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Enzyme Nomenclature
Information on EC 2.3.1.247 - 3-keto-5-aminohexanoate cleavage enzyme
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2.3.1.247 3-keto-5-aminohexanoate cleavage enzymeIUBMB Comments
Requires Zn2+. The enzyme, isolated from the bacteria Fusobacterium nucleatum and Cloacimonas acidaminovorans, is involved in the anaerobic fermentation of lysine.
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The enzyme appears in viruses and cellular organisms
Reaction Schemes
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
3-keto,5-aminohexanoate cleavage enzyme
FN1868
kce
3-keto,5-aminohexanoate cleavage enzyme
Fusobacterium nucleatum subsp. nucleatum ATCC 25586 / JCM14847
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-
kce
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
(5S)-5-amino-3-oxohexanoate + acetyl-CoA = L-3-aminobutanoyl-CoA + acetoacetate
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-
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(5S)-5-amino-3-oxohexanoate + acetyl-CoA = L-3-aminobutanoyl-CoA + acetoacetate
the enzyme shows a catalytic reaction mechanism that proceeds through deprotonation of the 3-keto-5-aminohexanoate substrate, nucleophilic addition onto an incoming acetyl-CoA, intramolecular transfer of the CoA moiety, and final retro-Claisen reaction leading to acetoacetate and 3-aminobutyryl-CoA, structure-function analysis, docking study and molecular modeling, detailed overview. Absence of detection of any covalent acyl-enzyme intermediate
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Claisen condensation
uncommon Claisen-type condensation
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PATHWAY SOURCE
PATHWAYS
BRENDA
KEGG
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SYSTEMATIC NAME
IUBMB Comments
(5S)-5-amino-3-oxohexanoate:acetyl-CoA ethylamine transferase
Requires Zn2+. The enzyme, isolated from the bacteria Fusobacterium nucleatum and Cloacimonas acidaminovorans, is involved in the anaerobic fermentation of lysine.
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
DL-3-aminobutanoyl-CoA + 2-methylacetoacetate
(5S)-5-amino-2-methyl-3-oxohexanoate + acetyl-CoA
(5S)-5-amino-3-oxohexanoate + acetyl-CoA
L-3-aminobutanoyl-CoA + acetoacetate
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-
-
-
r
(5S)-5-amino-3-oxohexanoate + acetyl-CoA
L-3-aminobutanoyl-CoA + acetoacetate
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preferred substrate, the substrate is cleaved between C-2 and C-3 to form C-2 and C-4 moieties
DL-3-aminobutyryl-CoA and acetoacetate are used in the reverse reaction assay
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r
(5S)-5-amino-3-oxohexanoate + acetyl-CoA
L-3-aminobutanoyl-CoA + acetoacetate
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-
-
-
r
(5S)-5-amino-3-oxohexanoate + acetyl-CoA
L-3-aminobutanoyl-CoA + acetoacetate
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preferred substrate, the substrate is cleaved between C-2 and C-3 to form C-2 and C-4 moieties
DL-3-aminobutyryl-CoA and acetoacetate are used in the reverse reaction assay
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r
(5S)-5-amino-3-oxohexanoate + acetyl-CoA
L-3-aminobutanoyl-CoA + acetoacetate
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-
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r
(5S)-5-amino-3-oxohexanoate + acetyl-CoA
L-3-aminobutanoyl-CoA + acetoacetate
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-
-
r
(5S)-5-amino-3-oxohexanoate + acetyl-CoA
L-3-aminobutanoyl-CoA + acetoacetate
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DL-3-aminobutanoyl-CoA and acetoacetate are used in the reverse reaction assay
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r
(5S)-5-amino-3-oxohexanoate + acetyl-CoA
L-3-aminobutanoyl-CoA + acetoacetate
Fusobacterium nucleatum subsp. nucleatum ATCC 25586 / JCM14847
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DL-3-aminobutanoyl-CoA and acetoacetate are used in the reverse reaction assay
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r
(5S)-5-amino-3-oxohexanoate + acetyl-CoA
L-3-aminobutanoyl-CoA + acetoacetate
Fusobacterium nucleatum subsp. nucleatum ATCC 25586 / JCM14847
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r
beta-alanyl-CoA + acetoacetate
?
Fusobacterium nucleatum subsp. nucleatum ATCC 25586 / JCM14847
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r
DL-3-aminobutanoyl-CoA + 2-methylacetoacetate
(5S)-5-amino-2-methyl-3-oxohexanoate + acetyl-CoA
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r
DL-3-aminobutanoyl-CoA + 2-methylacetoacetate
(5S)-5-amino-2-methyl-3-oxohexanoate + acetyl-CoA
Fusobacterium nucleatum subsp. nucleatum ATCC 25586 / JCM14847
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r
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
(5S)-5-amino-3-oxohexanoate + acetyl-CoA
L-3-aminobutanoyl-CoA + acetoacetate
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-
-
-
r
(5S)-5-amino-3-oxohexanoate + acetyl-CoA
L-3-aminobutanoyl-CoA + acetoacetate
-
-
-
-
r
(5S)-5-amino-3-oxohexanoate + acetyl-CoA
L-3-aminobutanoyl-CoA + acetoacetate
-
-
-
r
(5S)-5-amino-3-oxohexanoate + acetyl-CoA
L-3-aminobutanoyl-CoA + acetoacetate
-
-
-
r
(5S)-5-amino-3-oxohexanoate + acetyl-CoA
L-3-aminobutanoyl-CoA + acetoacetate
Fusobacterium nucleatum subsp. nucleatum ATCC 25586 / JCM14847
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-
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r
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Zn2+
dependent on, one metal ion per subunit and active site, coordinated by His46, His48, and Glu230 in the active site. The metal ion is situated at the bottom of a crevice accessible from two opposite openings, one of which is delimited by the mobile beta3-alpha3 loop
additional information
additional information
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no effect on enzyme activity by Co2+ and Mg2+ at 0.1 mM
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
EDTA
activates at low concentrations in the presence of a higher concentration of CoCl2, inhibits at 0.1-1.0 mM by 30%
potassium phosphate
4, 15, 30, 65, and 85% inhibition at 0.2, 0.4, 1.0, 10, and 100 mM, respectively
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
EDTA
activates at low concentrations in the presence of a higher concentration of CoCl2, inhibits at 0.1-1.0 mM by 30%
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
additional information
steady-state kinetic analysis of wild-type and mutant enzymes, overview
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0.208
(5S)-5-amino-3-oxohexanoate
wild-type enzyme, pH and temperature not specified in the publication
0.442
(5S)-5-amino-3-oxohexanoate
mutant E143Q, pH and temperature not specified in the publication
0.921
(5S)-5-amino-3-oxohexanoate
mutant E143G, pH and temperature not specified in the publication
1.181
(5S)-5-amino-3-oxohexanoate
mutant S82G, pH and temperature not specified in the publication
0.012
acetyl-CoA
wild-type enzyme, pH and temperature not specified in the publication
0.012
acetyl-CoA
mutant E143Q, pH and temperature not specified in the publication
0.024
acetyl-CoA
mutant E143G, pH and temperature not specified in the publication
0.046
acetyl-CoA
mutant S82G, pH and temperature not specified in the publication
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.13
(5S)-5-amino-3-oxohexanoate
mutant S82G, pH and temperature not specified in the publication
0.32
(5S)-5-amino-3-oxohexanoate
mutant E143Q, pH and temperature not specified in the publication
0.37
(5S)-5-amino-3-oxohexanoate
mutant E143G, pH and temperature not specified in the publication
2.69
(5S)-5-amino-3-oxohexanoate
wild-type enzyme, pH and temperature not specified in the publication
0.13
acetyl-CoA
mutant S82G, pH and temperature not specified in the publication
0.32
acetyl-CoA
mutant E143Q, pH and temperature not specified in the publication
0.37
acetyl-CoA
mutant E143G, pH and temperature not specified in the publication
2.69
acetyl-CoA
wild-type enzyme, pH and temperature not specified in the publication
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.1
(5S)-5-amino-3-oxohexanoate
mutant S82G, pH and temperature not specified in the publication
0.4
(5S)-5-amino-3-oxohexanoate
mutant E143G, pH and temperature not specified in the publication
0.7
(5S)-5-amino-3-oxohexanoate
mutant E143Q, pH and temperature not specified in the publication
12.9
(5S)-5-amino-3-oxohexanoate
wild-type enzyme, pH and temperature not specified in the publication
2.8
acetyl-CoA
mutant S82G, pH and temperature not specified in the publication
15.4
acetyl-CoA
mutant E143G, pH and temperature not specified in the publication
26.7
acetyl-CoA
mutant E143Q, pH and temperature not specified in the publication
224.2
acetyl-CoA
wild-type enzyme, pH and temperature not specified in the publication
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
5.2 - 8.1
50% of maximal activity at pH 5.2 and pH 8.1
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
Fusobacterium nucleatum subsp. nucleatum ATCC 25586 / JCM14847
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
metabolism
additional information
enzyme structure determination and analysis, the active site is situated in each monomer at the C-terminal face of the central beta-barrel with a metal ion coordinated by His46, His48, and Glu230, overview
evolution
gene cluster organization in putative lysine-fermenting bacteria, overview
evolution
the enzyme is a representative of a large family of prokaryotic hypothetical proteins, annotated as the domain of unknown function DUF849, it shows the ubiquitous triose phosphate isomerase (TIM) barrel fold and a Zn2+ cation reminiscent of metal-dependent class II aldolases
evolution
Fusobacterium nucleatum subsp. nucleatum ATCC 25586 / JCM14847
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gene cluster organization in putative lysine-fermenting bacteria, overview
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metabolism
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C-1 and C-2 of 3-oxo-5-aminohexanoate are converted mainly to acetoacetate and acetate, whereas C-3 to C-6 are converted mainly to 3-hydroxybutyrate or its coenzyme A thiolester. 3-Aminobutyryl-CoA is then deaminated to form crotonyl-CoA. The enzymes observed in extracts of Brevibacterium sp. can account for the conversion of 3,5-diaminohexanoate to acetyl-CoA, overview
metabolism
the enzyme is involved in the anaerobic fermentation of lysine
metabolism
the enzyme is involved in the fermentation pathway of lysine
metabolism
the enzyme is involved in the the 3-keto-5-aminohexanoate pathway of lysine degradation, tracer experiments on acetate and butyrate formation from lysine and acetate, overview
metabolism
Fusobacterium nucleatum subsp. nucleatum ATCC 25586 / JCM14847
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the enzyme is involved in the the 3-keto-5-aminohexanoate pathway of lysine degradation, tracer experiments on acetate and butyrate formation from lysine and acetate, overview
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metabolism
Fusobacterium nucleatum subsp. nucleatum ATCC 25586 / JCM14847
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the enzyme is involved in the fermentation pathway of lysine
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metabolism
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C-1 and C-2 of 3-oxo-5-aminohexanoate are converted mainly to acetoacetate and acetate, whereas C-3 to C-6 are converted mainly to 3-hydroxybutyrate or its coenzyme A thiolester. 3-Aminobutyryl-CoA is then deaminated to form crotonyl-CoA. The enzymes observed in extracts of Brevibacterium sp. can account for the conversion of 3,5-diaminohexanoate to acetyl-CoA, overview
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Show AA Sequence and Transmembrane Helices (417 entries)
Please use the AA Sequence and Transmembrane Helices Search for a specific query.
Please use the AA Sequence and Transmembrane Helices Search for a specific query.
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
30000
4 * 30000, SDS-PAGE, 4 * 31044, sequence calculation
31044
4 * 30000, SDS-PAGE, 4 * 31044, sequence calculation
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
homotetramer
homotetramer
each subunit of 276 residues shows the canonical (beta/alpha)8 TIM barrel fold, with a short additional C-terminal alpha-helix (alpa9) protruding at the N-terminal face of the barrel and three beta-turn extensions coming out from the barrel core, inserted in between beta2 and alpha2 (residues 49-58), beta4 and alpha4 (residues 112-119), and beta8 and alpha8 (residues 234-240)
homotetramer
4 * 30000, SDS-PAGE, 4 * 31044, sequence calculation
homotetramer
Fusobacterium nucleatum subsp. nucleatum ATCC 25586 / JCM14847
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4 * 30000, SDS-PAGE, 4 * 31044, sequence calculation
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
native state enzyme, as well as enzyme complexed with substrate (5S)-5-amino-3-oxohexanoate or product acetoacetate, X-ray diffraction structure determination and analysis at 1.28-1.84 A resolution, molecular replacement
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
D231G
site-directed mutagenesis, inactive mutant
R226G
site-directed mutagenesis, inactive mutant
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
native enzyme 143fold by anion exchange chromatography
native soluble enzyme 78fold by ammonium sulfate fractionation and anion exchange chromatography, followed by ultrafiltration and adsorption chromatography
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recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography, desalting gel filtration, anion exchange chromatography, and gel filtration
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene kce, DNA and amino acid sequence determination and analysis, genetic structure and comparison, recombinant expression of His-tagged enzyme in Escherichia coli strain BL21 DE3
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Barker, H.A.; Kahn, J.M.; Hedrick, L.
Pathway of lysine degradation in Fusobacterium nucleatum
J. Bacteriol.
152
201-207
1982
Fusobacterium nucleatum subsp. nucleatum (Q8RHX2), Fusobacterium nucleatum subsp. nucleatum ATCC 25586 / JCM14847 (Q8RHX2)
brenda
Barker, H.A.; Kahn, J.M.; Chew, S.
Enzymes involved in 3,5-diaminohexanoate degradation by Brevibacterium sp.
J. Bacteriol.
143
1165-1170
1980
Brevibacterium sp., Brevibacterium sp. L5
brenda
Kreimeyer, A.; Perret, A.; Lechaplais, C.; Vallenet, D.; Medigue, C.; Salanoubat, M.; Weissenbach, J.
Identification of the last unknown genes in the fermentation pathway of lysine
J. Biol. Chem.
282
7191-7197
2007
Fusobacterium nucleatum subsp. nucleatum (Q8RHX2), Fusobacterium nucleatum subsp. nucleatum ATCC 25586 / JCM14847 (Q8RHX2)
brenda
Bellinzoni, M.; Bastard, K.; Perret, A.; Zaparucha, A.; Perchat, N.; Vergne, C.; Wagner, T.; de Melo-Minardi, R.C.; Artiguenave, F.; Cohen, G.N.; Weissenbach, J.; Salanoubat, M.; Alzari, P.M.
3-Keto-5-aminohexanoate cleavage enzyme: a common fold for an uncommon Claisen-type condensation
J. Biol. Chem.
286
27399-27405
2011
Candidatus Cloacimonas acidaminovorans (B0VHH0)
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