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Literature summary 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.
    View publication on PubMedView publication on EuropePMC

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
2.3.1.247 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

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

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
2.3.1.247 additional information
-
 additional information steady-state kinetic analysis of wild-type and mutant enzymes, overview Candidatus Cloacimonas acidaminovorans
2.3.1.247 0.012
-
 acetyl-CoA wild-type enzyme, pH and temperature not specified in the publication Candidatus Cloacimonas acidaminovorans
2.3.1.247 0.012
-
 acetyl-CoA mutant E143Q, pH and temperature not specified in the publication Candidatus Cloacimonas acidaminovorans
2.3.1.247 0.024
-
 acetyl-CoA mutant E143G, pH and temperature not specified in the publication Candidatus Cloacimonas acidaminovorans
2.3.1.247 0.046
-
 acetyl-CoA mutant S82G, pH and temperature not specified in the publication Candidatus Cloacimonas acidaminovorans
2.3.1.247 0.208
-
 (5S)-5-amino-3-oxohexanoate wild-type enzyme, pH and temperature not specified in the publication Candidatus Cloacimonas acidaminovorans
2.3.1.247 0.442
-
 (5S)-5-amino-3-oxohexanoate mutant E143Q, pH and temperature not specified in the publication Candidatus Cloacimonas acidaminovorans
2.3.1.247 0.921
-
 (5S)-5-amino-3-oxohexanoate mutant E143G, pH and temperature not specified in the publication Candidatus Cloacimonas acidaminovorans
2.3.1.247 1.181
-
 (5S)-5-amino-3-oxohexanoate mutant S82G, pH and temperature not specified in the publication Candidatus Cloacimonas acidaminovorans

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
2.3.1.247 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)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
2.3.1.247 (5S)-5-amino-3-oxohexanoate + acetyl-CoA Candidatus Cloacimonas acidaminovorans
-
 L-3-aminobutanoyl-CoA + acetoacetate
-
 r

Organism

EC Number Organism UniProt Comment Textmining
2.3.1.247 Candidatus Cloacimonas acidaminovorans B0VHH0
-
-

Reaction

EC Number Reaction Comment Organism Reaction ID
2.3.1.247 (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)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
2.3.1.247 (5S)-5-amino-3-oxohexanoate + acetyl-CoA
-
 Candidatus Cloacimonas acidaminovorans L-3-aminobutanoyl-CoA + acetoacetate
-
 r

Subunits

EC Number Subunits Comment Organism
2.3.1.247 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

EC Number Synonyms Comment Organism
2.3.1.247 kce
-
 Candidatus Cloacimonas acidaminovorans

Turnover Number [1/s]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
2.3.1.247 0.13
-
 acetyl-CoA mutant S82G, pH and temperature not specified in the publication Candidatus Cloacimonas acidaminovorans
2.3.1.247 0.13
-
 (5S)-5-amino-3-oxohexanoate mutant S82G, pH and temperature not specified in the publication Candidatus Cloacimonas acidaminovorans
2.3.1.247 0.32
-
 acetyl-CoA mutant E143Q, pH and temperature not specified in the publication Candidatus Cloacimonas acidaminovorans
2.3.1.247 0.32
-
 (5S)-5-amino-3-oxohexanoate mutant E143Q, pH and temperature not specified in the publication Candidatus Cloacimonas acidaminovorans
2.3.1.247 0.37
-
 acetyl-CoA mutant E143G, pH and temperature not specified in the publication Candidatus Cloacimonas acidaminovorans
2.3.1.247 0.37
-
 (5S)-5-amino-3-oxohexanoate mutant E143G, pH and temperature not specified in the publication Candidatus Cloacimonas acidaminovorans
2.3.1.247 2.69
-
 acetyl-CoA wild-type enzyme, pH and temperature not specified in the publication Candidatus Cloacimonas acidaminovorans
2.3.1.247 2.69
-
 (5S)-5-amino-3-oxohexanoate wild-type enzyme, pH and temperature not specified in the publication Candidatus Cloacimonas acidaminovorans

General Information

EC Number General Information Comment Organism
2.3.1.247 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
2.3.1.247 metabolism the enzyme is involved in the anaerobic fermentation of lysine Candidatus Cloacimonas acidaminovorans
2.3.1.247 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]

EC Number kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
2.3.1.247 0.1
-
 (5S)-5-amino-3-oxohexanoate mutant S82G, pH and temperature not specified in the publication Candidatus Cloacimonas acidaminovorans
2.3.1.247 0.4
-
 (5S)-5-amino-3-oxohexanoate mutant E143G, pH and temperature not specified in the publication Candidatus Cloacimonas acidaminovorans
2.3.1.247 0.7
-
 (5S)-5-amino-3-oxohexanoate mutant E143Q, pH and temperature not specified in the publication Candidatus Cloacimonas acidaminovorans
2.3.1.247 2.8
-
 acetyl-CoA mutant S82G, pH and temperature not specified in the publication Candidatus Cloacimonas acidaminovorans
2.3.1.247 12.9
-
 (5S)-5-amino-3-oxohexanoate wild-type enzyme, pH and temperature not specified in the publication Candidatus Cloacimonas acidaminovorans
2.3.1.247 15.4
-
 acetyl-CoA mutant E143G, pH and temperature not specified in the publication Candidatus Cloacimonas acidaminovorans
2.3.1.247 26.7
-
 acetyl-CoA mutant E143Q, pH and temperature not specified in the publication Candidatus Cloacimonas acidaminovorans
2.3.1.247 224.2
-
 acetyl-CoA wild-type enzyme, pH and temperature not specified in the publication Candidatus Cloacimonas acidaminovorans