA
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0017 - 0.0162
(R)-8-amino-7-oxononanoic acid
0.08
2-amino-3-hydroxy-2-methylnonadioic acid
-
-
0.068
4-carboxybutyl(1-amino-1-carboxyethyl)phosphonate
-
-
0.007
8-amino-7-oxo-8-phosphonononanoic acid
-
-
0.0009 - 0.0152
8-amino-7-oxooctanoic acid
0.59 - 1.24
D-alanine
3.75
D-histidine
-
-
0.115
D-KAPA
-
pH 7.7, 25C, recombinant enzyme
0.99
L-cysteine
-
-
5.6
L-histidine
-
-
additional information
additional information
-
dimethyl-8-amino-7-oxooctanoic acid, an achiral substrate analogue, does not inhibit the enzyme
-
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.011
2,3-dichloronaphthalene-1,4-dione
Arabidopsis thaliana
-
pH 7.5, 30C
0.042
2-(furan-2-yl)-1H-benzimidazole
Arabidopsis thaliana
-
pH 7.5, 30C
0.056
2-[(1,1,2,2-tetrachloroethyl)sulfanyl]-3a,4,7,7a-tetrahydro-1H-isoindole-1,3(2H)-dione
Arabidopsis thaliana
-
pH 7.5, 30C
0.054
2-[(trichloromethyl)sulfanyl]-3a,4,7,7a-tetrahydro-1H-isoindole-1,3(2H)-dione
Arabidopsis thaliana
-
pH 7.5, 30C
0.0013
4-(1H-inden-3-yl)naphthalene-1,2-dione
Arabidopsis thaliana
-
pH 7.5, 30C
0.011
5,10-dioxo-5,10-dihydronaphtho[2,3-b][1,4]dithiine-2,3-dicarbonitrile
Arabidopsis thaliana
-
pH 7.5, 30C
0.0044
5,8-dihydronaphthalene-1,4-dione
0.0021
5-hydroxy-2-methylnaphthalene-1,4-dione
Arabidopsis thaliana
-
pH 7.5, 30C
0.0096
5-hydroxynaphthalene-1,4-dione
Arabidopsis thaliana
-
pH 7.5, 30C
0.0044
methyl 3-(5,6-dioxo-5,6-dihydronaphthalen-2-yl)propanoate
Arabidopsis thaliana
-
pH 7.5, 30C
0.0011
methyl 3-[8-(1H-inden-3-yl)-5,6-dioxo-5,6-dihydronaphthalen-2-yl]propanoate
Arabidopsis thaliana
-
pH 7.5, 30C
0.00063
methyl 3-[8-[(4-fluorophenyl)amino]-5,6-dioxo-5,6-dihydronaphthalen-2-yl]propanoate
Arabidopsis thaliana
-
pH 7.5, 30C
0.00059
methyl 3-[8-[(4-methylphenyl)amino]-5,6-dioxo-5,6-dihydronaphthalen-2-yl]propanoate
Arabidopsis thaliana
-
pH 7.5, 30C
0.041
N-[dichloro(fluoro)-l4-sulfanyl]-N',N'-dimethyl-N-phenylsulfuric diamide
Arabidopsis thaliana
-
pH 7.5, 30C
0.047
N-[dichloro(fluoromethyl)-lambda4-sulfanyl]-N',N'-dimethyl-N-(4-methylphenyl)sulfuric diamide
Arabidopsis thaliana
-
pH 7.5, 30C
0.0033
naphthalene-1,2-dione
Arabidopsis thaliana
-
pH 7.5, 30C
0.01985
triphenyltin acetate
Arabidopsis thaliana
-
pH 7.5, 37C
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.00225
-
partially purified enzyme
0.032
-
glycine, pimeloyl-CoA, pH 6.0, 60C
0.071
-
L-alanine, pimeloyl-CoA, pH 6.0, 60C
0.078
-
L-alanine, pimeloyl-CoA, pH 6.0, 60C
0.09 - 0.1
purified recombinant enzyme
0.272
-
L-alanine, acetyl-CoA, pH 6.0, 60C
0.897
-
glycine, acetyl-CoA, pH 6.0, 60C
2.46
-
L-alanine, pimeloyl-CoA, pH 6.0, 60C
additional information
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6.3 - 7.6
-
-
6.5 - 7.5
-
about half-maximal activity at pH 6.5 and pH 7.5
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
45 - 65
-
about half-maximal activity at 45C and 65C
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
-
expressed in most tissue
Manually annotated by BRENDA team
-
expressed in most tissue
Manually annotated by BRENDA team
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
PDB
SCOP
CATH
ORGANISM
UNIPROT
Burkholderia xenovorans (strain LB400)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4)
Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
41600
-
calculated from nucleotide sequence
41740
-
electrospray mass spectrometry, holoenzyme
46000
-
gel filtration
50000
recombinant His-tagged enzyme, gel filtration
additional information
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
homodimer
-
2 x 40000, SDS-PAGE
monomer
additional information
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
enzyme in complex with inhibitor trifluoroalanine, soaking of holo-enzyme crystals in a solution containing 10 mM L-trifluoroalanine and 10 mM pyridoxal-5'-phosphate in crystallization buffer containing 1.6 M ammonium sulfate and 200 mM 1,3-bis[tris(hydroxymethyl)methylamino]propane at pH 8.5, and rapidly frozen in liquid nitrogen, X-ray diffraction structure determination and analysis at 1.99 A resolution
-
Mg2+ added for structure analysis of the holoenzyme; pH 8.5-8.9, ammonium sulfate precipitation, apoenzyme, X-ray diffraction structure analysis with and without bound pyridoxyl-5'-phosphate, model, active site residues
-
pH 8.5-8.9, ammonium sulfate precipitation, apoenzyme, X-ray diffraction structure analysis with and without bound pyridoxyl-5'-phosphate, model, active site residues
-
pyridoxal-5'-phosphate-bound form, pH 7.5, precipitation with polyethylene glycol, 0.2 M (NH4)2SO4 , x-ray diffraction structure analysis
-
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
40
-
stable for one h
55
-
stable for one h
60
-
and below, stable
65
-
stable for one h
75
-
stable for one h
80
-
and above, inactivation
93
-
stable for one h
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
EDTA stabilizes during purification
-
freeze-thawing inactivates
-
proteinase inhibitors, e.g. PMSF, pepstatin A, stabilize during purification
-
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20C, 0.01 M phosphate buffer, pH 7.0, 5 mM 2-mercaptoethanol, 5 months
-
0C, several months
-
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
from Escherichia coli DH5alpha, ammonium sulfate fractionation, gel filtration, hydrophobic interaction chromatography, ion exchange chromatography
-
Glutathione Sepharose chromatography, GST-tag cleavage, Glutathione Sepharose chromatography
-
Glutathione Sepharose chromatography, GST-tag cleavage, Glutathione Sepharose chromatography, gel filtration
-
Glutathione Sepharose chromatography, GST-tag cleavage, Glutathione Sepharose chromatography, heat treatment with centrifugation
-
Glutathione Sepharose chromatography, GST-tag cleavage, Glutathione Sepharose chromatography, ion exchange chromatography
immobilized metal ion affinity chromatography (Ni2+), His-tag cleavage, immobilized metal ion affinity chromatography (Ni2+), gel filtration
-
maltose binding protein affinity chromatography
-
native enzyme partially by subcellular fractionation, recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography and gel filtration
partial; recombinant from E. coli overproducing strain
-
recombinant from E. coli
-
recombinant from E. coli overproducing strain
-
recombinant from overexpressing E. coli strain HMS174 (DE3)
-
recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affiinity chromatography and gel filtration to homogeneity
-
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
bioF gene overexpression in Escherichia coli
-
bioF gene, expression in strain HMS174 (DE3)
-
expressed in overproducing Escherichia coli strain C268/pTG3401
-
gene bioF, DNA and amino acid sequence determination and analysis, overexpression of His-tagged enzyme in Escherichia coli strain BL21(DE3)
gene Rv1569, overexpression of His-tagged enzyme in Escherichia coli strain BL21(DE3)
-
GST-fusion protein expressed in Escherichia coli JM109
His-tagged protein and murine 5-aminolevulinate synthase-fusion protein (single chain chimeric dimer) expressed in Escherichia coli HU227, R872 and DH5alpha
-
His-tagged protein expressed in Escherichia coli Rosetta-gami (DE3)
-
histidine-tagged enzyme is expressed in Escherichia coli C268
improved overexpression in Escherichia coli bioF- strain R874
-
maltose binding protein fusion protein expressed in Escherichia coli BL21-Gold(DE3)
-
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
K236A
-
active site lysine involved in the Schiff base linkage with the PLP cofactor
additional information
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
agriculture
-
possible target for design of inhibitors as herbicides and antibacterial agents
medicine
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