Information on EC 5.1.2.2 - mandelate racemase

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The expected taxonomic range for this enzyme is: Pseudomonas

EC NUMBER
COMMENTARY hide
5.1.2.2
-
RECOMMENDED NAME
GeneOntology No.
mandelate racemase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
(S)-mandelate = (R)-mandelate
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
racemization
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
4-hydroxymandelate degradation
-
-
Aminobenzoate degradation
-
-
mandelate degradation I
-
-
Microbial metabolism in diverse environments
-
-
4-hydroxymandelate degradation
-
-
SYSTEMATIC NAME
IUBMB Comments
mandelate racemase
-
CAS REGISTRY NUMBER
COMMENTARY hide
9024-04-8
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
strain isolated from soil, gene mdlA
UniProt
Manually annotated by BRENDA team
strain isolated from soil, gene mdlA
UniProt
Manually annotated by BRENDA team
ATCC12336
-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
physiological function
-
enzyme catalyzes the Mg2+-dependent 1,1-proton transfer that interconverts the enantiomers of mandelate
additional information
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
(2R)-2-(4-bromophenyl)-2-hydroxyacetamide
?
show the reaction diagram
-
22% of the activity with (R)-mandelate
-
-
?
(2R)-2-furyl(hydroxy)acetic acid
?
show the reaction diagram
-
24% of the activity with (R)-mandelate
-
-
?
(2R)-2-hydroxy-2-phenylacetamide
?
show the reaction diagram
-
15% of the activity with (R)-mandelate
-
-
?
(2R)-2-hydroxy-3-(1-H-imidazol-1-yl)propanoic acid
?
show the reaction diagram
-
5.4% of the activity with (R)-mandelate
-
-
?
(2R)-2-hydroxypentanoic acid
?
show the reaction diagram
-
1% of the activity with (R)-mandelate
-
-
?
(2R)-2-naphthylglycolate
(2S)-2-naphthylglycolate
show the reaction diagram
-
a non-natural substrate
-
-
?
(2R)-3-furyl(hydroxy)acetic acid
?
show the reaction diagram
-
38% of the activity with (R)-mandelate
-
-
?
(2R)-cyclohex-1-en-1-yl(hydroxy)acetic acid
?
show the reaction diagram
-
50% of the activity with (R)-mandelate
-
-
?
(2R)-hydroxy(2-naphthyl)acetic acid
?
show the reaction diagram
-
26% of the activity with (R)-mandelate
-
-
?
(2S)-hydroxy(2-thienyl)acetic acid
?
show the reaction diagram
-
59% of the activity with (R)-mandelate
-
-
?
(R)-(E)-2-hydroxy-3-pentenoic acid
?
show the reaction diagram
-
36% of the activity with (R)-mandelate
-
-
?
(R)-(E)-2-hydroxy-4-phenyl-3-butenoic acid
?
show the reaction diagram
-
53% of the activity with (R)-mandelate
-
-
?
(R)-2-naphthylglycolate
(S)-2-naphthylglycolate
show the reaction diagram
(R)-3-chloromandelate
(S)-3-chloromandelate
show the reaction diagram
-
a non-natural substrate
-
-
?
(R)-lactate
(S)-lactate
show the reaction diagram
-
-
-
-
?
(R)-mandelamide
(S)-mandelamide
show the reaction diagram
-
a non-natural substrate
-
-
?
(R)-mandelate
(S)-mandelate
show the reaction diagram
(R)-trifluorolactate
trifluorolactate
show the reaction diagram
-
racemization
-
-
?
(S)-2-hydroxy-3-butenoic acid
(R)-2-hydroxy-3-butenoic acid
show the reaction diagram
(S)-2-naphthylglycolate
(R)-2-naphthylglycolate
show the reaction diagram
(S)-lactate
(R)-lactate
show the reaction diagram
-
-
-
-
?
(S)-mandelate
(R)-mandelate
show the reaction diagram
(S)-mandelic acid amide
(R)-mandelic acid amide
show the reaction diagram
-
activity is enhanced by an electron-withdrawing substituent in the phenyl moiety
-
?
(S)-trifluorolactate
(R)-trifluorolactate
show the reaction diagram
-
-
-
-
?
(S)-trifluorolactate
trifluorolactate
show the reaction diagram
-
racemization
-
-
?
(S)-vinylglycolate
(R)-vinylglycolate
show the reaction diagram
-
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
?
show the reaction diagram
-
35% of the activity with (R)-mandelate
-
-
?
4-bromo-(R)-mandelate
4-bromo-(S)-mandelate
show the reaction diagram
-
376% of the activity with (R)-mandelate
-
-
r
4-bromo-D-mandelate
4-bromo-L-mandelate
show the reaction diagram
4-chloro-(R)-mandelate
4-chloro-(S)-mandelate
show the reaction diagram
-
326% of the activity with (R)-mandelate
-
-
r
4-chloro-D-mandelate
4-chloro-L-mandelate
show the reaction diagram
4-fluoro-(R)-mandelate
4-fluoro-(S)-mandelate
show the reaction diagram
-
96% of the activity with (R)-mandelate
-
-
r
4-hydroxy-(R)-mandelate
4-hydroxy-(S)-mandelate
show the reaction diagram
-
45% of the activity with (R)-mandelate
-
-
r
4-hydroxy-D-mandelate
4-hydroxy-L-mandelate
show the reaction diagram
4-methoxy-(R)-mandelate
4-methoxy-(S)-mandelate
show the reaction diagram
-
17% of the activity with (R)-mandelate
-
-
r
4-methoxy-D-mandelate
4-methoxy-L-mandelate
show the reaction diagram
-
-
-
-
5-chloro-(R)-mandelate
5-chloro-(S)-mandelate
show the reaction diagram
-
61% of the activity with (R)-mandelate
-
-
r
D-mandelate
L-mandelate
show the reaction diagram
p-(bromomethyl)mandelate
p-(methyl)benzoylformate + Br-
show the reaction diagram
p-hydroxy-D-mandelate
p-hydroxy-L-mandelate
show the reaction diagram
-
-
-
-
S-mandelate
R-mandelate
show the reaction diagram
-
-
-
-
?
additional information
?
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
(S)-mandelate
(R)-mandelate
show the reaction diagram
D-mandelate
L-mandelate
show the reaction diagram
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Divalent metal ions
Fe2+
-
absolute requirement for a divalent metal ion: Mg2+, Mn2+, Ni2+, Co2+ or Fe2+
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
(R)-2-hydroxybutyrate
-
-
(R)-2-naphthylglycolate
-
-
(R)-alpha-Phenylglycerate
-
-
(R)-atrolactate
-
-
(R)-lactate
-
-
(R,S)-1-hydroxyethylphosphonate
-
transition state analogue inhibitor
(R,S)-1-naphthylglycolate
-
competitive
(R,S)-2,2,2-trifluoro-1-hydroxyethylphosphonate
-
transition state analogue inhibitor
(R,S)-2-naphthylglycolate
-
-
(R,S)-alpha-hydroxybenzylphosphonate
(R,S)-methyl-alpha-hydroxybenzylphosphonate
-
-
(S)-2-hydroxybutyrate
-
-
(S)-2-naphthylglycolate
-
-
(S)-alpha-Phenylglycerate
-
-
(S)-cyclohexylphenylglycolate
-
-
(S)-lactate
-
-
1,1-diphenyl-1-hydroxymethylphosphonate
-
modest competitive inhibitor
1-hydroxy-2-naphthoic acid
-
reversible
2-Hydroxybutyrate
-
competitive
2-naphthohydroxamate
2-naphtholhydroxamate
-
-
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
3-Hydroxy-2-naphthoic acid
4-Hydroxycoumarin
alpha-hydroxyisobutyrate
-
substrate-product analogue inhibitor
alpha-Phenylglycidate
-
irreversible
Anthranil-3-carboxylic acid
-
reversible
benzilate
Benzoate
benzohydroxamate
benzoylformate
-
-
benzoylhydroxamate
-
-
benzoylphosphonate
-
-
benzylphosphonate
-
-
Coumarilic acid
-
reversible
Cupferron
diphenylacetate
-
-
Diphenylacetic acid
-
-
diphosphate
-
-
DL-alpha-Phenylglycerate
-
competitive
DL-alpha-Phenylglycidate
DL-Atrolactate
-
-
DL-beta-Phenyllactate
-
-
iodoacetamide
-
weak noncompetitive inhibitor
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
naphthoate
-
mixed-type inhibition
NEM
-
weak noncompetitive inhibitor
p-chloromercuribenzoate
-
weak noncompetitive inhibitor
phenylacetate
-
-
Phenylmercaptoacetate
-
-
Phenyloxyacetate
-
-
salicylate
styrene oxide
-
-
Tartronate
-
competitive
trans-beta-Phenylglycidate
-
irreversible
additional information
-
no inhibition by p-chloromercuribenzoate
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
Sucrose
additional information
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1.2 - 4.2
(2R)-2-naphthylglycolate
3.5
(R)-2-Hydroxy-3-butenoic acid
-
-
0.35 - 4.4
(R)-2-naphthylglycolate
1.1 - 4.4
(R)-2-naphtylglyconate
1.27 - 3.92
(R)-3-chloromandelate
1.13 - 1.24
(R)-mandelamide
0.29 - 5.4
(R)-mandelate
1.2
(R)-trifluorolactate
-
pH 7.5, 25C, recombinant wild-type enzyme
0.41 - 2.9
(S)-2-naphthylglycolate
0.55 - 2.9
(S)-2-naphtylglyconate
0.3 - 6.1
(S)-Mandelate
1.74
(S)-trifluorolactate
-
pH 7.5, 25C, recombinant wild-type enzyme
0.256
4-Bromo-D-mandelate
-
-
0.29
4-Hydroxy-D-mandelate
-
-
0.33
4-Methoxy-D-mandelate
-
-
0.1
D(-)-mandelate
0.093 - 0.63
D-mandelate
0.04 - 4.2
Mg2+
additional information
additional information
-
Michaelis-Menten kinetics
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
46 - 147
(2R)-2-naphthylglycolate
240
(R)-2-Hydroxy-3-butenoic acid
Pseudomonas putida
-
-
5.4 - 147
(R)-2-naphthylglycolate
5.4 - 147
(R)-2-naphtylglyconate
388 - 2020
(R)-3-chloromandelate
11.03 - 21.17
(R)-mandelamide
0.018 - 1150
(R)-mandelate
2
(R)-trifluorolactate
Pseudomonas putida
-
pH 7.5, 25C, recombinant wild-type enzyme
250
(S)-2-Hydroxy-3-butenoic acid
Pseudomonas putida
-
-
2.95 - 101
(S)-2-naphthylglycolate
2.95 - 101
(S)-2-naphtylglyconate
0.012 - 1124
(S)-Mandelate
2.5
(S)-trifluorolactate
Pseudomonas putida
-
pH 7.5, 25C, recombinant wild-type enzyme
1070
D-mandelate
Pseudomonas putida
-
-
additional information
additional information
-
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
20.1 - 85
(2R)-2-naphthylglycolate
194879
249 - 1300
(R)-3-chloromandelate
194878
9.79 - 17.1
(R)-mandelamide
3385
650
(R)-mandelate
Pseudomonas putida
-
pH 7.5, 25C, recombinant wild-type enzyme
735
1.6
(R)-trifluorolactate
Pseudomonas putida
-
pH 7.5, 25C, recombinant wild-type enzyme
194876
620 - 8000
(S)-Mandelate
431
1.4
(S)-trifluorolactate
Pseudomonas putida
-
pH 7.5, 25C, recombinant wild-type enzyme
194877
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
17.3 - 98
(R)-2-hydroxybutyrate
0.16 - 33
(R)-2-naphthylglycolate
0.95 - 3.3
(R)-atrolactate
32
(R)-lactate
-
pH 7.5, 25C, recombinant wild-type enzyme
40.2
(R,S)-1-hydroxyethylphosphonate
-
pH 7.5, 25C, recombinant wild-type enzyme
1.9
(R,S)-1-naphthylglycolate
-
25C, pH 7.5
0.67
(R,S)-2,2,2-trifluoro-1-hydroxyethylphosphonate
-
pH 7.5, 25C, recombinant wild-type enzyme
0.52
(R,S)-2-naphthylglycolate
-
25C, pH 7.5
0.0047 - 0.238
(R,S)-alpha-hydroxybenzylphosphonate
5.1
(R,S)-methyl-alpha-hydroxybenzylphosphonate
-
-
11.4 - 71
(S)-2-hydroxybutyrate
0.48 - 5
(S)-2-naphthylglycolate
0.5
(S)-cyclohexylphenylglycolate
-
wild-type enzyme
26.1
(S)-lactate
-
pH 7.5, 25C, recombinant wild-type enzyme
0.00591 - 1.41
1,1-diphenyl-1-hydroxymethylphosphonate
0.023 - 0.19
2-naphthohydroxamate
0.023 - 0.19
2-naphtholhydroxamate
0.027
3,3,3-trifluoro-2-hydroxy-2-(trifluoromethyl)-propanoate
-
pH 7.5, 25C, recombinant wild-type enzyme
5.5
alpha-hydroxyisobutyrate
-
pH 7.5, 25C, recombinant wild-type enzyme
0.67 - 45
benzilate
0.0117 - 0.216
benzohydroxamate
0.0093
benzohydroxamic acid
-
-
0.65
benzoylformate
-
-
0.3
benzoylphosphonate
-
-
3.5
benzylphosphonate
-
-
0.00267
Cupferron
-
-
4.5
diphenylacetate
-
wild-type enzyme
0.00279
N-hydroxyformanilide
-
-
0.2
phenylacetate
-
-
1.8
Tartronate
-
pH 7.5, 25C, recombinant wild-type enzyme
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7 - 8.5
wild type enzyme
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
39000
-
8 * 39000
40700
-
mutants V22A, V26A and V29A
40710
-
mutants V26A/V26L and T24S
40730
-
wild type
40740
-
mutants V22I, V26L and V29L
40760
-
mutants A25V and V22I/V29L
40780
-
mutants V22F, V26F and V29F
42000
-
SDS-PAGE
69500
-
4 * 69500, SDS-PAGE
200000
-
gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
homooctamer
-
generated from a tetramer of dimers
octamer
-
8 * 39000
tetramer
-
4 * 69500, SDS-PAGE
additional information
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
-
mutant E317Q
-
of mutant K166R
-
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, 21C, 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
-
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
recombinant enzyme exhibits only a slight loss of activity when the enzyme is dialyzed without 200 mM NaCl at 4C 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 -70C in the presence of 200 mM NaCl
-
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
by metal ion affinity chromatography
-
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
-
wild type and mutant E317Q
-
wild type and mutant K166R
-
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
cloning of fusions proteins in Escherichia coli
-
expressed ind Escherichia coli
-
expression in Escherichia coli
-
gene mdlA, coexpression of mandelate racemase and mandelate dehydrogenase in Escherichia coli strain BL21(DE3), subcloning in Escherichia coli strain TG1
overexpression in Escherichia coli strain BL21(DE3)
-
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
-
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
C92S/C264S/K166C
-
site-directed mutagenesis
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
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
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
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/V29L
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
Y54F
-
site-directed mutagenesis
Y54L
-
site-directed mutagenesis
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
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
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
Show AA Sequence (298 entries)
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