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Enzyme Nomenclature
Information on EC 5.1.1.20 - L-Ala-D/L-Glu epimerase
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5.1.1.20 L-Ala-D/L-Glu epimeraseIUBMB Comments
The enzyme, characterized from the bacteria Escherichia coli and Bacillus subtilis, is involved in the recycling of the murein peptide, of which L-Ala-D-Glu is a component. In vitro the enzyme from Escherichia coli epimerizes several L-Ala-L-X dipeptides with broader specificity than the enzyme from Bacillus subtilis.
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The expected taxonomic range for this enzyme is: Bacteria, Archaea
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
AEE
L-Ala-D/L-Glu epimerase
YfkA
YfkB
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
L-alanyl-D-glutamate = L-alanyl-L-glutamate
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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
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
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
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PATHWAY SOURCE
PATHWAYS
MetaCyc
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SYSTEMATIC NAME
IUBMB Comments
L-alanyl-D-glutamate epimerase
The enzyme, characterized from the bacteria Escherichia coli and Bacillus subtilis, is involved in the recycling of the murein peptide, of which L-Ala-D-Glu is a component. In vitro the enzyme from Escherichia coli epimerizes several L-Ala-L-X dipeptides with broader specificity than the enzyme from Bacillus subtilis.
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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
L-Ala-L-His
L-Ala-D-His
L-Ala-L-His is epimerized by YcjG at pH 8 but not at pH 6
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r
L-Ala-D-Glu
L-Ala-L-Glu
the enzyme is involved in the recycling of the murein peptide, of which L-Ala-D-Glu is a component. The murein hydrolases degrade peptidoglycan to the final dipeptide L-Ala-D-Glu. If L-Ala-D-Glu is epimerized to L-Ala-L-Glu, hydrolysis can occur with bacterial dipeptidases
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r
additional information
?
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no activity with L-Ala-L-Arg, L-Ala-L-Lys, L-Ala-L-Pro, L-Glu-L-Glu, L-Lys-L-Glu, L-Pro-L-Glu, L-Lys-L-Ala, or D-Ala-D-Ala
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?
additional information
?
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no activity with L-Ala-L-Arg, L-Ala-L-Lys, L-Ala-L-Pro, L-Glu-L-Glu, L-Lys-L-Glu, L-Pro-L-Glu, L-Lys-L-Ala, or D-Ala-D-Ala
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?
additional information
?
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The kinetic parameters suggest that L-Ala-D/L-Glu is the intrinsic substrate for the enzyme
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?
additional information
?
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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
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?
additional information
?
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The kinetic parameters suggest that L-Ala-D/L-Glu is the intrinsic substrate for the enzyme
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?
additional information
?
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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
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?
additional information
?
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no activity with L-Ala-L-Arg, L-Ala-L-Lys, L-Ala-L-Pro, L-Glu-L-Glu, L-Lys-L-Glu, L-Pro-L-Glu, L-Lys-L-Ala, or D-Ala-D-Ala
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?
additional information
?
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no activity with L-Ala-L-Arg, L-Ala-L-Lys, L-Ala-L-Pro, L-Glu-L-Glu, L-Lys-L-Glu, L-Pro-L-Glu, L-Lys-L-Ala, or D-Ala-D-Ala
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?
additional information
?
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The kinetic parameters suggest that L-Ala-D/L-Glu is the intrinsic substrate for the enzyme
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?
additional information
?
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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
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?
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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
L-Ala-D-Glu
L-Ala-L-Glu
the enzyme is involved in the recycling of the murein peptide, of which L-Ala-D-Glu is a component. The murein hydrolases degrade peptidoglycan to the final dipeptide L-Ala-D-Glu. If L-Ala-D-Glu is epimerized to L-Ala-L-Glu, hydrolysis can occur with bacterial dipeptidases
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r
additional information
?
-
The kinetic parameters suggest that L-Ala-D/L-Glu is the intrinsic substrate for the enzyme
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?
additional information
?
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The kinetic parameters suggest that L-Ala-D/L-Glu is the intrinsic substrate for the enzyme
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?
additional information
?
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The kinetic parameters suggest that L-Ala-D/L-Glu is the intrinsic substrate for the enzyme
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?
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
8.5
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
37
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
physiological function
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
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
evolution
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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
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physiological function
the enzyme is involved in the recycling of the murein peptide, of which L-Ala-D-Glu is a component
physiological function
the enzyme is involved in the recycling of the murein peptide, of which L-Ala-D-Glu is a component
physiological function
the enzyme participates in murein peptide metabolism
physiological function
the enzyme participates in murein peptide metabolism
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
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
physiological function
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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
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Show AA Sequence and Transmembrane Helices (261 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
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
monomer
additional information
additional information
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
additional information
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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
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additional information
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
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
crystal structure of YkfB in apoform and in complex with L-Ala-D/L-Glu
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
D297G
I19A/D297G
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the mutant enzyme shows o-succinylbenzoate synthase activity. Substitutions for Ile19 increases the growth rate relative to that for the D297G progenitor
I19C/D297G
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the mutant enzyme shows o-succinylbenzoate synthase activity. Substitutions for Ile19 increases the growth rate relative to that for the D297G progenitor
I19F/D297G
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the mutant enzyme shows o-succinylbenzoate synthase activity. Substitutions for Ile19 increases the growth rate relative to that for the D297G progenitor
I19L/D297G
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the mutant enzyme shows o-succinylbenzoate synthase activity. Substitutions for Ile19 increases the growth rate relative to that for the D297G progenitor
I19N/D297G
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the mutant enzyme shows o-succinylbenzoate synthase activity. Substitutions for Ile19 increases the growth rate relative to that for the D297G progenitor
I19S/D297G
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the mutant enzyme shows o-succinylbenzoate synthase activity. Substitutions for Ile19 increases the growth rate relative to that for the D297G progenitor
I19T/D297G
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the mutant enzyme shows o-succinylbenzoate synthase activity. Substitutions for Ile19 increases the growth rate relative to that for the D297G progenitor
I19V/D297G
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the mutant enzyme shows o-succinylbenzoate synthase activity. Substitutions for Ile19 increases the growth rate relative to that for the D297G progenitor
I19W/D297G
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the mutant enzyme shows o-succinylbenzoate synthase activity. Substitutions for Ile19 increases the growth rate relative to that for the D297G progenitor
I19Y/D297G
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the mutant enzyme shows o-succinylbenzoate synthase activity. Substitutions for Ile19 increases the growth rate relative to that for the D297G progenitor
D297G
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the mutant enzyme shows o-succinylbenzoate synthase activity at low level that is sufficient to permit anaerobic growth by an o-succinylbenzoate synthase-deficient strain of Escherichia coli, wild-type enzyme show
D297G
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the mutation is located at the end of the eighth beta-strand of the (beta/alpha)8-barrel. The mutant enzyme has no detectable muconate lactonizing activity. The mutant enzyme catalyzes the o-succinylbenzoate synthase reaction
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Schmidt, D.M.; Hubbard, B.K.; Gerlt, J.A.
Evolution of enzymatic activities in the enolase superfamily: functional assignment of unknown proteins in Bacillus subtilis and Escherichia coli as L-Ala-D/L-Glu epimerases
Biochemistry
40
15707-15715
2001
Bacillus subtilis (O34508), Bacillus subtilis, Escherichia coli (P51981), Escherichia coli
brenda
Gulick, A.M.; Schmidt, D.M.; Gerlt, J.A.; Rayment, I.
Evolution of enzymatic activities in the enolase superfamily: crystal structures of the L-Ala-D/L-Glu epimerases from Escherichia coli and Bacillus subtilis
Biochemistry
40
15716-15724
2001
Bacillus subtilis (O34508), Escherichia coli (P51981)
brenda
Schmidt, D.M.; Mundorff, E.C.; Dojka, M.; Bermudez, E.; Ness, J.E.; Govindarajan, S.; Babbitt, P.C.; Minshull, J.; Gerlt, J.A.
Evolutionary potential of (beta/alpha)8-barrels: functional promiscuity produced by single substitutions in the enolase superfamily
Biochemistry
42
8387-8393
2003
Escherichia coli
brenda
Klenchin, V.A.; Schmidt, D.M.; Gerlt, J.A.; Rayment, I.
Evolution of enzymatic activities in the enolase superfamily: structure of a substrate-liganded complex of the L-Ala-D/L-Glu epimerase from Bacillus subtilis
Biochemistry
43
10370-10378
2004
Bacillus subtilis (O34508), Bacillus subtilis
brenda
Vick, J.E.; Schmidt, D.M.; Gerlt, J.A.
Evolutionary potential of (beta/alpha)8-barrels: in vitro enhancement of a "new" reaction in the enolase superfamily
Biochemistry
44
11722-11729
2005
Escherichia coli
brenda
Ogasawara, Y.; Dairi, T.
Peptide epimerization machineries found in microorganisms
Front. Microbiol.
9
156
2018
Bacillus subtilis (O34400), Escherichia coli (P51981), Bacillus subtilis 168 (O34400)
brenda
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