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Information on EC 2.3.1.47 - 8-amino-7-oxononanoate synthase and Organism(s) Escherichia coli and UniProt Accession P12998

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IUBMB Comments
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 .
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This record set is specific for:
Escherichia coli
UNIPROT: P12998
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Word Map
The taxonomic range for the selected organisms is: Escherichia coli
The enzyme appears in selected viruses and cellular organisms
Synonyms
dapa at, 8-amino-7-oxononanoate synthase, 7,8-diaminopelargonic acid aminotransferase, 8-amino-7-oxopelargonate synthase, kapas, kapa synthase, 7-keto-8-aminopelargonic acid synthase, biof protein, 7-keto-8-aminopelargonic acid synthetase, atbiof, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7-keto-8-aminopelargonate synthase
-
8-amino-7-oxononanoate synthase
-
AON synthase
-
7,8-diaminopelargonic acid aminotransferase
-
-
7-KAP synthetase
-
-
7-keto-8-aminopelargonate synthetase
-
-
-
-
7-keto-8-aminopelargonic acid synthase
-
-
7-keto-8-aminopelargonic acid synthetase
-
-
-
-
7-keto-8-aminopelargonic synthetase
-
-
-
-
7-oxo-8-aminononanoate synthase
-
-
-
-
8-amino-7-oxononanoate synthase
-
-
8-amino-7-oxopelargonate synthase
-
-
-
-
bioF protein
-
-
DAPA AT
-
-
KAPA synthetase
-
-
synthase, 7-oxo-8-aminononanoate
-
-
-
-
synthetase, 7-keto-8-aminopelargonate
-
-
-
-
additional information
-
the enzyme is a member of the alpha-oxoamine synthase enzyme family
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 mechanism
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
decarboxylation
-
condensation
-
Claisen condensation
-
decarboxylation
-
-
condensation
-
-
Acyl group transfer
-
-
-
-
PATHWAY SOURCE
PATHWAYS
-
-, -, -, -
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
-
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
6-carboxyhexanoyl-CoA + L-alanine
8-amino-7-oxononanoate + CoA + CO2
show the reaction diagram
L-alanine + pimeloyl-CoA
8-amino-7-oxononanoate + CoA + CO2
show the reaction diagram
-
-
-
?
pimeloyl-CoA + L-alanine
8-amino-7-oxononanoate + CO2 + CoA
show the reaction diagram
-
-
-
?
pimeloyl-[acyl carrier protein] + L-alanine
8-amino-7-oxononanoate + CO2 + [acyl carrier protein]
show the reaction diagram
-
-
-
?
(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
-
37°C, direct assay with 100 mM N-(2-hydroxyethyl)piperazine-N'-(2-propanesulfonic acid) buffer (pH 8.6), 0.1 mM pyridoxal 5'-phosphate, varying S-adenosyl-L-methionine, 9 microM (S)-8-amino-7-oxononanoic acid, varying inhibitor concentration
-
-
?
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
-
?
L-alanine + pimeloyl-CoA
8-amino-7-oxononanoate + CoA + CO2
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
-
-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
6-carboxyhexanoyl-CoA + L-alanine
8-amino-7-oxononanoate + CoA + CO2
show the reaction diagram
(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
-
37°C, direct assay with 100 mM N-(2-hydroxyethyl)piperazine-N'-(2-propanesulfonic acid) buffer (pH 8.6), 0.1 mM pyridoxal 5'-phosphate, varying S-adenosyl-L-methionine, 9 microM (S)-8-amino-7-oxononanoic acid, varying inhibitor concentration
-
-
?
6-carboxyhexanoyl-CoA + L-alanine
8-amino-7-oxononanoate + CoA + CO2
show the reaction diagram
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
pyridoxal 5'-phosphate
pyridoxal 5'-phosphate
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
(R)-8-amino-7-oxononanoic acid
-
no inhibition up to 15 microM with 94.6% ee (S)-enantiomer as substrate, beyond that strong inhibitor of both enzyme forms, binding to active site
8-Amino-7-oxononanoate
-
product inhibition in vivo
D/L-histidine
-
-
L-cysteine
-
-
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
additional information
-
concentration above 10 mM of Ca2+, Mg2+, and Mn2+ cause slow precipitation of the enzyme
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.25 - 0.5
L-alanine
0.01 - 0.025
pimeloyl-CoA
0.5 - 0.9
L-alanine
0.025 - 0.07
pimeloyl-CoA
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.028 - 0.06
L-alanine
0.000833 - 0.001
pimeloyl-CoA
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.11 - 0.12
L-alanine
2.33 - 2.67
pimeloyl-CoA
2.4
pimeloyl-CoA
-
pH not specified in the publication, temperature not specified in the publication
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0033 - 0.0153
(R)-8-amino-7-oxononanoic acid
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7
-
assay at
7.5
-
assay at
additional information
-
pI: 7.0
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6.3 - 7.6
-
-
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
37
-
assay at
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
41600
-
calculated from nucleotide sequence
41690
-
1 * 41690, native enzyme with bound cofactor, mass spectrometry
41740
-
electrospray mass spectrometry, holoenzyme
44000
-
x * 44000, SDS-PAGE
additional information
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
homodimer
2 x 40000, SDS-PAGE
?
-
x * 44000, SDS-PAGE
dimer
-
2 * ?
monomer
-
1 * 41690, native enzyme with bound cofactor, mass spectrometry
additional information
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
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
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
-
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
K236A
active site lysine involved in the Schiff base linkage with the PLP cofactor
additional information
-
natural mutants with altered enzyme activity
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
40
-
stable for one h
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
from Escherichia coli DH5alpha, ammonium sulfate fractionation, gel filtration, hydrophobic interaction chromatography, ion exchange chromatography
Ni-NTA column chromatography
recombinant from E. coli
Glutathione Sepharose chromatography, GST-tag cleavage, Glutathione Sepharose chromatography, ion exchange chromatography
-
recombinant from E. coli
-
recombinant from overexpressing E. coli strain HMS174 (DE3)
-
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
bioF gene overexpression in Escherichia coli
expressed in Escherichia coli BL21(DE3) cells
His-tagged protein and murine 5-aminolevulinate synthase-fusion protein (single chain chimeric dimer) expressed in Escherichia coli HU227, R872 and DH5alpha
bioF gene overexpression in Escherichia coli
-
bioF gene, expression in strain HMS174 (DE3)
-
GST-fusion protein expressed in Escherichia coli JM109
-
histidine-tagged enzyme is expressed in Escherichia coli C268
-
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
medicine
-
enzyme is a potential target for antimycobacterial drugs
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Eidenberg, M.A.; Star, C.
Synthesis of 7-oxo-8-aminopelargonic acid, a biotin vitamer, in cell-free extracts of Escherichia coli biotin auxotrophs
J. Bacteriol.
96
1291-1297
1968
Escherichia coli
Manually annotated by BRENDA team
Otsuka, A.J.; Buoncristiani, M.R.; Howard, P.K.; Flamm, J.; Johnson, C.; Yamamoto, R.; Uchida, K.; Cook, C.; Ruppert, J.; Matsuzaki, J.
The Escherichia coli biotin biosynthetic enzyme sequences predicted from the nucleotide sequence of the bio operon
J. Biol. Chem.
263
19577-19585
1988
Escherichia coli
Manually annotated by BRENDA team
Izumi, Y.; Sato, K.; Tani, Y.; Ogata, K.
Distribution of 7-keto-8-aminopelargonic acid synthetase in bacteria and the control mechanism of the enzyme activity
Agric. Biol. Chem.
37
1335-1340
1973
Alcaligenes faecalis, Bacillus subtilis, Citrobacter freundii, Enterobacter cloacae, Erwinia aroidea, Escherichia coli, Klebsiella aerogenes, Kocuria rosea, Lysinibacillus sphaericus, Pseudomonas fluorescens
-
Manually annotated by BRENDA team
Webster, S.P.; Campopiano, D.J.; Alexeev, D.; Alexeeva, M.; Watt, R.M.; Sawyer, L.; Baxter, R.L.
Characterization of 8-amino-7-oxononanoate synthase: a bacterial PLP-dependent, acyl CoA condensing enzyme
Biochem. Soc. Trans.
26
S268
1998
Lysinibacillus sphaericus, Escherichia coli
Manually annotated by BRENDA team
Alexeev, D.; Alexeeva, M.; Baxter, R.L.; Campopiano, D.J.; Webster, S.P.; Sawyer, L.
The crystal structure of 8-amino-7-oxononanoate synthase: a bacterial PLP-dependent, acyl-CoA-condensing enzyme
J. Mol. Biol.
284
401-419
1998
Escherichia coli (P12998), Escherichia coli
Manually annotated by BRENDA team
Webster, S.P.; Alexeev, D.; Campopiano, D.J.; Watt, R.M.; Alexeeva, M.; Sawyer, L.; Baxter, R.L.
Mechanism of 8-amino-7-oxononanoate synthase: spectroscopic, kinetic, and crystallographic studies
Biochemistry
39
516-528
2000
Escherichia coli
Manually annotated by BRENDA team
Kerbarh, O.; Campopiano, D.J.; Baxter, R.L.
Mechanism of alpha-oxoamine synthases: identification of the intermediate Claisen product in the 8-amino-7-oxononanoate synthase reaction
Chem. Commun. (Camb. )
2006
60-62
2006
Escherichia coli
Manually annotated by BRENDA team
Alexeev, D.; Baxter, R.L.; Campopiano, D.J.; Kerbarh, O.; Sawyer, L.; Tomczyk, N.; Watt, R.; Webster, S.P.
Suicide inhibition of alpha-oxamine synthases: structures of the covalent adducts of 8-amino-7-oxononanoate synthase with trifluoroalanine
Org. Biomol. Chem.
4
1209-1212
2006
Escherichia coli
Manually annotated by BRENDA team
Mann, S.; Colliandre, L.; Labesse, G.; Ploux, O.
Inhibition of 7,8-diaminopelargonic acid aminotransferase from Mycobacterium tuberculosis by chiral and achiral anologs of its substrate: biological implications
Biochimie
91
826-834
2009
Escherichia coli, Escherichia coli C268, Mycobacterium tuberculosis
Manually annotated by BRENDA team
Turbeville, T.D.; Zhang, J.; Adams, W.C.; Hunter, G.A.; Ferreira, G.C.
Functional asymmetry for the active sites of linked 5-aminolevulinate synthase and 8-amino-7-oxononanoate synthase
Arch. Biochem. Biophys.
511
107-117
2011
Escherichia coli (P12998)
Manually annotated by BRENDA team
Kubota, T.; Izumi, Y.
Detection and characterization of a thermophilic biotin biosynthetic enzyme, 7-keto-8-aminopelargonic acid synthase, from various thermophiles
Biosci. Biotechnol. Biochem.
76
685-690
2012
Acetivibrio thermocellus, Acetivibrio thermocellus ATCC 27405, Aquifex aeolicus, Escherichia coli, Geobacillus kaustophilus, Geobacillus kaustophilus JCM 12893, Symbiobacterium thermophilum, Symbiobacterium thermophilum IAM14863, Thermosynechococcus vestitus
Manually annotated by BRENDA team
Manandhar, M.; Cronan, J.E.
A Canonical biotin synthesis enzyme, 8-amino-7-oxononanoate synthase (BioF), utilizes different acyl chain donors in Bacillus subtilis and Escherichia coli
Appl. Environ. Microbiol.
84
e02084-17
2018
Bacillus subtilis (P53556), Bacillus subtilis, Bacillus subtilis 168 (P53556), Escherichia coli (P12998), Escherichia coli
Manually annotated by BRENDA team