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Information on EC 5.1.1.20 - L-Ala-D/L-Glu epimerase and Organism(s) Bacillus subtilis and UniProt Accession O34508

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EC Tree
     5 Isomerases
         5.1 Racemases and epimerases
             5.1.1 Acting on amino acids and derivatives
                5.1.1.20 L-Ala-D/L-Glu epimerase
IUBMB 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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Bacillus subtilis
UNIPROT: O34508
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The taxonomic range for the selected organisms is: Bacillus subtilis
The expected taxonomic range for this enzyme is: Bacteria, Archaea
Synonyms
l-ala-d/l-glu epimerase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
L-Ala-D/L-Glu epimerase
-
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
L-alanyl-D-glutamate = L-alanyl-L-glutamate
show the reaction diagram
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
PATHWAY SOURCE
PATHWAYS
-
-
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.
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
L-Ala-D-Asp
L-Ala-L-Asp
show the reaction diagram
-
-
-
r
L-Ala-D-Glu
L-Ala-L-Glu
show the reaction diagram
L-Ala-D-Met
L-Ala-L-Met
show the reaction diagram
-
-
-
r
L-Ala-L-Asp
L-Ala-D-Asp
show the reaction diagram
-
-
-
r
L-Ala-L-Glu
L-Ala-D-Glu
show the reaction diagram
-
-
-
r
L-Ala-L-Leu
L-Ala-D-Leu
show the reaction diagram
-
-
-
r
L-Ala-L-Met
L-Ala-D-Met
show the reaction diagram
-
-
-
r
L-Ala-L-Ser
L-Ala-D-Ser
show the reaction diagram
-
-
-
r
L-Pro-L-Glu
L-Pro-D-Glu
show the reaction diagram
-
-
-
r
L-Ser-L-Glu
L-Ser-D-Glu
show the reaction diagram
-
-
-
r
L-alanyl-D-glutamate
L-alanyl-L-glutamate
show the reaction diagram
-
-
-
?
additional information
?
-
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
L-Ala-D-Glu
L-Ala-L-Glu
show the reaction diagram
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
-
-
r
L-alanyl-D-glutamate
L-alanyl-L-glutamate
show the reaction diagram
-
-
-
?
additional information
?
-
The kinetic parameters suggest that L-Ala-D/L-Glu is the intrinsic substrate for the enzyme
-
-
?
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.028
L-Ala-D-Asp
pH 8.5, 37°C
0.32
L-Ala-D-Glu
pH 8.5, 37°C
0.51
L-Ala-D-Met
pH 8.5, 37°C
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.053
L-Ala-D-Asp
pH 8.5, 37°C
15
L-Ala-D-Glu
pH 8.5, 37°C
1.1
L-Ala-D-Met
pH 8.5, 37°C
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1.9
L-Ala-D-Asp
pH 8.5, 37°C
47
L-Ala-D-Glu
pH 8.5, 37°C
2.2
L-Ala-D-Met
pH 8.5, 37°C
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
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
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
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
39472
x * 39472, calculated from sequence
39500
x * 39500, electrospray ionization mass spectrometry
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
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
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
crystals are grown by hanging drop methods at room temperature
structure of the complex of L-Ala-L-Glu with the enzyme
crystal structure of YkfB in apoform and in complex with L-Ala-D/L-Glu
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli
gene yfkA or yfkB
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
Manually annotated by BRENDA team
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)
Manually annotated by BRENDA team
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
Manually annotated by BRENDA team
Ogasawara, Y.; Dairi, T.
Peptide epimerization machineries found in microorganisms
Front. Microbiol.
9
156
2018
Bacillus subtilis (O34400), Bacillus subtilis 168 (O34400), Escherichia coli (P51981)
Manually annotated by BRENDA team