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Enzyme Nomenclature
Information on EC 5.1.2.2 - mandelate racemase
for references in articles please use BRENDA:EC5.1.2.2
Word Map on EC 5.1.2.2
- 5.1.2.2
- s-mandelate
-
kenyon
-
alpha-proton
- muconate
-
gerlt
-
1,1-proton
- benzohydroxamate
-
petsko
-
kozarich
- galactarate
- benzoylformate
- d-glucarate
-
fujita
-
ransom
- mitra
- synthesis
- biotechnology
- analysis
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The expected taxonomic range for this enzyme is: Pseudomonas
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EC NUMBER 
COMMENTARY 
5.1.2.2
-
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RECOMMENDED NAME
GeneOntology No.
mandelate racemase
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
(S)-mandelate = (R)-mandelate
one-base acceptor mechanism, functional asymmetry at the active site
-
(S)-mandelate = (R)-mandelate
His297 and Asp270 function together as a catalytic dyad
(S)-mandelate = (R)-mandelate
enzyme does not catalyze an intermolecular proton transfer to achieve racemization. The enzyme operates via a one-acceptor mechanism, in which the proton abstracted from one stereochemical face of a substrate molecule is returned to the opposite face of the same carbon of the substrate molecule
-
(S)-mandelate = (R)-mandelate
pathway involving a carbanion intermediate
-
(S)-mandelate = (R)-mandelate
reaction proceeds via a two-base mechanism in which Lys166 abstracts the alpha-proton from (S)-mandelate and His297 abstracts the alpha-proton from (R)-mandelate; the enzyme contains two distinct general acid/base catalysts: Lys166 which abstracts the alpha-proton from (S)-mandelate, and His297, which abstracts the alpha-proton from (R)-mandelate
-
(S)-mandelate = (R)-mandelate
two-base mechanism in which the conjugate acid of the R-specific base is monoprotic and in which the S-specific base may be an amino group
-
(S)-mandelate = (R)-mandelate
importance of beta,gamma-unsaturation in promoting facile racemization of the substrate alpha-proton
-
-
-
(S)-mandelate = (R)-mandelate
one pot enantioconvergent synthesis of R-mandelic acid ester from racemic mandelic acid is achieved by a novel aqueous/organic two-phase system with two-enzyme process consisting of (1) lipase-catalyzed enantioselective esterification of racemic mandelic acid in organic solvent and (2) in situ racemization of unreacted isomer, S-mandelic acid in aqueous phase by recombinant mandelate racemase
-
(S)-mandelate = (R)-mandelate
enzyme does not catalyze an intermolecular proton transfer to achieve racemization. The enzyme operates via a one-acceptor mechanism, in which the proton abstracted from one stereochemical face of a substrate molecule is returned to the opposite face of the same carbon of the substrate molecule
-
-
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
racemization
racemization
-
-
-
-
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
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SYSTEMATIC NAME
IUBMB Comments
mandelate racemase
-
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CAS REGISTRY NUMBER
COMMENTARY
9024-04-8
-
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
285168, 285169, 285170, 285172, 285173, 285174, 285175, 285176, 285179, 285181, 285184, 285187, 285188, 285189, 285190, 285191, 285192, 285193, 285194, 285195, 3649, 4814, 650147, 661344, 661581, 672613, 677136
-
-
-
Uniprot
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
physiological function
-
enzyme catalyzes the Mg2+-dependent 1,1-proton transfer that interconverts the enantiomers of mandelate
additional information
additional information
-
the enzyme's 20s loop likely undergoes a significant conformational change upon binding (R)-mandelate
additional information
-
development and evaluation of a virtual mutant screening method based on the binding energy in the transition state, the method is beneficial in enzyme rational redesign and helps to better understand the catalytic properties of the enzyme, and it is effective in predicting the trend of mutational effects on catalysis, molecular dynamic simulation, overview
additional information
-
significance of Ser139 in mandelate racemization, the active site residue S139 forms a hydrogen bond with one carboxyl oxygen of the substrate mandelate, residues S139 and E317 of mandelate racemase have a synergistic effect on transition state stabilization, overview
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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
(2R)-2-(4-bromophenyl)-2-hydroxyacetamide
?
-
22% of the activity with (R)-mandelate
-
-
?
(2R)-2-furyl(hydroxy)acetic acid
?
-
24% of the activity with (R)-mandelate
-
-
?
(2R)-2-hydroxy-2-phenylacetamide
?
-
15% of the activity with (R)-mandelate
-
-
?
(2R)-2-hydroxy-3-(1-H-imidazol-1-yl)propanoic acid
?
-
5.4% of the activity with (R)-mandelate
-
-
?
(2R)-2-hydroxypentanoic acid
?
-
1% of the activity with (R)-mandelate
-
-
?
(2R)-2-naphthylglycolate
(2S)-2-naphthylglycolate
-
a non-natural substrate
-
-
?
(2R)-3-furyl(hydroxy)acetic acid
?
-
38% of the activity with (R)-mandelate
-
-
?
(2R)-cyclohex-1-en-1-yl(hydroxy)acetic acid
?
-
50% of the activity with (R)-mandelate
-
-
?
(2R)-hydroxy(2-naphthyl)acetic acid
?
-
26% of the activity with (R)-mandelate
-
-
?
(2S)-hydroxy(2-thienyl)acetic acid
?
-
59% of the activity with (R)-mandelate
-
-
?
(R)-(E)-2-hydroxy-3-pentenoic acid
?
-
36% of the activity with (R)-mandelate
-
-
?
(R)-(E)-2-hydroxy-4-phenyl-3-butenoic acid
?
-
53% of the activity with (R)-mandelate
-
-
?
(R)-3-chloromandelate
(S)-3-chloromandelate
-
a non-natural substrate
-
-
?
(S)-mandelic acid amide
(R)-mandelic acid amide
-
activity is enhanced by an electron-withdrawing substituent in the phenyl moiety
-
?
(S)-vinylglycolate
(R)-vinylglycolate
-
two-step quite symmetric process through a dianionic enolic intermediate that is formed after the abstraction of the alpha-protein of vinylglycolate by a basic enzymatic residue and is then reprotonated by another residue
-
?
2-hydroxybut-3-enoic acid
?
-
35% of the activity with (R)-mandelate
-
-
?
4-bromo-(R)-mandelate
4-bromo-(S)-mandelate
-
376% of the activity with (R)-mandelate
-
-
r
4-chloro-(R)-mandelate
4-chloro-(S)-mandelate
-
326% of the activity with (R)-mandelate
-
-
r
4-fluoro-(R)-mandelate
4-fluoro-(S)-mandelate
-
96% of the activity with (R)-mandelate
-
-
r
4-hydroxy-(R)-mandelate
4-hydroxy-(S)-mandelate
-
45% of the activity with (R)-mandelate
-
-
r
4-methoxy-(R)-mandelate
4-methoxy-(S)-mandelate
-
17% of the activity with (R)-mandelate
-
-
r
5-chloro-(R)-mandelate
5-chloro-(S)-mandelate
-
61% of the activity with (R)-mandelate
-
-
r
(R)-mandelate
(S)-mandelate
-
wild-type enzyme shows slightly higher affinity for (S)-mandelate than for (R)-mandelate, but catalyzes the turnover of (R)-mandelate slightly more rapidly
-
-
r
(S)-2-hydroxy-3-butenoic acid
(R)-2-hydroxy-3-butenoic acid
-
maximal racemization rate is 35% relative to mandelate
-
-
(S)-mandelate
(R)-mandelate
-
catalyzes the Mg2+-dependent 1,1-proton transfer that interconverts the enantiomers, catalysis is done via a two-base mechanism
-
-
r
D-mandelate
L-mandelate
-
strictly inducible enzyme. Inducers: D-mandelate, L-mandelate, benzoylformate
-
-
-
D-mandelate
L-mandelate
-
first enzyme in the bacterial pathway that converts mandelic acid to benzoic acid
-
-
-
D-mandelate
L-mandelate
-
first enzyme of pathway of oxidation of D,L-mandelate that permits certain strains of Pseudomonas putida to use mandelate as a sole source of carbon and energy
-
-
-
p-(bromomethyl)mandelate
p-(methyl)benzoylformate + Br-
-
-
i.e. alpha-carboxy-alpha-hydroxy-p-xylylene
-
additional information
?
-
-
not racemized: 4-hydroxy-3-methoxymandelate, 3,4-dihydroxymandelate
-
-
-
additional information
?
-
-
efficient racemization of 2-hydroxy-2-heteroaryl-acetic acid derivatives. Steric limitations for aryl-substituted mandelate derivatives are elucidated to be particularly striking for o-substituents, whereas m- and p-analogues are freely accepted as well as heteroaryl and naphthyl analogs. The electronic character of substituents is found to play an important role: whereas electron-withdrawing substituents dramatically enhance the racemization rates, electron-donating analogs cause a depletion
-
?
additional information
?
-
-
no activity with phenyl glycine and mandelic acid hydrazide
-
?
additional information
?
-
-
mandelate racemase catalyzes the Mg2+-dependent 1,1-proton transfer that interconverts the enantiomers of mandelate
-
-
-
additional information
?
-
-
substrate recognition and binding method, overview. Mandelate racemase from Pseudomonas putida catalyzes the interconversion of the enantiomers of mandelic acid and a variety of aryl- and heteroaryl-substituted mandelate derivatives. beta,gamma-Unsaturation is not an absolute requirement for catalysis and that mandelate racemase can bind and catalyze the racemization of (S)- and (R)-trifluorolactate. The enzyme catalyzes hydrogen-deuterium exchange at the alpha-postion of trifluorolactate
-
-
-
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NATURAL SUBSTRATES
NATURAL PRODUCTS
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
(S)-mandelate
(R)-mandelate
-
catalyzes the Mg2+-dependent 1,1-proton transfer that interconverts the enantiomers, catalysis is done via a two-base mechanism
-
-
r
D-mandelate
L-mandelate
-
strictly inducible enzyme. Inducers: D-mandelate, L-mandelate, benzoylformate
-
-
-
D-mandelate
L-mandelate
-
first enzyme in the bacterial pathway that converts mandelic acid to benzoic acid
-
-
-
D-mandelate
L-mandelate
-
first enzyme of pathway of oxidation of D,L-mandelate that permits certain strains of Pseudomonas putida to use mandelate as a sole source of carbon and energy
-
-
-
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Co2+
Divalent metal ions
Fe2+
-
absolute requirement for a divalent metal ion: Mg2+, Mn2+, Ni2+, Co2+ or Fe2+
Mg2+
Mn2+
Ni2+
Co2+
-
absolute requirement for a divalent metal ion; Mg2+, Mn2+, Ni2+, Co2+ or Fe2+ satisfy the divalent metal ion requirement
Divalent metal ions
-
increase the affinity of the enzyme for the substrate. No absolute requirement
Divalent metal ions
-
the required divalent metal ion is ligated by the carboxyl groups of Asp195, Glu221, and Glu247, which emanate from the carboxy-terminal ends of strands 3, 4 and 5, respectively
Mg2+
-
absolute requirement for a divalent metal ion; Mg2+, Mn2+, Ni2+, Co2+ or Fe2+ satisfy the divalent metal ion requirement
Mg2+
-
Km: 0.65 mM for wild-type enzyme and 0.34 mM for mutant enzyme N197A
Mn2+
-
absolute requirement for a divalent metal ion; Mg2+, Mn2+, Ni2+, Co2+ or Fe2+ satisfy the divalent metal ion requirement
Mn2+
-
enzyme binds 0.9 mol Mn2+ per mol of subunit with a dissociation constant of 0.008 mM. Also six additional Mn2+ bind to the enzyme much more weakly, with a dissociation constant of 1.5 mM
Ni2+
-
absolute requirement for a divalent metal ion; Mg2+, Mn2+, Ni2+, Co2+ or Fe2+ satisfy the divalent metal ion requirement
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INHIBITORS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
(R,S)-2,2,2-trifluoro-1-hydroxyethylphosphonate
-
transition state analogue inhibitor
3,3,3-trifluoro-2-hydroxy-2-(trifluoromethyl)-propanoate
-
a substrate-product analogue and a potent competitive inhibitor with both (R)-mandelate and (R)-trifluorolactate. The inhibitor exhibits a different binding mode with the two trifluoromethyl groups closely packed against the 20s loop and the carboxylate bridging the two active site Broensted acid-base catalysts Lys166 and His297
N-hydroxyformanilide
-
potent competitive inhibitor, MR can bind either the protonated or deprotonated forms of N-hydroxyformanilide, with a 10fold greater affinity for the latter form
(R,S)-alpha-hydroxybenzylphosphonate
-
transition state analogue inhibitor
benzohydroxamate
-
a reasonable mimic of the transition state and/or intermediate that chelates the active site divalent metal ion and is bound in a conformation with the phenyl ring coplanar with the hydroxamate moiety, active site binding, structure comparison with bound Cupferron, overview
Cupferron
-
a reasonable mimic of the transition state and/or intermediate that chelates the active site divalent metal ion and is bound in a conformation with the phenyl ring coplanar with the diazeniumdiolate moiety, active site binding, structure comparison with bound benzohydroxamate, overview
DL-alpha-Phenylglycidate
-
binds at the active site of the enzyme, complete and irreversible inhibition in presence of Mg2+. Both D- and L-mandelate protect from inactivation
EDTA
-
activity is fully restored upon addition of certain divalent metal ions. Mg2+ is the most effective, followed by Co2+, Ni2+, Mn2+ and Fe2+
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
Sucrose
-
slight activating effect of sucrose on mutant enzyme efficiency. In presence of polymeric viscosogens poly(ethylene glycol) and Ficoll, no effect on turnover number or the ratio of turnover number and Km-value for the wild-type enzyme is observed
Sucrose
-
higher viscosity by addition of up to 35% sucrose elevates the enzyme activity
additional information
-
the activity of the enzyme immobilized through ionic binding onto DEAE- and TEAE-cellulose is significantly enhanced as compared to the native protein, i.e. 2.7fold and 2.5fold
-
additional information
-
activation of mandelate racemase via immobilization in lyotropic liquid crystals for biocatalysis in organic solvents: application and modeling
-
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
additional information
-
Michaelis-Menten kinetics
-
3.5
(2R)-2-naphthylglycolate
-
pH 7.5, 25°C, wild-type enzyme, in presence of 20 mM MgCl2
1.9
(R)-2-naphthylglycolate
-
mutant A25V, pH 7.5, 25°C; mutant V22A, pH 7.5, 25°C
3.5
(R)-2-naphthylglycolate
-
wild-type, pH 7.5, 25°C, presence of 20 mM Mg2+
3.7
(R)-2-naphthylglycolate
-
mutant V22I/V29L, pH 7.5, 25°C, presence of 20 mM Mg2+
4.2
(R)-2-naphthylglycolate
-
mutant V22I, pH 7.5, 25°C, presence of 20 mM Mg2+
1.9
(R)-2-naphtylglyconate
-
pH 7.5 at 25°C, 3.3 mM Mg2+, mutant A25V; pH 7.5 at 25°C, 3.3 mM Mg2+, mutant V22A
3.7
(R)-2-naphtylglyconate
-
pH 7.5 at 25°C, 3.3 mM Mg2+, mutant V22I/V29L
4.4
(R)-2-naphtylglyconate
-
pH 7.5 at 25°C, 3.3 mM Mg2+, mutant V26A/V29L
0.9
(R)-mandelate
-
mutant V29F, pH 7.5, 25°C; pH 7.5 at 25°C, 3.3 mM Mg2+, mutant V29F
0.91
(R)-mandelate
-
mutant V26A, pH 7.5, 25°C; pH 7.5 at 25°C, 3.3 mM Mg2+, mutant V26A
1.1
(R)-mandelate
-
mutant A25V, pH 7.5, 25°C; pH 7.5 at 25°C, 3.3 mM Mg2+, mutant A25V
1.2
(R)-mandelate
-
pH 7.5 at 25°C, 3.3 mM Mg2+, wild-type; wild-type, pH 7.5, 25°C
1.4
(R)-mandelate
-
mutant V26A/V29L, pH 7.5, 25°C; pH 7.5 at 25°C, 3.3 mM Mg2+, mutant V26A/V29L
1.47
(R)-mandelate
-
pH 7.5 at 25°C, 20 mM Mg2+, wild-type; wild-type, pH 7.5, 25°C, presence of 20 mM Mg2+
1.7
(R)-mandelate
-
mutant V26L, pH 7.5, 25°C; mutant V29L, pH 7.5, 25°C; pH 7.5 at 25°C, 3.3 mM Mg2+, mutant V26L; pH 7.5 at 25°C, 3.3 mM Mg2+, mutant V29L
1.8
(R)-mandelate
-
mutant V26F, pH 7.5, 25°C; pH 7.5 at 25°C, 3.3 mM Mg2+, mutant V26F
2.8
(R)-mandelate
-
mutant T24S, pH 7.5, 25°C; mutant V22I/V29L, pH 7.5, 25°C, presence of 20 mM Mg2+; pH 7.5 at 25°C, 3.3 mM Mg2+, mutant T24S; pH 7.5 at 25°C, 3.3 mM Mg2+, mutant V22I/V29L
2.9
(R)-mandelate
-
mutant V22I, pH 7.5, 25°C, presence of 20 mM Mg2+; pH 7.5 at 25°C, 3.3 mM Mg2+, mutant V22I
4.4
(R)-mandelate
-
mutant V22A, pH 7.5, 25°C; mutant V22F, pH 7.5, 25°C; pH 7.5 at 25°C, 3.3 mM Mg2+, mutant V22A; pH 7.5 at 25°C, 3.3 mM Mg2+, mutant V22F
5
(R)-mandelate
-
mutant V29A, pH 7.5, 25°C; pH 7.5 at 25°C, 3.3 mM Mg2+, mutant V29A
0.62
(S)-2-naphthylglycolate
-
mutant V22F, pH 7.5, 25°C; mutant V26L, pH 7.5, 25°C
1.6
(S)-2-naphthylglycolate
-
wild-type, pH 7.5, 25°C, presence of 20 mM Mg2+
2.4
(S)-2-naphthylglycolate
-
mutant V22I/V29L, pH 7.5, 25°C, presence of 20 mM Mg2+
2.9
(S)-2-naphthylglycolate
-
mutant V22I, pH 7.5, 25°C, presence of 20 mM Mg2+
0.62
(S)-2-naphtylglyconate
-
pH 7.5 at 25°C, 3.3 mM Mg2+, mutant V22F; pH 7.5 at 25°C, 3.3 mM Mg2+, mutant V26L
1.7
(S)-2-naphtylglyconate
-
pH 7.5 at 25°C, 3.3 mM Mg2+, mutant V26A/V29L
2.4
(S)-2-naphtylglyconate
-
pH 7.5 at 25°C, 3.3 mM Mg2+, mutant V26A/V29L
0.3
(S)-Mandelate
-
recombinant mandelate racemase, putative misfolded form with N-terminal hexahistidine tag, Na-HEPES buffer (0.1 M, pH 7.5), 3.3 mM MgCl2
0.6
(S)-Mandelate
-
mutant V29L, pH 7.5, 25°C; pH 7.5 at 25°C, 3.3 mM Mg2+, mutant V29L
0.6
(S)-Mandelate
-
recombinant mrIII fusion protein bearing an N-terminal StrepII-tag and a C-terminal decahistidine tag, Na-HEPES buffer (0.1 M, pH 7.5), 3.3 mM MgCl2
0.8
(S)-Mandelate
-
recombinant mandelate racemase represents correctly folded enzyme with N-terminal hexahistidine tag, in Na-HEPES buffer (0.1 M, pH 7.5),3.3 mM MgCl2
0.97
(S)-Mandelate
-
pH 7.5 at 25°C, 3.3 mM Mg2+, wild-type; wild-type, pH 7.5, 25°C
1.07
(S)-Mandelate
-
pH 7.5 at 25°C, 20 mM Mg2+, wild-type; wild-type, pH 7.5, 25°C, presence of 20 mM Mg2+
1.1
(S)-Mandelate
-
mutant V26A/V29L, pH 7.5, 25°C; mutant V26F, pH 7.5, 25°C; mutant V26L, pH 7.5, 25°C; mutant V29F, pH 7.5, 25°C; pH 7.5 at 25°C, 3.3 mM Mg2+, mutant V26A/V29L; pH 7.5 at 25°C, 3.3 mM Mg2+, mutant V26F; pH 7.5 at 25°C, 3.3 mM Mg2+, mutant V26L; pH 7.5 at 25°C, 3.3 mM Mg2+, mutant V29F
1.1
(S)-Mandelate
-
recombinant mandelate racemase, replacement of the N-terminal hexahistidine tag by a StrepII-tag appears to ameliorate the folding problem yielding a single enzyme species, Na-HEPES buffer (0.1 M, pH 7.5), 3.3 mM MgCl2
1.5
(S)-Mandelate
-
mutant V22I/V29L, pH 7.5, 25°C, presence of 20 mM Mg2+; pH 7.5 at 25°C, 3.3 mM Mg2+, mutant V26A/V29L
1.7
(S)-Mandelate
-
mutant V22I, pH 7.5, 25°C, presence of 20 mM Mg2+; mutant V26A, pH 7.5, 25°C; pH 7.5 at 25°C, 3.3 mM Mg2+, mutant V22I; pH 7.5 at 25°C, 3.3 mM Mg2+, mutant V26A
1.8
(S)-Mandelate
-
mutant A25V, pH 7.5, 25°C; pH 7.5 at 25°C, 3.3 mM Mg2+, mutant A25V
3
(S)-Mandelate
-
mutant T24S, pH 7.5, 25°C; pH 7.5 at 25°C, 3.3 mM Mg2+, mutant T24S
3.4
(S)-Mandelate
-
mutant V22A, pH 7.5, 25°C; pH 7.5 at 25°C, 3.3 mM Mg2+, mutant V22A
3.9
(S)-Mandelate
-
mutant V29A, pH 7.5, 25°C; pH 7.5 at 25°C, 3.3 mM Mg2+, mutant V29A
6.1
(S)-Mandelate
-
mutant V22F, pH 7.5, 25°C; pH 7.5 at 25°C, 3.3 mM Mg2+, mutant V22F
0.04
Mg2+
-
pH 7.5, mutant V22A, addition of either 10 mM (R)- or (S)-mandelate; pH 7.5, mutant V22F, addition of either 10 mM (R)- or (S)-mandelate
0.05
Mg2+
-
pH 7.5, mutant V26F, addition of either 10 mM (R)- or (S)-mandelate
0.08
Mg2+
-
pH 7.5, mutant V29A, addition of either 10 mM (R)- or (S)-mandelate
0.12
Mg2+
-
pH 7.5, mutant V26L, addition of either 10 mM (R)- or (S)-mandelate
0.15
Mg2+
-
pH 7.5, mutant V26A, addition of either 10 mM (R)- or (S)-mandelate
0.22
Mg2+
-
pH 7.5, mutant V29F, addition of either 10 mM (R)- or (S)-mandelate
0.29
Mg2+
-
pH 7.5, mutant T24S, addition of either 10 mM (R)- or (S)-mandelate
0.34
Mg2+
-
pH 7.5, wild-type, addition of either 10 mM (R)- or (S)-mandelate
0.47
Mg2+
-
pH 7.5, mutant V29L, addition of either 10 mM (R)- or (S)-mandelate
0.51
Mg2+
-
pH 7.5, mutant V26A/V29L, addition of either 10 mM (R)- or (S)-mandelate
0.64
Mg2+
-
pH 7.5, mutant A25V, addition of either 10 mM (R)- or (S)-mandelate
3.8
Mg2+
-
pH 7.5, mutant V22I, addition of either 10 mM (R)- or (S)-mandelate
4.2
Mg2+
-
pH 7.5, mutant V22I/V29L, addition of either 10 mM (R)- or (S)-mandelate
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
70
(2R)-2-naphthylglycolate
-
pH 7.5, 25°C, wild-type enzyme, in presence of 20 mM MgCl2
10.5
(R)-2-naphthylglycolate
-
mutant V22I/V29L, pH 7.5, 25°C, presence of 20 mM Mg2+
70
(R)-2-naphthylglycolate
-
wild-type, pH 7.5, 25°C, presence of 20 mM Mg2+
147
(R)-2-naphthylglycolate
-
mutant V22I, pH 7.5, 25°C, presence of 20 mM Mg2+
3 - 6
(R)-mandelate
-
mutant V26L, pH 7.5, 25°C; pH 7.5, 3.3 mM Mg2+, mutant V26L
13
(R)-mandelate
-
mutant A25V, pH 7.5, 25°C; pH 7.5, 3.3 mM Mg2+, mutant A25V
33
(R)-mandelate
-
mutant V26F, pH 7.5, 25°C; pH 7.5, 3.3 mM Mg2+, mutant V26F
53
(R)-mandelate
-
mutant V29F, pH 7.5, 25°C; pH 7.5, 3.3 mM Mg2+, mutant V29F
82
(R)-mandelate
-
mutant V22A, pH 7.5, 25°C; pH 7.5, 3.3 mM Mg2+, mutant V22A
98
(R)-mandelate
-
mutant V22F, pH 7.5, 25°C; pH 7.5, 3.3 mM Mg2+, mutant V22F
102
(R)-mandelate
-
mutant T24S, pH 7.5, 25°C; pH 7.5, 3.3 mM Mg2+, mutant T24S
106
(R)-mandelate
-
mutant V26A/V29L, pH 7.5, 25°C; pH 7.5, 3.3 mM Mg2+, mutant V26A/V29L
240
(R)-mandelate
-
mutant V29A, pH 7.5, 25°C; pH 7.5, 3.3 mM Mg2+, mutant V29A
300
(R)-mandelate
-
mutant V29L, pH 7.5, 25°C; pH 7.5, 3.3 mM Mg2+, mutant V29L
304
(R)-mandelate
-
mutant V26A, pH 7.5, 25°C; pH 7.5, 3.3 mM Mg2+, mutant V26A
552
(R)-mandelate
-
pH 7.5, 3.3 mM Mg2+, wild-type; wild-type, pH 7.5, 25°C
620
(R)-mandelate
-
pH 7.5, 20 mM Mg2+, wild-type; wild-type, pH 7.5, 25°C, presence of 20 mM Mg2+
1010
(R)-mandelate
-
mutant V22I/V29L, pH 7.5, 25°C, presence of 20 mM Mg2+; pH 7.5, 3.3 mM Mg2+, mutant V22I/V29L
1150
(R)-mandelate
-
mutant V22I, pH 7.5, 25°C, presence of 20 mM Mg2+; pH 7.5, 3.3 mM Mg2+, mutant V22I
7.1
(S)-2-naphthylglycolate
-
mutant V22I/V29L, pH 7.5, 25°C, presence of 20 mM Mg2+
38.4
(S)-2-naphthylglycolate
-
wild-type, pH 7.5, 25°C, presence of 20 mM Mg2+
101
(S)-2-naphthylglycolate
-
mutant V22I, pH 7.5, 25°C, presence of 20 mM Mg2+
22
(S)-Mandelate
-
mutant A25V, pH 7.5, 25°C; mutant V26F, pH 7.5, 25°C; pH 7.5, 3.3 mM Mg2+, mutant A25V; pH 7.5, 3.3 mM Mg2+, mutant V26F
23
(S)-Mandelate
-
mutant V26L, pH 7.5, 25°C; pH 7.5, 3.3 mM Mg2+, mutant V26L
53
(S)-Mandelate
-
mutant V29F, pH 7.5, 25°C; pH 7.5, 3.3 mM Mg2+, mutant V29F
77
(S)-Mandelate
-
mutant V22A, pH 7.5, 25°C; pH 7.5, 3.3 mM Mg2+ mutant V22A
89
(S)-Mandelate
-
mutant V26A/V29L, pH 7.5, 25°C; pH 7.5, 3.3 mM Mg2+, mutant V26A/V29L
98
(S)-Mandelate
-
mutant V22F, pH 7.5, 25°C; pH 7.5, 3.3 mM Mg2+, mutant V22F
120
(S)-Mandelate
-
mutant T24S, pH 7.5, 25°C; pH 7.5, 3.3 mM Mg2+, mutant T24S
176
(S)-Mandelate
-
mutant V29A, pH 7.5, 25°C; pH 7.5, 3.3 mM Mg2+, mutant V29A
180
(S)-Mandelate
-
mutant V29L, pH 7.5, 25°C; pH 7.5, 3.3 mM Mg2+, mutant V29L
190
(S)-Mandelate
-
recombinant mandelate racemase, putative misfolded form with N-terminal hexahistidine tag, Na-HEPES buffer (0.1 M, pH 7.5), 3.3 mM MgCl2
470
(S)-Mandelate
-
pH 7.5, 3.3 mM Mg2+, wild-type; wild-type, pH 7.5, 25°C
472
(S)-Mandelate
-
recombinant mandelate racemase fusion protein bearing an N-terminal StrepII-tag and a C-terminal decahistidine tag, Na-HEPES buffer (0.1 M, pH 7.5), 3.3 mM MgCl2
492
(S)-Mandelate
-
pH 7.5, 20 mM Mg2+, wild-type; wild-type, pH 7.5, 25°C, presence of 20 mM Mg2+
550
(S)-Mandelate
-
mutant V26A, pH 7.5, 25°C; pH 7.5, 3.3 mM Mg2+, mutant V26A
710
(S)-Mandelate
-
mutant V22I/V29L, pH 7.5, 25°C, presence of 20 mM Mg2+; pH 7.5, 3.3 mM Mg2+, mutant V26A/V29L
740
(S)-Mandelate
-
mutant V22I, pH 7.5, 25°C, presence of 20 mM Mg2+; pH 7.5, 3.3 mM Mg2+, mutant V22I
940
(S)-Mandelate
-
recombinant mandelate racemase represents correctly folded enzyme, with N-terminal hexahistidine tag, in Na-HEPES buffer (0.1 M, pH 7.5), 3.3 mM MgCl2
1124
(S)-Mandelate
-
recombinant enzyme replacement of the N-terminal hexahistidine tag by a StrepII-tag appears to ameliorate the folding problem yielding a single enzyme species, Na-HEPES buffer (0.1 M, pH 7.5), 3.3 mM MgCl2
additional information
additional information
dependence of turnover number on pH
-
additional information
additional information
-
dependence of turnover number on pH
-
additional information
additional information
-
the turnover number of the mutant enzyme is unaffected by varying solvent viscosity
-
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
20.1
(2R)-2-naphthylglycolate
-
pH 7.5, 25°C, wild-type enzyme, in presence of 20 mM MgCl2
1100
(S)-Mandelate
-
recombinant mandelate racemase, replacement of the N-terminal hexahistidine tag by a StrepII-tag appears to ameliorate the folding problem yielding a single enzyme species, Na-HEPES buffer (0.1 M, pH 7.5), 3.3 mM MgCl2
1200
(S)-Mandelate
-
recombinant mandelate racemase, represents correctly folded enzyme with N-terminal hexahistidine tag, in Na-HEPES buffer (0.1 M, pH 7.5), 3.3 mM MgCl2
7300
(S)-Mandelate
-
recombinant mandelate racemase, putative misfolded form with N-terminal hexahistidine tag, Na-HEPES buffer (0.1 M, pH 7.5), 3.3 mM MgCl2
8000
(S)-Mandelate
-
recombinant mandelate racemase, fusion protein bearing an N-terminal StrepII-tag and a C-terminal decahistidine tag, Na-HEPES buffer (0.1 M, pH 7.5), 3.3 mM MgCl2
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Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
40.2
(R,S)-1-hydroxyethylphosphonate
-
pH 7.5, 25°C, recombinant wild-type enzyme
0.67
(R,S)-2,2,2-trifluoro-1-hydroxyethylphosphonate
-
pH 7.5, 25°C, recombinant wild-type enzyme
0.027
3,3,3-trifluoro-2-hydroxy-2-(trifluoromethyl)-propanoate
-
pH 7.5, 25°C, recombinant wild-type enzyme
0.0047
(R,S)-alpha-hydroxybenzylphosphonate
-
25°C, pH 7.5, wild-type enzyme
0.0047
(R,S)-alpha-hydroxybenzylphosphonate
-
pH 7.5, 25°C, recombinant wild-type enzyme
0.238
(R,S)-alpha-hydroxybenzylphosphonate
-
25°C, pH 7.5, mutant enzyme N197A
0.023
2-naphtholhydroxamate
-
wild-type, pH 7.5, 25°C, presence of 20 mM Mg2+
0.112
2-naphtholhydroxamate
-
mutant V22I/V29L, pH 7.5, 25°C, presence of 20 mM Mg2+
0.19
2-naphtholhydroxamate
-
mutant V22I, pH 7.5, 25°C, presence of 20 mM Mg2+
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
-
applicability of the electrochemical quarz crystal nanobalance technique to measure the adsorption behavior of an enzyme and its substrate at a platinum electrode
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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PDB
SCOP
CATH
ORGANISM
UNIPROT
Polaromonas sp. (strain JS666 / ATCC BAA-500)
Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4)
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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SUBUNITS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
-
striking structural similarity of mandelate racemase with muconate lactonizing enzyme
additional information
-
the enzyme is composed of three distinct structural domains: an N-terminal capping domain consisting of a three-stranded beta-sheet with an antiparallel four-alpha-helix bundle, a central domain consisting of a (beta/alpha)7 beta-barrel, and a short C-terminal domain composed of external beta-strands
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Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
crystallographic evidence for stereospecific alkylation by (R)-alpha-phenylglycidate
-
identification of the active site and possible catalytic residues at 2.5 A resolution
-
purified recombinant homooctameric wild-type enzyme complexed with two analogues of the putative aci-carboxylate intermediate, benzohydroxamate and Cupferron, X-ray diffraction structure at 2.2 A resolution
-
wild-type and C92S/C264S/K166C mutant enzymes in complex with inhibitors benzilate, 3,3,3-trifluoro-2-hydroxy-2-(trifluoromethyl)-propanoate and tratronate, hanging drop vapor diffusion method, mixing of 0.002 ml of each protein and reservoir solution, the protein solution contains for 3,3,3-trifluoro-2-hydroxy-2-(trifluoromethyl)-propanoate-enzyme crystals 3.3 mM MgCl2, 1 mM inhibitor, and HEPES, 50 mM, pH 7.5, and for the reservoir solution 20% w/v, 120 mM glycine, 70 mM KNO3, and 0.1 M Tris-HCl, pH 8.0, for tartronate-enzyme crystals , 6.0 mg/ml protein, 3.3 mM MgCl2, 20 mM sodium tartronate, and 50 mM HEPES, pH 7.5, and 14% w/v PEG 1500 , 100 mM glycine, and 0.1 M triethanolamin, pH 8.5, as reservoir solution, and for mutant enzyme-benzilate crystals, mutant protein in 3.3 mM MgCl2, 20 mM benzilate, and 50 mM HEPES, pH 7.5, reservoir solution containing 15% w/v PEG 1500, 150 mM glycine, 50 mM NaCl, and 0.1 M HEPES, pH 7.5, equilibration against 0.5 ml reservoir solution, 21°C, and 50% humidity, X-ray diffraction structure determination and analysis at 1.68-1.89 A resolution
-
X-ray crystal structure of mandelate racemase solved at 2.5 A resolution, reveals that the sescondary, tertiary and quarternary structures of mandelate racemase and muconate lactonizing enzyme are remarkably similar
-
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GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
recombinant enzyme exhibits only a slight loss of activity when the enzyme is dialyzed without 200 mM NaCl at 4°C for 8 h, a loss of 20% of its activity when the enzyme is stored for 1 h on ice in the absence of BSA (but stable in the presence of 0.1% BSA), and a 30% reduction in Vmax after storage for 20 days at -70°C in the presence of 200 mM NaCl
-
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
purification of recombinant MR as a fusion protein with an N-terminal hexahistidine tag using immobilized-nickel ion affinity chromatography and elution with a linear gradient of EDTA
-
recombinant Strep-tagged wild-type and mutant enzymes from Escherichia coli strain BL21(DE3) by affinity chromatography and dialysis
-
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
gene mdlA, coexpression of mandelate racemase and mandelate dehydrogenase in Escherichia coli strain BL21(DE3), subcloning in Escherichia coli strain TG1
overexpression of Strep-tagged wild-type and mutant enzymes in Escherichia coli strain BL21(DE3)
-
Recombinant MR from is overproduced from Escherichia coli strain BL21(DE3) cells transformed with a pET-15b plasmid containing the MR open reading frame. This construct encodes the MR gene product with an N-terminal hexahistidine tag. Mutants are produced by site-directed mutagenesis
-
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
A25V
D270N
structure of D270N with (S)-atrolactate bound in the active site reveals no geometric alterations when compared to the structure of the wild type enzyme complexed with (S)-atrolactate, with the exception that the side chain of His297 is tilted and displaced about 0.5A away from Asn270 and towards the (S)-atrolactate. The turnover number for both (R)-mandelate and (S)-mandelate are reduced 10000fold
E317Q
-
E317Q with 3400fold reduced turnover number for (R)-mandelate and 29000fold reduced turnover number for (S)-mandelate. E317Q mutant enzyme does not catalyze detectable elimination of Br- from either enantiomer of p-(bromomethyl)mandelate. E317Q mutant enzyme is irreversibly inactivated by racemic alpha-phenylglycidate at a rate comparable to that measured for wild type enzyme
F52W
-
compared to wild-type enzyme the catalytic preference of the mutant enzyme is reversed and catalytic efficiency is reduced. Mutant enzyme exhibits higher affinity for (R)-mandelate than for (S)-mandelate, and a higher turnover number with (S)-mandelate as the substrate, relative to that with (R)-mandelate
F52W/Y54W
-
compared to wild-type enzyme the catalytic preference of the mutant enzyme is reversed and catalytic efficiency is reduced. Mutant enzyme exhibits higher affinity for (R)-mandelate than for (S)-mandelate, and a higher turnover number with (S)-mandelate as the substrate, relative to that with (R)-mandelate
H297N
K166E
-
K166R retains low level of racemase activity. K166R mutant catalyzes the elimination of Br- from only the (R)-enantiomer of (R,S)-p-(bromomethyl)mandelate
N197A
S139A
-
site-directed mutagenesis, the mutation leads to a significant reduction of catalytic efficiency by about 45fold and 60fold in R to S and S to R directions
T24S
V22A
V22F
V22I
V22I/V29L
-
Catalytic efficiencies (kcat/Km) for all mutants are reduced between 6- and 40fold with the exception of V22I, V26A, V29L, and V22I/V29L which have near wildtype efficiencies with mandelate; variation of the hydrophobic loop, catalytic efficiency similar to wild-type
V26A
V26A/V29L
V26F
V26I
-
site-directed mutagenesis, the mutant shows 2fold higher catalytic efficiency towards R-mandelamide than the wild-type enzyme
V26I/Y54V
-
site-directed mutagenesis, the mutant shows 5.2fold higher catalytic efficiency towards (3R)-3-chloromandelic acid than the wild-type enzyme
V26L
V29A
V29F
V29L
Y54Q
-
compared to wild-type enzyme the catalytic preference of the mutant enzyme is reversed and catalytic efficiency is reduced. Mutant enzyme exhibits higher affinity for (R)-mandelate than for (S)-mandelate, and a higher turnover number with (S)-mandelate as the substrate, relative to that with (R)-mandelate
additional information
A25V
-
Catalytic efficiencies (kcat/Km) for all mutants are reduced between 6- and 40fold with the exception of V22I, V26A, V29L, and V22I/V29L which have near wildtype efficiencies with mandelate; variation of the hydrophobic loop, decrease in catalytic efficiency
H297N
-
H297N has no detectable mandelate racemase activity. However, H297N catalyzes the stereospecific elimination of Br- from racemic p-(bromomethyl)mandelate to give p-(methyl)benzoylformate in 45% yield at a rate equal to that measured for wild type enzyme
H297N
-
H297N, which is inactive as a racemase catalyzes the stereospecific exchange of the alpha-proton of S- but not R-mandelate with solvent D2O at a rate that is 30% of that of the wild type enzyme
N197A
-
Kcat for (R)-mandelate reduced 30fold, Kcat for (S)-mandelate reduced 179fold relative to wild-type
N197A
-
turnover number is reduced 30fold for (R)-mandelate and 179fold for (S)-mandelate relative to wild-type enzyme. The ratio of turnover number to Km-value is reduced 208fold for (R)-mandelate and 556fold for (S)-mandelate, 3.5fold reduction in affinity for the substrate analogue (R)-atrolactate, but 51fold and 18fold reduction in affinity for alpha-hydroxybenzylphosphonate and benzohydroxamate, respectively
N197A
-
slight activating effect of sucrose on mutant enzyme efficiency. In presewnce of polymeric viscosogens poly(ethylene glycol) and Ficoll, no effect on turnover number or the ratio of turnover number and Km-value for the wild-type enzyme is observed
T24S
-
Catalytic efficiencies (kcat/Km) for all mutants are reduced between 6- and 40fold with the exception of V22I, V26A, V29L, and V22I/V29L which have near wildtype efficiencies with mandelate; variation of the hydrophobic loop, decrease in catalytic efficiency
V22A
-
Catalytic efficiencies (kcat/Km) for all mutants are reduced between 6- and 40fold with the exception of V22I, V26A, V29L, and V22I/V29L which have near wildtype efficiencies with mandelate; variation of the hydrophobic loop, decrease in catalytic efficiency
V22F
-
Catalytic efficiencies (kcat/Km) for all mutants are reduced between 6- and 40fold with the exception of V22I, V26A, V29L, and V22I/V29L which have near wildtype efficiencies with mandelate; variation of the hydrophobic loop, decrease in catalytic efficiency
V22I
-
Catalytic efficiencies (kcat/Km) for all mutants are reduced between 6- and 40fold with the exception of V22I, V26A, V29L, and V22I/V29L which have near wildtype efficiencies with mandelate; variation of the hydrophobic loop. For mandelate, catalytic efficiency similar to wild-type. For substrate 2-naphthylglycolate, increase in catalytic efficiency
V26A
-
Catalytic efficiencies (kcat/Km) for all mutants are reduced between 6- and 40fold with the exception of V22I, V26A, V29L, and V22I/V29L which have near wildtype efficiencies with mandelate; variation of the hydrophobic loop, catalytic efficiency similar to wild-type
V26A/V29L
-
Catalytic efficiencies (kcat/Km) for all mutants are reduced between 6- and 40fold with the exception of V22I, V26A, V29L, and V22I/V29L which have near wildtype efficiencies with mandelate; variation of the hydrophobic loop, decrease in catalytic efficiency
V26F
-
Catalytic efficiencies (kcat/Km) for all mutants are reduced between 6- and 40fold with the exception of V22I, V26A, V29L, and V22I/V29L which have near wildtype efficiencies with mandelate; variation of the hydrophobic loop, decrease in catalytic efficiency
V26L
-
Catalytic efficiencies (kcat/Km) for all mutants are reduced between 6- and 40fold with the exception of V22I, V26A, V29L, and V22I/V29L which have near wildtype efficiencies with mandelate; variation of the hydrophobic loop, decrease in catalytic efficiency
V29A
-
Catalytic efficiencies (kcat/Km) for all mutants are reduced between 6- and 40fold with the exception of V22I, V26A, V29L, and V22I/V29L which have near wildtype efficiencies with mandelate; variation of the hydrophobic loop, decrease in catalytic efficiency
V29F
-
Catalytic efficiencies (kcat/Km) for all mutants are reduced between 6- and 40fold with the exception of V22I, V26A, V29L, and V22I/V29L which have near wildtype efficiencies with mandelate; variation of the hydrophobic loop, decrease in catalytic efficiency
V29L
-
Catalytic efficiencies (kcat/Km) for all mutants are reduced between 6- and 40fold with the exception of V22I, V26A, V29L, and V22I/V29L which have near wildtype efficiencies with mandelate; variation of the hydrophobic loop. For mandelate, catalytic efficiency similar to wild-type. For substrate 2-naphthylglycolate, increase in catalytic efficiency
V29L
-
site-directed mutagenesis, the mutant shows 2fold higher catalytic efficiency towards R-2-naphthylglycolate than the wild-type enzyme
additional information
mandelate racemase and mandelate dehydrogenase are coexpressed in Escherichia coli for the synthesis of benzoylformate by converting racemic mandelate
additional information
-
mandelate racemase and mandelate dehydrogenase are coexpressed in Escherichia coli for the synthesis of benzoylformate by converting racemic mandelate
-
additional information
-
development and evaluation of a virtual mutant screening method for non-natural substrates based on the binding energy in the transition state, the method is beneficial in enzyme rational redesign and helps to better understand the catalytic properties of the enzyme, and it is effective in predicting the trend of mutational effects on catalysis, molecular dynamic simulation, overview
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
analysis
-
direct kinetic assay for mandelate racemase using circular dichroic measurement
biotechnology
-
the demonstrated application of a membrane bioreactor will be a useful method for large-scale dynamic kinetic resulution (DKR) of mandelic acid and for possible other bioconversions in organic media
synthesis
synthesis
-
DEAE-cellulose-immobilized mandelate racemase can be efficiently used in repeated batch reactions for the racemization of (R)-mandelic acid under mild conditions
synthesis
mandelate racemase and mandelate dehydrogenase, coexpressed in Escherichia coli, are useful for the synthesis of benzoylformate by converting racemic mandelate
synthesis
-
mandelate racemase and mandelate dehydrogenase, coexpressed in Escherichia coli, are useful for the synthesis of benzoylformate by converting racemic mandelate
-
synthesis
-
DEAE-cellulose-immobilized mandelate racemase can be efficiently used in repeated batch reactions for the racemization of (R)-mandelic acid under mild conditions
-
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LINKS TO OTHER DATABASES (specific for EC-Number 5.1.2.2)
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