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Information on EC 5.1.1.5 - lysine racemase for references in articles please use BRENDA:EC5.1.1.5Word Map on EC 5.1.1.5
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The expected taxonomic range for this enzyme is: Bacteria, Eukaryota
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L-lysine = D-lysine
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racemization
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L-lysine degradation V
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lysine racemase
The enzyme is involved in a lysine catabolic pathway.
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lyr
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gene OEOE0162
UniProt
brenda
gene lyr
UniProt
brenda
gene lyr
UniProt
brenda
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brenda
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brenda
from garden soil, the lyr gene may have only recently evolved from Escherichia coli N-acetyl-gamma-glutamyl-phosphate reductase and Deinococcus radiodurans N-acyl amino acid racemase, the partial regions of both enzymes might have been combined to evolve a novel enzyme, in which the new catalytic sites are created for catalyzing the racemization of lysine
UniProt
brenda
from soil, the lyr gene may have recently evolved from Escherichia coli N-acetyl-gamma-glutamyl-phosphate reductase and Deinococcus radiodurans N-acyl amino acid racemase, the partial regions of both enzymes might have been combined to evolve a novel enzyme, in which the new catalytic sites are created for catalyzing the racemization of lysine
UniProt
brenda
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additional information
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active site structure and substrate docking modeling, overview
additional information
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active site structure and substrate docking modeling, overview
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D-lysine
L-lysine
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r
D-ornithine
L-ornithine
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r
L-Ornithine
D-Ornithine
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-
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r
additional information
?
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L-arginine
D-arginine
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-
-
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r
L-arginine
D-arginine
weaker activity
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?
L-arginine
D-arginine
weaker activity
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?
L-arginine
D-arginine
-
-
-
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r
L-lysine
D-lysine
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-
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?
L-lysine
D-lysine
-
-
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r
L-lysine
D-lysine
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?
L-lysine
D-lysine
-
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-
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r
L-lysine
D-lysine
preferred substrate
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?
L-lysine
D-lysine
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?
L-lysine
D-lysine
preferred substrate
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?
L-lysine
D-lysine
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r
L-lysine
D-lysine
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D-lysine is used by the transgenic plants as nitrogen source
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r
L-lysine
D-lysine
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enzyme exhibits higher specific activity toward lysine in the L-lysine to D-lysine direction than in the reverse reaction
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r
additional information
?
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the Oenococcus oeni lysine racemase has a specific activity towards basic amino acids, residues Thr224 and Trp355 are important for enzyme substrate specificity
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additional information
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the Oenococcus oeni lysine racemase has a specific activity towards basic amino acids, residues Thr224 and Trp355 are important for enzyme substrate specificity
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additional information
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enzyme residue S394 residue plays a crucial role in determining the preference of Lyr to lysine and arginine. No activity by wild-type and mutant enzyme with alanine, methionine, histidine, tryptophan, leucine, glutamine, asparagine and serine
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additional information
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enzyme residue S394 residue plays a crucial role in determining the preference of Lyr to lysine and arginine. No activity by wild-type and mutant enzyme with alanine, methionine, histidine, tryptophan, leucine, glutamine, asparagine and serine
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additional information
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lysine racemase, although functionally inactive for growth purposes, may still have regulatory significance in permitting cross-induction of D-lysine-related enzymes by L-lysine, and vice versa
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additional information
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L-Lys gives rise to L-pipecolate that is utilized in the biosynthesis of the piperidine alkaloids 1-acetoxy-6-aminooctahydroindolizine and 3,4,5-trihydroxyoctahydro-1-pyridine. D-Lys is converted to D-N6-acetyllysine prior to further catabolism
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additional information
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L-lysine
D-lysine
Q04HB7
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?
L-lysine
D-lysine
M4GGR9
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?
L-lysine
D-lysine
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r
L-lysine
D-lysine
M4GGR9
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?
L-lysine
D-lysine
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-
-
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r
L-lysine
D-lysine
C7ACH5
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D-lysine is used by the transgenic plants as nitrogen source
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r
L-lysine
D-lysine
C7ACH5
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enzyme exhibits higher specific activity toward lysine in the L-lysine to D-lysine direction than in the reverse reaction
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r
additional information
?
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the Oenococcus oeni lysine racemase has a specific activity towards basic amino acids, residues Thr224 and Trp355 are important for enzyme substrate specificity
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additional information
?
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Q04HB7
the Oenococcus oeni lysine racemase has a specific activity towards basic amino acids, residues Thr224 and Trp355 are important for enzyme substrate specificity
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additional information
?
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lysine racemase, although functionally inactive for growth purposes, may still have regulatory significance in permitting cross-induction of D-lysine-related enzymes by L-lysine, and vice versa
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additional information
?
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L-Lys gives rise to L-pipecolate that is utilized in the biosynthesis of the piperidine alkaloids 1-acetoxy-6-aminooctahydroindolizine and 3,4,5-trihydroxyoctahydro-1-pyridine. D-Lys is converted to D-N6-acetyllysine prior to further catabolism
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pyridoxal 5'-phosphate
dependent on
pyridoxal 5'-phosphate
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dependent on, cofactor binding residues of the enzyme are Thr245, Gly262, Tyr78, Gly263, Arg173, and Arg260, overview
pyridoxal 5'-phosphate
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dependent on
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Co2+
addition of 2 mM extrinsic divalent ions enhances the enzyme activity up to 114.5%
Mg2+
addition of 2 mM extrinsic divalent ions enhances the enzyme activity up to 83.6
Mn2+
addition of 2 mM extrinsic divalent ions enhances the enzyme activity up to 97.3%
Zn2+
analyzing of bound metal ions in purified Lyr with an inductively coupled plasma spectrometer shows that dialyzed Lyr contains 0.77 mol of Zn2+ per mol of the dimeric enzyme, while cobalt, magnesium, manganese, nickel, or copper ions are absent
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dipicolinic acid
complete inhibition by metal-chelating agents in 50 mM Tris-HCl buffer (pH 8.0) at 30°C
EDTA
complete inhibition by metal-chelating agents in 50 mM Tris-HCl buffer (pH 8.0) at 30°C
hydroxylamine
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completely inhibition of the enzyme's L-Lys racemization at 5 mM, partially restored by the addition of pyridoxal 5'-phosphate
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22
D-ornithine
pH 8.0, 30°C, recombinant wild-type enzyme
27
L-ornithine
pH 8.0, 30°C, recombinant wild-type enzyme
1 - 2
D-Lysine
pH 8.0, 30°C, recombinant mutant T224I
9.8
D-Lysine
pH 8.0, 30°C, recombinant wild-type enzyme
21
D-Lysine
pH 8.0, 30°C, recombinant mutant W355Y
23.48
D-Lysine
in 50 mM Tris-HCl (pH 8.0), 2 mM cobalt chloride at 30°C
31
D-Lysine
pH 8.0, 30°C, recombinant mutant T224I/W355Y
1 - 2.5
L-arginine
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pH 8.0, 50°C, recombinant mutant S394C
1 - 7
L-arginine
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pH 8.0, 50°C, recombinant mutant S394T
14.9
L-arginine
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pH 9.0, 50°C, recombinant His-tagged wild-type enzyme
14.9
L-arginine
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pH 8.0, 50°C, recombinant wild-type enzyme
17.1
L-arginine
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pH 8.0, 50°C, recombinant mutant S394N
17.8
L-arginine
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pH 8.0, 50°C, recombinant mutant S394Y
47.7
L-arginine
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pH 9.0, 50°C, recombinant His-tagged mutant T391Y
75.5
L-arginine
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pH 9.0, 50°C, recombinant His-tagged mutant T391Y/S394Y
2 - 3
L-lysine
pH 8.0, 30°C, recombinant mutant W355Y
2 - 6
L-lysine
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pH 8.0, 50°C, recombinant mutant S394C; pH 8.0, 50°C, recombinant mutant S394N
11
L-lysine
pH 8.0, 30°C, recombinant wild-type enzyme
15
L-lysine
pH 8.0, 30°C, recombinant mutant T224I
16.21
L-lysine
in 50 mM Tris-HCl (pH 8.0), 2 mM cobalt chloride at 30°C
21.8
L-lysine
-
pH 9.0, 50°C, recombinant His-tagged wild-type enzyme
21.8
L-lysine
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pH 8.0, 50°C, recombinant wild-type enzyme
25.2
L-lysine
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pH 8.0, 50°C, recombinant mutant S394T
26.5
L-lysine
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pH 8.0, 50°C, recombinant mutant S394Y
27
L-lysine
pH 8.0, 30°C, recombinant mutant T224I/W355Y
34.3
L-lysine
-
pH 9.0, 50°C, recombinant His-tagged mutant T391Y/S394Y
37.6
L-lysine
-
pH 9.0, 50°C, recombinant His-tagged mutant T391Y
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1.83
D-ornithine
pH 8.0, 30°C, recombinant wild-type enzyme
1.83
L-ornithine
pH 8.0, 30°C, recombinant wild-type enzyme
0.15
D-Lysine
pH 8.0, 30°C, recombinant mutant T224I/W355Y
0.28
D-Lysine
pH 8.0, 30°C, recombinant mutant T224I
0.88
D-Lysine
pH 8.0, 30°C, recombinant mutant W355Y
2.16
D-Lysine
in 50 mM Tris-HCl (pH 8.0), 2 mM cobalt chloride at 30°C
2.83
D-Lysine
pH 8.0, 30°C, recombinant wild-type enzyme
0.38
L-arginine
-
pH 9.0, 50°C, recombinant His-tagged mutant T391Y/S394Y
10.17
L-arginine
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pH 9.0, 50°C, recombinant His-tagged mutant T391Y
10.83
L-arginine
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pH 9.0, 50°C, recombinant His-tagged wild-type enzyme
10.83
L-arginine
-
pH 8.0, 50°C, recombinant wild-type enzyme
16.2
L-arginine
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pH 8.0, 50°C, recombinant mutant S394C
17.45
L-arginine
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pH 8.0, 50°C, recombinant mutant S394T
18.75
L-arginine
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pH 8.0, 50°C, recombinant mutant S394N
19.67
L-arginine
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pH 8.0, 50°C, recombinant mutant S394Y
0.16
L-lysine
pH 8.0, 30°C, recombinant mutant T224I/W355Y
0.32
L-lysine
pH 8.0, 30°C, recombinant mutant T224I
1.03
L-lysine
pH 8.0, 30°C, recombinant mutant W355Y
2.57
L-lysine
-
pH 9.0, 50°C, recombinant His-tagged mutant T391Y/S394Y
3.5
L-lysine
pH 8.0, 30°C, recombinant wild-type enzyme
5.1
L-lysine
in 50 mM Tris-HCl (pH 8.0), 2 mM cobalt chloride at 30°C
14.93
L-lysine
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pH 8.0, 50°C, recombinant mutant S394Y
23.07
L-lysine
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pH 9.0, 50°C, recombinant His-tagged mutant T391Y
31.25
L-lysine
-
pH 8.0, 50°C, recombinant mutant S394N
50.68
L-lysine
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pH 8.0, 50°C, recombinant mutant S394C
55.43
L-lysine
-
pH 9.0, 50°C, recombinant His-tagged wild-type enzyme
55.43
L-lysine
-
pH 8.0, 50°C, recombinant wild-type enzyme
62.5
L-lysine
-
pH 8.0, 50°C, recombinant mutant S394T
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0.08
D-ornithine
pH 8.0, 30°C, recombinant wild-type enzyme
0.07
L-ornithine
pH 8.0, 30°C, recombinant wild-type enzyme
0.005
D-Lysine
pH 8.0, 30°C, recombinant mutant T224I/W355Y
0.023
D-Lysine
pH 8.0, 30°C, recombinant mutant T224I
0.042
D-Lysine
pH 8.0, 30°C, recombinant mutant W355Y
0.28
D-Lysine
pH 8.0, 30°C, recombinant wild-type enzyme
0.005
L-arginine
-
pH 9.0, 50°C, recombinant His-tagged mutant T391Y/S394Y
0.21
L-arginine
-
pH 9.0, 50°C, recombinant His-tagged mutant T391Y
0.73
L-arginine
-
pH 9.0, 50°C, recombinant His-tagged wild-type enzyme
0.006
L-lysine
pH 8.0, 30°C, recombinant mutant T224I/W355Y
0.025
L-lysine
pH 8.0, 30°C, recombinant mutant T224I
0.045
L-lysine
pH 8.0, 30°C, recombinant mutant W355Y
0.075
L-lysine
-
pH 9.0, 50°C, recombinant His-tagged mutant T391Y/S394Y
0.32
L-lysine
pH 8.0, 30°C, recombinant wild-type enzyme
0.61
L-lysine
-
pH 9.0, 50°C, recombinant His-tagged mutant T391Y
2.55
L-lysine
-
pH 9.0, 50°C, recombinant His-tagged wild-type enzyme
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1.68
substrate 10 mM D-lysine, in 50 mM Tris-HCl (pH 8.0), 2 mM cobalt chloride at 30°C
3.61
substrate 10 mM L-lysine, in 50 mM Tris-HCl (pH 8.0), 2 mM cobalt chloride at 30°C
568
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purified recombinant His-tagged enzyme, substrate L-arginine, pH 8.0, 50°C
887
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purified recombinant His-tagged mutant S394Y, substrate L-lysine, pH 8.0, 50°C
980
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purified recombinant His-tagged mutant S394C, substrate L-arginine, pH 8.0, 50°C
1043
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purified recombinant His-tagged mutant S394T, substrate L-arginine, pH 8.0, 50°C
1185
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purified recombinant His-tagged mutant S394Y, substrate L-arginine, pH 8.0, 50°C
1200
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purified recombinant His-tagged mutant S394N, substrate L-arginine, pH 8.0, 50°C
1633
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purified recombinant His-tagged mutant S394N, substrate L-lysine, pH 8.0, 50°C
2356
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purified recombinant His-tagged mutant S394C, substrate L-lysine, pH 8.0, 50°C
2828
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purified recombinant His-tagged enzyme, substrate L-lysine, pH 8.0, 50°C
3127
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purified recombinant His-tagged mutant S394T, substrate L-lysine, pH 8.0, 50°C
additional information
enzyme is incubated in 1 ml of reaction mixture containing 50 mM Tris-HCl (pH 8.0), 2 mM cobalt chloride and 10 mM L- or D-lysine at 30°C, Lyr activities in 4 week old wild type and transgenic tobacco plants are determined, the specific activity of Lyr in the transgenic T2 plants selected on L-lysine ranges from 0.77 to 1.06 mU/mg protein, although transgenic plants exhibit considerable variation in enzyme activities, no phenotypic dissimilarities associated with L-lysine selection are found, suggesting that the Lyr gene as a selectable marker could be effective over a range of expression levels
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8 - 9
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recombinant His-tagged enzyme, substrate L-lysine
8
50 mM Tris-HCl
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30
assay at
50
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assay at
50
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recombinant His-tagged enzyme, substrate L-lysine
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42700
protein composed of 393 amino acids with the calculated molecular mass, confirmed by SDS-PAGE
43000
determined by SDS-PAGE and Western Blot analysis
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purified recombinant His-tagged enzyme, sitting drop vapor diffusion method, mixing of 2.5 mg/ml protein with 0.1 M sodium acetate, pH 4.6, 0.05 M lithium chloride, and 29% w/v PEG 8000, 20°C, X-ray diffraction structure determination and analysis at 1.74 A resolution
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5 - 9
about 15% of maximal activity is observed at pHs of below 5 and above 9
701800
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50
the enzyme shows considerable stability at 50°C, with a half-life of about 3 days
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by nickel chelate affinity chromatography
recombinant His-tagged wild-type and mutant enzymes from Escherichia coli strain BL21(DE3)
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recombinant His6-tagged wild-type and mutant enzymes from Escherichia coli strain BL21(DE3) by nickel affinity chromatography
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expression in Escherichia coli
expression of His6-tagged wild-type and mutant enzymes in Escherichia coli strain BL21(DE3)
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gene lyr, expression of His-tagged wild-type and mutant enzymes in Escherichia coli strain BL21(DE3)
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gene OEOE0162, DNA and amino acid sequence determination and analysis, expression of the enzyme in Escherichia coli strain BL21
transformation of the lyr gene in Nicotiana benthamiana and Arabidopsis thaliana plants by means of Agrobacterium tumefaciens strains LBA4404 and GV3101, transgenic plants produce normal roots that penetrate into the selection medium and are healthy, the Lyr gene is found to be expressed as a protein in all the transgenic lines
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to investigate the effect of Lyr expression on the amino acid profile of the host cells, the composition of free amino acids in the leaves of wild-type and transgenic tobacco plants is determined, the results reveal a substantial 40fold and a marginal 4fold increase of free L-aspartate content in the wild-type and transgenic plants, respectively, grown on L-lysine medium as compared to plants grown on medium containing D-lysine or without lysine supplement
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T224I
site-directed mutagenesis, the mutant shows significantly decreased activity compared to the wild-type enzyme
T224I/W355Y
site-directed mutagenesis, the double mutant shows significantly decreased activity compared to the wild-type enzyme
W355Y
site-directed mutagenesis, the mutant shows significantly decreased activity compared to the wild-type enzyme
A165K/N174L/T391Y
-
site-directed mutagenesis, the mutant shows no activity towards L-Ala, L-Lys, or L-Arg
N174L
-
site-directed mutagenesis, inactive mutant
R173A
-
site-directed mutagenesis, inactive mutant
R173K
-
site-directed mutagenesis, inactive mutant
S394C
-
site-directed mutagenesis, the mutant shows 1.5fold increased activity with L-arginine compared to the wild-type enzyme
S394N
-
site-directed mutagenesis, the mutant shows about 2.2fold increased activity with L-arginine compared to the wild-type enzyme
S394T
-
site-directed mutagenesis, the mutant shows 1.8fold increased activity with L-arginine compared to the wild-type enzyme
S394Y
-
site-directed mutagenesis, the mutant shows 2.1fold increased activity with L-arginine compared to the wild-type enzyme
T391Y
-
site-directed mutagenesis, the mutant shows 47% reduced activity with L-lysine compared to the wild-type enzyme
T391Y/S394Y
-
site-directed mutagenesis,the mutant exhibits significantly reduced specific activity towards L-Lys (6% residual activity) and toward L-Arg (0.9% residual activity)
A165K/N174L/T391Y
-
site-directed mutagenesis, the mutant shows no activity towards L-Ala, L-Lys, or L-Arg
-
N174L
-
site-directed mutagenesis, inactive mutant
-
R173A
-
site-directed mutagenesis, inactive mutant
-
R173K
-
site-directed mutagenesis, inactive mutant
-
S394C
-
site-directed mutagenesis, the mutant shows 1.5fold increased activity with L-arginine compared to the wild-type enzyme
-
S394N
-
site-directed mutagenesis, the mutant shows about 2.2fold increased activity with L-arginine compared to the wild-type enzyme
-
S394T
-
site-directed mutagenesis, the mutant shows 1.8fold increased activity with L-arginine compared to the wild-type enzyme
-
S394Y
-
site-directed mutagenesis, the mutant shows 2.1fold increased activity with L-arginine compared to the wild-type enzyme
-
T391Y
-
site-directed mutagenesis, the mutant shows 47% reduced activity with L-lysine compared to the wild-type enzyme
-
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biotechnology
enzyme is a novel non-antibiotic selectable marker for plant transformation
molecular biology
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the enzyme is valuable to serve as a novel non-antibiotic selectable marker in the generation of transgenic plants
molecular biology
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the enzyme is valuable to serve as a novel non-antibiotic selectable marker in the generation of transgenic plants
-
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ARGR_PSETA
409
43976
Swiss-Prot
LYSR_OENOB
Oenococcus oeni (strain ATCC BAA-331 / PSU-1)
371
41354
Swiss-Prot
A0A0P1GIY9_9RHOB
93
9585
TrEMBL
A0A136MRW8_9BACT
188
20260
TrEMBL
A0A0N7M119_9RHOB
176
18939
TrEMBL
C7ACH5_9BACT
393
42694
TrEMBL
M4GGR9_PROMI
407
44917
TrEMBL
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Guengerich, F.P.; Broquist, H.P.
Biosynthesis of slaframine, (1S,6S,8aS)-1-acetoxy-6-aminooctahydroindolizine, a parasympathomimetic alkaloid of fungal origin. II. The origin of pipecolic acid
Biochemistry
12
4270-4274
1973
Slafractonia leguminicola
brenda
Chang, Y.F.; Adams, E.
D-lysine catabolic pathway in Pseudomonas putida: interrelations with L-lysine catabolism
J. Bacteriol.
117
753-764
1974
Pseudomonas putida
brenda
Chen, I.; Lin, W.; Hsu, S.; Thiruvengadam, V.; Hsu, W.
Isolation and characterization of a novel lysine racemase from a soil metagenomic library
Appl. Environ. Microbiol.
75
5161-5166
2009
uncultured bacterium (C7ACH5)
brenda
Chen, I.C.; Thiruvengadam, V.; Lin, W.D.; Chang, H.H.; Hsu, W.H.
Lysine racemase: a novel non-antibiotic selectable marker for plant transformation
Plant Mol. Biol.
72
153-169
2010
uncultured bacterium (C7ACH5)
brenda
Kato, S.; Hemmi, H.; Yoshimura, T.
Lysine racemase from a lactic acid bacterium, Oenococcus oeni: structural basis of substrate specificity
J. Biochem.
152
505-508
2012
Oenococcus oeni, Oenococcus oeni (Q04HB7)
brenda
Wu, H.M.; Kuan, Y.C.; Chu, C.H.; Hsu, W.H.; Wang, W.C.
Crystal structures of lysine-preferred racemases, the non-antibiotic selectable markers for transgenic plants
PLoS ONE
7
e48301
2012
Proteus mirabilis (M4GGR9), Proteus mirabilis BCRC10725 (M4GGR9), Proteus mirabilis BCRC10725
brenda
Kuan, Y.; Kao, C.; Chen, C.; Chen, C.; Hu, H.; Hsu, W.
Biochemical characterization of a novel lysine racemase from Proteus mirabilis BCRC10725
Process Biochem.
46
1914-1920
2011
Proteus mirabilis (M4GGR9), Proteus mirabilis BCRC10725 (M4GGR9)
-
brenda
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