Information on EC 1.4.3.19 - glycine oxidase

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The enzyme appears in viruses and cellular organisms

EC NUMBER
COMMENTARY hide
1.4.3.19
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RECOMMENDED NAME
GeneOntology No.
glycine oxidase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
2-iminoacetate + H2O = glyoxylate + NH3
show the reaction diagram
(1b)
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-
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glycine + H2O + O2 = glyoxylate + NH3 + H2O2
show the reaction diagram
glycine + O2 = 2-iminoacetate + H2O2
show the reaction diagram
(1a)
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-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
oxidation
redox reaction
-
-
-
-
reduction
-
-
-
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
butanol and isobutanol biosynthesis (engineered)
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glyphosate degradation II
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Metabolic pathways
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Thiamine metabolism
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SYSTEMATIC NAME
IUBMB Comments
glycine:oxygen oxidoreductase (deaminating)
A flavoenzyme containing non-covalently bound FAD. The enzyme from Bacillus subtilis is active with glycine, sarcosine, N-ethylglycine, D-alanine, D-alpha-aminobutyrate, D-proline, D-pipecolate and N-methyl-D-alanine. It differs from EC 1.4.3.3, D-amino-acid oxidase, due to its activity on sarcosine and D-pipecolate. The intermediate 2-iminoacetate is used directly by EC 2.8.1.10, thiazole synthase.
CAS REGISTRY NUMBER
COMMENTARY hide
39307-16-9
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SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
cephalosporin C + H2O + O2
?
show the reaction diagram
cyclopropylglycine + H2O + O2
?
show the reaction diagram
D-2-aminobutyrate + H2O + O2
2-oxobutyrate + H2O2
show the reaction diagram
-
as active as sarcosine
-
-
?
D-2-aminobutyrate + H2O + O2
? + NH3 + H2O2
show the reaction diagram
-
2.2% of the activity with sarcosine
-
-
?
D-4-hydroxyphenylglycine + H2O + O2
?
show the reaction diagram
D-Ala + H2O + O2
? + NH3 + H2O2
show the reaction diagram
D-Ala + H2O + O2
pyruvate + NH3 + H2O2
show the reaction diagram
D-alanine + H2O + O2
pyruvate + NH3 + H2O2
show the reaction diagram
D-aminobutanoate + H2O + O2
? + H2O2
show the reaction diagram
-
30% of the activity with sarcosine
-
-
?
D-Arg + H2O + O2
? + H2O2
show the reaction diagram
-
about 35% of the activity with sarcosine
-
-
?
D-arginine + H2O + O2
?
show the reaction diagram
D-aspartate + H2O + O2
?
show the reaction diagram
D-glutamate + H2O + O2
?
show the reaction diagram
-
0.2% activity compared to glycine
-
-
?
D-His + H2O + O2
? + H2O2
show the reaction diagram
-
about 25% of the activity with sarcosine
-
-
?
D-Ile + H2O + O2
3-methyl-2-oxopentanoate + H2O2
show the reaction diagram
-
about 30% of the activity with sarcosine
-
-
?
D-Leu + H2O + O2
4-methyl-2-oxopentanoate + H2O2
show the reaction diagram
-
about 35% of the activity with sarcosine
-
-
?
D-lysine + H2O + O2
?
show the reaction diagram
-
0.2% activity compared to glycine
-
-
?
D-methionine + H2O + O2
4-(methylsulfanyl)-2-oxobutanoic acid + NH3 + H2O2
show the reaction diagram
D-methionine + H2O + O2
?
show the reaction diagram
-
-
-
-
?
D-norvaline + H2O + O2
2-oxopentanoic acid + NH3 + H2O2
show the reaction diagram
D-phenylalanine + H2O + O2
phenylpyruvate + NH3 + H2O2
show the reaction diagram
D-pipecolate + H2O + O2
?
show the reaction diagram
D-pipecolate + H2O + O2
? + H2O2
show the reaction diagram
D-Pro + H2O + O2
? + H2O2
show the reaction diagram
-
about 120% of the activity with sarcosine
-
-
?
D-Pro + H2O + O2
? + NH3 + H2O2
show the reaction diagram
D-proline + H2O + O2
?
show the reaction diagram
D-Val + H2O + O2
3-methyl-2-oxobutanoate + H2O2
show the reaction diagram
-
about 35% of the activity with sarcosine
-
-
?
D-Val + H2O + O2
? + NH3 + H2O2
show the reaction diagram
-
4.8% of the activity with sarcosine
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-
?
D-valine + H2O + O2
3-methyl-2-oxobutanoic acid + NH3 + H2O2
show the reaction diagram
glycine + H2O + O2
glyoxylate + NH3 + H2O2
show the reaction diagram
glycine + O2 + H2O
glyoxylate + H2O2 + NH3
show the reaction diagram
glycine ethyl ester + H2O + O2
?
show the reaction diagram
-
30.7% activity compared to glycine
-
-
?
glycine-ethyl-ester + H2O + O2
?
show the reaction diagram
glycine-ethyl-ester + H2O + O2
? + H2O2
show the reaction diagram
glyphosate + H2O + O2
? + H2O2
show the reaction diagram
-
110% of the activity with sarcosine
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-
?
N-ethylglycine + H2O + O2
?
show the reaction diagram
-
0.3% activity compared to glycine
-
-
?
N-ethylglycine + H2O + O2
glyoxylate + ethylamine + H2O2
show the reaction diagram
N-ethylglycine + H2O + O2
glyoxylate + NH3 + H2O2
show the reaction diagram
N-methyl-D-Ala + H2O + O2
? + H2O2
show the reaction diagram
-
75% of the activity with sarcosine
-
-
?
N-methyl-D-Ala + H2O + O2
? + NH3 + H2O2
show the reaction diagram
-
16.9% of the activity with sarcosine
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-
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N-methyl-D-Ala + H2O + O2
pyruvate + methylamine + H2O2
show the reaction diagram
-
about 110% of the activity with sarcosine
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-
?
sarcosine + H2O + O2
?
show the reaction diagram
sarcosine + H2O + O2
glyoxylate + methylamine + H2O2
show the reaction diagram
additional information
?
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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
cyclopropylglycine + H2O + O2
?
show the reaction diagram
O31616
enzyme is required for the biosynthesis of the thiazole moiety of thiamine diphosphate
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-
?
D-4-hydroxyphenylglycine + H2O + O2
?
show the reaction diagram
D-alanine + H2O + O2
pyruvate + NH3 + H2O2
show the reaction diagram
D-glutamate + H2O + O2
?
show the reaction diagram
-
0.2% activity compared to glycine
-
-
?
D-lysine + H2O + O2
?
show the reaction diagram
-
0.2% activity compared to glycine
-
-
?
D-proline + H2O + O2
?
show the reaction diagram
glycine + H2O + O2
glyoxylate + NH3 + H2O2
show the reaction diagram
glycine + O2 + H2O
glyoxylate + H2O2 + NH3
show the reaction diagram
glycine ethyl ester + H2O + O2
?
show the reaction diagram
-
30.7% activity compared to glycine
-
-
?
glycine-ethyl-ester + H2O + O2
?
show the reaction diagram
-
-
-
-
?
N-ethylglycine + H2O + O2
?
show the reaction diagram
-
0.3% activity compared to glycine
-
-
?
N-ethylglycine + H2O + O2
glyoxylate + ethylamine + H2O2
show the reaction diagram
-
-
-
-
?
sarcosine + H2O + O2
?
show the reaction diagram
sarcosine + H2O + O2
glyoxylate + methylamine + H2O2
show the reaction diagram
-
-
-
-
?
additional information
?
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
flavin
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flavoprotein
pyrroloquinoline quinone
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-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
no enhancement of enzyme activity in the presence of metal cations
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
acetone
22% residual activity after 30 min incubation at 30% (v/v)
acetonitrile
complete inhibition at 30% (v/v)
Ag2+
-
2.0 mM
Cd2+
-
2.0 mM
Co2+
there is a sharp decrease in activity when 1 mM Co2+ is added to the reaction assay
Cu2+
-
2.0 mM
diethylether
73% residual activity after 30 min incubation at 30% (v/v)
ethyl acetate
19% residual activity after 30 min incubation at 30% (v/v)
Hg2+
-
2.0 mM
hydroxylamine
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methanol
54% residual activity after 30 min incubation at 30% (v/v)
methylhydrazine
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N,N-Dimethyl formamide
17% residual activity after 30 min incubation at 30% (v/v)
PCMB
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2.0 mM
phenylhydrazine
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Semicarbazide
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Zn2+
there is a sharp decrease in activity when 1 mM Zn2+ is added to the reaction assay
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1.17
cyclopropylglycine
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-
81
D-Ala
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-
4 - 2000
D-alanine
221.8 - 2000
D-pipecolate
46 - 76.5
D-Pro
2.06 - 285
D-proline
0.99 - 3.8
Gly
0.18 - 105
glycine
0.29 - 1.8
glycine-ethyl-ester
0.5 - 87
glyphosate
0.71 - 2.8
N-ethyl-glycine
0.22 - 2.8
N-ethylglycine
0.15 - 0.45
O2
0.22 - 11
sarcosine
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1.14
cyclopropylglycine
Bacillus subtilis
-
-
0.4 - 1.1
D-Ala
0.33 - 1.5
D-alanine
1.3 - 3.5
D-Pro
0.3 - 1.35
D-proline
1.2 - 4
Gly
0.3 - 4.1
glycine
0.7 - 1.8
glyphosate
1.4
N-ethylglycine
Bacillus subtilis
-
-
0.47 - 4.2
sarcosine
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.19
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crude extract
0.21
-
purification step ultrafiltration
0.568
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wild-type enzyme
0.9
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mutant enzyme I15V, from crude extract
1.06
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His-tagged chimeric glycine oxidase
1.2
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purification step HiTrap chelating chromatography
1.75
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crude extract, at 37°C and pH 8.5
8.6
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mutant enzyme I15V, after 9.3fold purification
14
cell free extract, when glycine is used as a substrate, at pH 8.0 and 37°C
960
after 68.6fold purification, when glycine is used as a substrate, at pH 8.0 and 37°C
1000
after 68.6fold purification, when D-alanine is used as a substrate, at pH 8.0 and 37°C
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
10
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reaction with sarcosine
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7 - 9
about 75% activity at pH 7.0, more than 50% activity is retained between pH 7.5 and 8.5, about 60% activity at pH 9.0. The enzyme activity decreases sharply below pH 7.0 and above pH 9.0. There is a negligible amount of activity at pH below 5.0 and above 10.0
8 - 11
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pH 8.0: about 55% of maximal activity, pH 11.0: about 55% of maximal activity, reaction with sarcosine
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
-
increase in activity with no evidence for any plateau or decrease up to 60°C, reaction with sarcosine
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
15 - 60
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increase in activity with no evidence for any plateau or decrease up to 60°C, reaction with sarcosine
40 - 55
the enzyme exhibits almost 80% of its activity at temperatures 40 and 55°C. The activity sharply decreases above 55°C
60
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activation during the first 15 min, with slow decrease thereafter
pI VALUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5.8
calculated from amino acid sequence
6
-
theoretical value, His-tagged chimeric enzyme; theoretical value, wild-type enzyme
PDB
SCOP
CATH
ORGANISM
UNIPROT
Bacillus subtilis (strain 168)
Bacillus subtilis (strain 168)
Bacillus subtilis (strain 168)
Bacillus subtilis (strain 168)
Geobacillus kaustophilus (strain HTA426)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
40500
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4 * 40500, gel filtration
40760
4 * 40760, MALDI-TOF mass spectrometry
40761
4 * 40761, calculated from amino acid sequence
40762
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x * 40763, recombinant enzyme, mass spectrometry, x * 40762, sequence calculation
40763
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x * 40763, recombinant enzyme, mass spectrometry, x * 40762, sequence calculation
46600
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4 * 46600, recombinant glycine oxidase, SDS-PAGE
49400
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4 * 49400, recombinant His-tagged chimeric glycine oxidase
159000
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gel filtration
160000
162000
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gel filtration
166400
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recombinant His-tagged chimeric glycine oxidase, gel filtration
172000
187600
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recombinant glycine oxidase, gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
homotetramer
tetramer
additional information
-
the isolated apoprotein of glycine oxidase shows high protein fluorescence, high exposure of hydrophobic surfaces, and low temperature stability as compared to the holoenzyme
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
hanging drop vapor diffusion method
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pH STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
4 - 9
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a great decrease in stability is only produced at pH values below pH 4.0, shows good stability between pH 6.0 and 9.0
689934
6.5 - 10
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the tetrameric oligomeric state of the holoenzyme is not affected within this range
696494
6.5 - 9.5
7 - 8
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optimal range for stability
696494
7 - 8.5
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25°C, 300 min, maximal stability
655429
7.5 - 8.5
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25°C, 5 h, most stable
440361
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
25
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5 h, most stable between pH 7.5 and 8.5
34.7
-
melting temperature, mutant G51R/A54R, determined by following protein and flavin fluorescence
35
-
pH 7.0, 30 min, stable up to
41.3
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melting temperature, mutant G51R, determined by following protein and flavin fluorescence
44.8
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melting temperature, mutant A54R, determined by following protein and flavin fluorescence
45.3
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melting temperature, mutant G51S/A54R, determined by following protein and flavin fluorescence
45.7
-
melting temperature, mutant G51S/A54R/H244A, determined by following protein and flavin fluorescence
46
-
Tm-value, after 30 min
48
-
melting temperature, apoprotein
50
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pH 7.0, 30 min, about 75% loss of activity
60 - 80
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at 60°C, the I15V mutant shows a similar profile than the wild type enzyme but with lower residual activity after 20 min, at 65°C the mutant goes through activation (160%) during the first 15 min, the activity then falls with a time-dependent trend and reaches a half-life value similar to the wild type enzyme, at higher temperatures (70-80°C) the activity decreases rapidly in both cases, but with half-life value higher for I15V mutant than for wild type enzyme
60
-
pH 7.0, 30 min, complete loss of activity
95
-
heat treatment of the protein at 95°C for 5 min results in the release of the FAD cofactor
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
tetrameric enzyme is strongly resistant to proteolysis, only the N-terminus is sensitive to proteases
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thiocyanate, up to 1 mM, decreases stability of the tetrameric enzyme in solution
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STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-80°C, 75 mM sodium diphosphate buffer pH 8.5 containing 10% glycerol, several months, no loss of activity
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-80°C, 75 mM sodium diphosphate buffer, pH 8.5, 10% glycerol
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-80°C, 75 mM sodium diphosphate, pH 8.5, 10% glycerol, stable for months
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-80°C, pH 7.5, both glycine oxidase and His-tagged glycine oxidase are stable for months
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
100 kDa ultrafiltration, HisTrap FF Ni2+-chelating affinity column chromatography, and phenyl-Sepharose FF hydrophobic column chromatography
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ammonium sulfate precipitation, Resource Q column chromatography and Resource ISO column chromatography
HiTrap chelating affinity chromatography
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HiTrap FF chelating affinity column chromatography and phenyl-Sepharose FF hydrophobic column chromatography
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purification of apoprotein
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recombinant enzyme expressed in Escherichia coli
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using ultrafiltation and a HiTrap chelating affinity column
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wild-type enzyme and His-tagged chimeric glycine oxidase
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
cloning of the glycine oxidase gene from Bacillus subtilis ATCC 6633 into the Rosetta Escherichia coli strain which contains the pRARE plasmid, inserting of the gene into the pET28a expression vector
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expressed in Escherichia coli BL21(DE3)CodonPlus-RIL cells
expressed in Escherichia coli Rosetta (DE3) cells
expressed in Escherichia coli Rosetta (DE3) cells Rosetta under the strong inducible T7 promotor of the pET28a vector
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expressed in Escherichia coli strain BL21(DE3)pLysS
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expression in Escherichia coli
production of a recombinant plasmid, pT7-GO by insertion of the DNA encoding for glycine oxidase into the multiple cloning site of the expression vector pT7.7. The pT7-glycine oxidase encodes a fully active fusion protein with six additional residues at the N-terminus of glycine oxidase. In BL21(DE3)pLysS Escherichia coli cells, and under optimal isopropyl thio-beta-D-galactoside induction conditions, soluble and active chimeric glycine oxidase is expressed up to 1.14 U per mg of cell. An N-terminally His-tagged glycine oxidase is also successfully expressed in Escherichia coli as a soluble protein and a fully active holoenzyme
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
A45H/G300C
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monomeric in solution. Upon incubation of apoprotein with FAD, neither FAD binding nor enzymatic activity is observed. Slow elimination of urea from partially unfolded mutant in presence of a large excess of FAD and 30% glyccerol does not produce the holoenzyme
A54R
-
20fold increase in Km for glyphosate
G300C
-
upon incubation of apoprotein with FAD, neither FAD binding nor enzymatic activity is observed. Slow elimination of urea from partially unfolded mutant in presence of a large excess of FAD and 30% glycerol does not produce the holoenzyme
G51R
-
4000fold increase in the specificity constant for substrate glyphosate
G51R/A54R
-
5800fold increase in the specificity constant for substrate glyphosate
G51S/A54R
-
3100fold increase in the specificity constant for substrate glyphosate
G51S/A54R/H244A
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210fold increase in catalytic activity and 15000fold increase in the specificity constant for substrate glyphosate. The alpha2-alpha3-loop assumes a different conformation, residue R54 may be the key residue in stabilizing glyphosate binding
H244A
-
2fold increase in expression yield
H244F
-
shows increased kcat value for glycine compared to the wild type enzyme, the mutation does not affect the expression of glycine oxidase and the physicochemical properties of bound FAD
H244N
-
shows increased kcat value for glycine compared to the wild type enzyme, the mutation does not affect the expression of glycine oxidase and the physicochemical properties of bound FAD
H244Q
-
shows increased kcat value compared to the wild type enzyme, the mutation does not affect the expression of glycine oxidase and the physicochemical properties of bound FAD
I15V
-
the mutant exhibits a 7fold higher specific activity compared to the wild type enzyme
Y241H
-
100fold increase in the specificity constant for substrate glyphosate
Renatured/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
the isolated apoprotein species is present in solution as a monomer which rapidly recovers its tertiary structure and converts into the tetrameric holoenzyme following incubation with free FAD. The reconstitution process follows a particular two-stage process, the spectral properties of the reconstituted holoenzyme are virtually indistinguishable from those observed with native glycine oxidase, while the activity is only recovered to about 50%. The urea-induced unfolding process of glycine oxidase can be considered as a two-step process. Only a single transition at 4.5 M urea concentration is observed for the apoprotein form. The chemical denaturation of glycine oxidase holoenzyme is partially reversible
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Show AA Sequence (897 entries)
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