Information on EC 5.1.1.5 - lysine racemase

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The expected taxonomic range for this enzyme is: Bacteria, Eukaryota

EC NUMBER
COMMENTARY hide
5.1.1.5
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RECOMMENDED NAME
GeneOntology No.
lysine racemase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
L-lysine = D-lysine
show the reaction diagram
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-
-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
racemization
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
L-lysine degradation V
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-
Lysine degradation
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-
lysine metabolism
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SYSTEMATIC NAME
IUBMB Comments
lysine racemase
The enzyme is involved in a lysine catabolic pathway.
CAS REGISTRY NUMBER
COMMENTARY hide
9024-10-6
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ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
gene OEOE0162
UniProt
Manually annotated by BRENDA team
gene lyr
UniProt
Manually annotated by BRENDA team
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-
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Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
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
D-lysine
L-lysine
show the reaction diagram
-
-
-
r
D-ornithine
L-ornithine
show the reaction diagram
-
-
-
r
L-arginine
D-arginine
show the reaction diagram
L-Lys
D-Lys
show the reaction diagram
-
-
-
-
L-lysine
D-lysine
show the reaction diagram
L-Ornithine
D-Ornithine
show the reaction diagram
-
-
-
r
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
L-lysine
D-lysine
show the reaction diagram
additional information
?
-
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
pyridoxal 5'-phosphate
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
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
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
dipicolinic acid
complete inhibition by metal-chelating agents in 50 mM Tris-HCl buffer (pH 8.0) at 30C
EDTA
complete inhibition by metal-chelating agents in 50 mM Tris-HCl buffer (pH 8.0) at 30C
hydroxylamine
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1 - 31
D-Lysine
22
D-ornithine
pH 8.0, 30C, recombinant wild-type enzyme
1 - 75.5
L-arginine
2 - 37.6
L-lysine
27
L-ornithine
pH 8.0, 30C, recombinant wild-type enzyme
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.15 - 2.83
D-Lysine
1.83
D-ornithine
Oenococcus oeni
Q04HB7
pH 8.0, 30C, recombinant wild-type enzyme
0.38 - 19.67
L-arginine
0.16 - 62.5
L-lysine
1.83
L-ornithine
Oenococcus oeni
Q04HB7
pH 8.0, 30C, recombinant wild-type enzyme
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.005 - 0.28
D-Lysine
1531
0.08
D-ornithine
Oenococcus oeni
Q04HB7
pH 8.0, 30C, recombinant wild-type enzyme
2550
0.005 - 0.73
L-arginine
123
0.006 - 2.55
L-lysine
134
0.07
L-ornithine
Oenococcus oeni
Q04HB7
pH 8.0, 30C, recombinant wild-type enzyme
192
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
1.68
substrate 10 mM D-lysine, in 50 mM Tris-HCl (pH 8.0), 2 mM cobalt chloride at 30C
3.61
substrate 10 mM L-lysine, in 50 mM Tris-HCl (pH 8.0), 2 mM cobalt chloride at 30C
568
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purified recombinant His-tagged enzyme, substrate L-arginine, pH 8.0, 50C
887
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purified recombinant His-tagged mutant S394Y, substrate L-lysine, pH 8.0, 50C
980
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purified recombinant His-tagged mutant S394C, substrate L-arginine, pH 8.0, 50C
1043
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purified recombinant His-tagged mutant S394T, substrate L-arginine, pH 8.0, 50C
1185
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purified recombinant His-tagged mutant S394Y, substrate L-arginine, pH 8.0, 50C
1200
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purified recombinant His-tagged mutant S394N, substrate L-arginine, pH 8.0, 50C
1633
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purified recombinant His-tagged mutant S394N, substrate L-lysine, pH 8.0, 50C
2356
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purified recombinant His-tagged mutant S394C, substrate L-lysine, pH 8.0, 50C
2828
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purified recombinant His-tagged enzyme, substrate L-lysine, pH 8.0, 50C
3127
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purified recombinant His-tagged mutant S394T, substrate L-lysine, pH 8.0, 50C
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 30C, 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
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
8 - 9
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recombinant His-tagged enzyme, substrate L-lysine
9
-
assay at
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
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
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
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, 20C, X-ray diffraction structure determination and analysis at 1.74 A resolution
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pH STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5 - 9
about 15% of maximal activity is observed at pHs of below 5 and above 9
701800
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
50
the enzyme shows considerable stability at 50C, with a half-life of about 3 days
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
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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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
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
EXPRESSION
ORGANISM
UNIPROT
LITERATURE
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
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
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
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site-directed mutagenesis, the mutant shows no activity towards L-Ala, L-Lys, or L-Arg
N174L
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site-directed mutagenesis, inactive mutant
R173A
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site-directed mutagenesis, inactive mutant
R173K
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site-directed mutagenesis, inactive mutant
S394C
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site-directed mutagenesis, the mutant shows 1.5fold increased activity with L-arginine compared to the wild-type enzyme
S394N
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site-directed mutagenesis, the mutant shows about 2.2fold increased activity with L-arginine compared to the wild-type enzyme
S394T
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site-directed mutagenesis, the mutant shows 1.8fold increased activity with L-arginine compared to the wild-type enzyme
S394Y
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site-directed mutagenesis, the mutant shows 2.1fold increased activity with L-arginine compared to the wild-type enzyme
T391Y
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site-directed mutagenesis, the mutant shows 47% reduced activity with L-lysine compared to the wild-type enzyme
T391Y/S394Y
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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
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site-directed mutagenesis, the mutant shows no activity towards L-Ala, L-Lys, or L-Arg
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N174L
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site-directed mutagenesis, inactive mutant
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R173A
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site-directed mutagenesis, inactive mutant
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R173K
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site-directed mutagenesis, inactive mutant
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S394C
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site-directed mutagenesis, the mutant shows 1.5fold increased activity with L-arginine compared to the wild-type enzyme
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S394N
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site-directed mutagenesis, the mutant shows about 2.2fold increased activity with L-arginine compared to the wild-type enzyme
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S394T
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site-directed mutagenesis, the mutant shows 1.8fold increased activity with L-arginine compared to the wild-type enzyme
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S394Y
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site-directed mutagenesis, the mutant shows 2.1fold increased activity with L-arginine compared to the wild-type enzyme
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T391Y
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site-directed mutagenesis, the mutant shows 47% reduced activity with L-lysine compared to the wild-type enzyme
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
biotechnology
enzyme is a novel non-antibiotic selectable marker for plant transformation
molecular biology