Literature summary for 2.3.1.247 extracted from

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 (2011), J. Biol. Chem., 286, 27399-27405.

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Crystallization (Commentary)

Crystallization (Comment)	Organism
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	Candidatus Cloacimonas acidaminovorans

Protein Variants

Protein Variants	Comment	Organism
D231G	site-directed mutagenesis, inactive mutant	Candidatus Cloacimonas acidaminovorans
E143G	site-directed mutagenesis	Candidatus Cloacimonas acidaminovorans
E143Q	site-directed mutagenesis	Candidatus Cloacimonas acidaminovorans
R226G	site-directed mutagenesis, inactive mutant	Candidatus Cloacimonas acidaminovorans
S82G	site-directed mutagenesis	Candidatus Cloacimonas acidaminovorans

KM Value [mM]

KM Value [mM]	KM Value Maximum [mM]	Substrate	Comment	Organism	Structure
additional information	-	additional information	steady-state kinetic analysis of wild-type and mutant enzymes, overview	Candidatus Cloacimonas acidaminovorans
0.012	-	acetyl-CoA	wild-type enzyme, pH and temperature not specified in the publication	Candidatus Cloacimonas acidaminovorans
0.012	-	acetyl-CoA	mutant E143Q, pH and temperature not specified in the publication	Candidatus Cloacimonas acidaminovorans
0.024	-	acetyl-CoA	mutant E143G, pH and temperature not specified in the publication	Candidatus Cloacimonas acidaminovorans
0.046	-	acetyl-CoA	mutant S82G, pH and temperature not specified in the publication	Candidatus Cloacimonas acidaminovorans
0.208	-	(5S)-5-amino-3-oxohexanoate	wild-type enzyme, pH and temperature not specified in the publication	Candidatus Cloacimonas acidaminovorans
0.442	-	(5S)-5-amino-3-oxohexanoate	mutant E143Q, pH and temperature not specified in the publication	Candidatus Cloacimonas acidaminovorans
0.921	-	(5S)-5-amino-3-oxohexanoate	mutant E143G, pH and temperature not specified in the publication	Candidatus Cloacimonas acidaminovorans
1.181	-	(5S)-5-amino-3-oxohexanoate	mutant S82G, pH and temperature not specified in the publication	Candidatus Cloacimonas acidaminovorans

Metals/Ions

Metals/Ions	Comment	Organism	Structure
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	Candidatus Cloacimonas acidaminovorans

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.	Reac.
(5S)-5-amino-3-oxohexanoate + acetyl-CoA	Candidatus Cloacimonas acidaminovorans	-	L-3-aminobutanoyl-CoA + acetoacetate	-	r

Organism

Organism	UniProt	Comment	Textmining
Candidatus Cloacimonas acidaminovorans	B0VHH0	-	-

Reaction

Reaction	Comment	Organism	Reaction ID
(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	Candidatus Cloacimonas acidaminovorans	a

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
(5S)-5-amino-3-oxohexanoate + acetyl-CoA	-	Candidatus Cloacimonas acidaminovorans	L-3-aminobutanoyl-CoA + acetoacetate	-	r

Subunits

Subunits	Comment	Organism
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)	Candidatus Cloacimonas acidaminovorans

Synonyms

Synonyms	Comment	Organism
kce	-	Candidatus Cloacimonas acidaminovorans

Turnover Number [1/s]

Turnover Number Minimum [1/s]	Turnover Number Maximum [1/s]	Substrate	Comment	Organism	Structure
0.13	-	acetyl-CoA	mutant S82G, pH and temperature not specified in the publication	Candidatus Cloacimonas acidaminovorans
0.13	-	(5S)-5-amino-3-oxohexanoate	mutant S82G, pH and temperature not specified in the publication	Candidatus Cloacimonas acidaminovorans
0.32	-	acetyl-CoA	mutant E143Q, pH and temperature not specified in the publication	Candidatus Cloacimonas acidaminovorans
0.32	-	(5S)-5-amino-3-oxohexanoate	mutant E143Q, pH and temperature not specified in the publication	Candidatus Cloacimonas acidaminovorans
0.37	-	acetyl-CoA	mutant E143G, pH and temperature not specified in the publication	Candidatus Cloacimonas acidaminovorans
0.37	-	(5S)-5-amino-3-oxohexanoate	mutant E143G, pH and temperature not specified in the publication	Candidatus Cloacimonas acidaminovorans
2.69	-	acetyl-CoA	wild-type enzyme, pH and temperature not specified in the publication	Candidatus Cloacimonas acidaminovorans
2.69	-	(5S)-5-amino-3-oxohexanoate	wild-type enzyme, pH and temperature not specified in the publication	Candidatus Cloacimonas acidaminovorans

General Information

General Information	Comment	Organism
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	Candidatus Cloacimonas acidaminovorans
metabolism	the enzyme is involved in the anaerobic fermentation of lysine	Candidatus Cloacimonas acidaminovorans
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	Candidatus Cloacimonas acidaminovorans

kcat/KM [mM/s]

kcat/KM Value [1/mMs^-1]	kcat/KM Value Maximum [1/mMs^-1]	Substrate	Comment	Organism	Structure
0.1	-	(5S)-5-amino-3-oxohexanoate	mutant S82G, pH and temperature not specified in the publication	Candidatus Cloacimonas acidaminovorans
0.4	-	(5S)-5-amino-3-oxohexanoate	mutant E143G, pH and temperature not specified in the publication	Candidatus Cloacimonas acidaminovorans
0.7	-	(5S)-5-amino-3-oxohexanoate	mutant E143Q, pH and temperature not specified in the publication	Candidatus Cloacimonas acidaminovorans
2.8	-	acetyl-CoA	mutant S82G, pH and temperature not specified in the publication	Candidatus Cloacimonas acidaminovorans
12.9	-	(5S)-5-amino-3-oxohexanoate	wild-type enzyme, pH and temperature not specified in the publication	Candidatus Cloacimonas acidaminovorans
15.4	-	acetyl-CoA	mutant E143G, pH and temperature not specified in the publication	Candidatus Cloacimonas acidaminovorans
26.7	-	acetyl-CoA	mutant E143Q, pH and temperature not specified in the publication	Candidatus Cloacimonas acidaminovorans
224.2	-	acetyl-CoA	wild-type enzyme, pH and temperature not specified in the publication	Candidatus Cloacimonas acidaminovorans

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Release 2023.1 (January 2023)