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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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Word Map
The enzyme appears in viruses and cellular organisms
Synonyms
AE epimerase, AEE, L-Ala-D/L-Glu epimerase, YcjG, YfkA, YfkB, YkfB, 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
AEE
L-Ala-D/L-Glu epimerase
YcjG
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
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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
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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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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
O34508
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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O34400
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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O34400
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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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
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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
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
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the enzyme is involved in the recycling of the murein peptide, of which L-Ala-D-Glu is a component
physiological function
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the enzyme is involved in the recycling of the murein peptide, of which L-Ala-D-Glu is a component
physiological function
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the enzyme participates in murein peptide metabolism
physiological function
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the enzyme participates in murein peptide metabolism
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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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
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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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UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
Sequence
AEEP_BACTN
Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482)
383
0
42168
Swiss-Prot
AEEP_CLOAB
Clostridium acetobutylicum (strain ATCC 824 / DSM 792 / JCM 1419 / LMG 5710 / VKM B-1787)
358
0
38905
Swiss-Prot
AEEP_FRATN
Francisella tularensis subsp. novicida (strain U112)
356
0
39122
Swiss-Prot
AEEP_THEMA
Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
345
0
38664
Swiss-Prot
A0A4Z9EG07_SALET
321
0
34602
TrEMBL
A0A4Z8YF42_SALET
321
0
34622
TrEMBL
A0A4Y6PFE9_SALAN
321
0
34606
TrEMBL
A0A501BCT6_SALET
321
0
34636
TrEMBL
A0A4Z9HQA1_SALET
321
0
34694
TrEMBL
A0A2S6U4D4_9PROT
192
0
20806
TrEMBL
A0A4Y6N2C3_SALET
321
0
34648
TrEMBL
A0A2S6UG59_9PROT
139
0
14393
TrEMBL
A0A500F8G7_SALET
321
0
34620
TrEMBL
A0A2S6UL53_9PROT
358
0
37694
TrEMBL
A0A399FEC7_9DEIN
358
0
39579
TrEMBL
A0A501XS82_9SPHN
328
0
34250
TrEMBL
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PDB
SCOP
CATH
UNIPROT
ORGANISM
Bacillus subtilis (strain 168)
Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482)
Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482)
Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482)
Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482)
Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
monomer
additional information
?
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x * 39472, calculated from sequence; x * 39500, electrospray ionization mass spectrometry
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x * 34955, calculated from sequence; x * 34994, electrospray ionization mass spectrometry
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
-
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 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
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
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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, Bacillus subtilis (O34508), Escherichia coli, Escherichia coli (P51981)
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, Bacillus subtilis (O34508)
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 168 (O34400), Bacillus subtilis (O34400), Escherichia coli (P51981)
brenda
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