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Literature summary for 5.1.1.20 extracted from

  • Ogasawara, Y.; Dairi, T.
    Peptide epimerization machineries found in microorganisms (2018), Front. Microbiol., 9, 156 .
    View publication on PubMedView publication on EuropePMC
Search for more literature for 5.1.1.20

Cloned(Commentary)

Cloned (Comment) Organism
gene ycjG Escherichia coli
gene yfkA or yfkB Bacillus subtilis

Crystallization (Commentary)

Crystallization (Comment) Organism
crystal structure of YcjG in apoform Escherichia coli
crystal structure of YkfB in apoform and in complex with L-Ala-D/L-Glu Bacillus subtilis

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
L-alanyl-D-glutamate Escherichia coli
-
 L-alanyl-L-glutamate
-
 ?
L-alanyl-D-glutamate Bacillus subtilis
-
 L-alanyl-L-glutamate
-
 ?
L-alanyl-D-glutamate Bacillus subtilis 168
-
 L-alanyl-L-glutamate
-
 ?
additional information Escherichia coli The kinetic parameters suggest that L-Ala-D/L-Glu is the intrinsic substrate for the enzyme ?
-
 ?
additional information Bacillus subtilis The kinetic parameters suggest that L-Ala-D/L-Glu is the intrinsic substrate for the enzyme ?
-
 ?
additional information Bacillus subtilis 168 The kinetic parameters suggest that L-Ala-D/L-Glu is the intrinsic substrate for the enzyme ?
-
 ?

Organism

Organism UniProt Comment Textmining
Bacillus subtilis O34400
-
-
Bacillus subtilis 168 O34400
-
-
Escherichia coli P51981
-
-

Reaction

Reaction Comment Organism Reaction ID
L-alanyl-D-glutamate = L-alanyl-L-glutamate a two-base reaction mechanism typical for enolase superfamily enzymes, Mg2+-assisted general base-catalyzed abstraction of the alpha-proton of a carboxylic acid and stabilization of an enolate anion intermediate, overview Escherichia coli
a
L-alanyl-D-glutamate = L-alanyl-L-glutamate a two-base reaction mechanism typical for enolase superfamily enzymes, Mg2+-assisted general base-catalyzed abstraction of the alpha-proton of a carboxylic acid and stabilization of an enolate anion intermediate, overview Bacillus subtilis
a

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
L-alanyl-D-glutamate
-
 Escherichia coli L-alanyl-L-glutamate
-
 ?
L-alanyl-D-glutamate
-
 Bacillus subtilis L-alanyl-L-glutamate
-
 ?
L-alanyl-D-glutamate
-
 Bacillus subtilis 168 L-alanyl-L-glutamate
-
 ?
additional information The kinetic parameters suggest that L-Ala-D/L-Glu is the intrinsic substrate for the enzyme Escherichia coli ?
-
 ?
additional information The kinetic parameters suggest that L-Ala-D/L-Glu is the intrinsic substrate for the enzyme Bacillus subtilis ?
-
 ?
additional information epimerization of the L-Glu residue is confirmed by NMR and MS analysis. Analyzing substrate specificity with dipeptides composed of different amino acids, YcjG shows a broad substrate specificity against dipeptides with L-Ala at the N-terminus but narrow specificity against dipeptides with L-Glu at the C-terminus Escherichia coli ?
-
 ?
additional information epimerization of the L-Glu residue is confirmed by NMR and MS analysis. Analyzing substrate specificity with dipeptides composed of different amino acids, YkfB has a narrow substrate specificity against both N- and C-terminal substrates Bacillus subtilis ?
-
 ?
additional information The kinetic parameters suggest that L-Ala-D/L-Glu is the intrinsic substrate for the enzyme Bacillus subtilis 168 ?
-
 ?
additional information epimerization of the L-Glu residue is confirmed by NMR and MS analysis. Analyzing substrate specificity with dipeptides composed of different amino acids, YkfB has a narrow substrate specificity against both N- and C-terminal substrates Bacillus subtilis 168 ?
-
 ?

Subunits

Subunits Comment Organism
More the enzyme structure comprises an N-terminal capping domain and a C-terminal (beta/alpha)7beta-barrel, and the active site is located in the barrel domain. The Mg2+ ion forms a bidentate interaction with the alpha-carbonyl group of the Glu of the substrate and the alpha-carbon center to be epimerized is located between two conserved lysine residues Escherichia coli
More the enzyme structure comprises an N-terminal capping domain and a C-terminal (beta/alpha)7beta-barrel, and the active site is located in the barrel domain. The Mg2+ ion forms a bidentate interaction with the alpha-carbonyl group of the Glu of the substrate and the alpha-carbon center to be epimerized is located between two conserved lysine residues, K162 and K268 in YkfB Bacillus subtilis

Synonyms

Synonyms Comment Organism
L-Ala-D/L-Glu epimerase
-
 Escherichia coli
L-Ala-D/L-Glu epimerase
-
 Bacillus subtilis
YcjG
-
 Escherichia coli
YfkA
-
 Bacillus subtilis
YfkB
-
 Bacillus subtilis

General Information

General Information Comment Organism
evolution the enzyme belongs to the enolase superfamily enzymes. The enzyme reaction shows the common enolase family reaction mechanism: Mg2+-assisted general base-catalyzed abstraction of the alpha-proton of a carboxylic acid and stabilization of an enolate anion intermediate. The fate of the intermediate is determined by the active site of each enzyme to produce the specific product Escherichia coli
evolution the enzyme belongs to the enolase superfamily enzymes. The enzyme reaction shows the common enolase family reaction mechanism: Mg2+-assisted general base-catalyzed abstraction of the alpha-proton of a carboxylic acid and stabilization of an enolate anion intermediate. The fate of the intermediate is determined by the active site of each enzyme to produce the specific product Bacillus subtilis
physiological function YcjG is a L-Ala-D/LGlu epimerases, which converts L-Ala-D-Glu into L-Ala-L-Glu for degradation and recycling of peptidoglycan Escherichia coli
physiological function YfkB is a L-Ala-D/LGlu epimerases, which converts L-Ala-D-Glu into L-Ala-L-Glu for degradation and recycling of peptidoglycan Bacillus subtilis