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Enzyme Nomenclature
Information on EC 5.1.1.5 - lysine racemase
for references in articles please use BRENDA:EC5.1.1.5
Word Map on EC 5.1.1.5
- 5.1.1.5
- d-lysine
- putida
-
non-antibiotic
- l-pipecolate
-
enantiomers
- molecular biology
- biotechnology
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The expected taxonomic range for this enzyme is: Bacteria, Eukaryota
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EC NUMBER 
COMMENTARY 
5.1.1.5
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RECOMMENDED NAME
GeneOntology No.
lysine racemase
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
L-lysine = D-lysine
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-
-
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
racemization
racemization
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-
-
-
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
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SYSTEMATIC NAME
IUBMB Comments
lysine racemase
The enzyme is involved in a lysine catabolic pathway.
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CAS REGISTRY NUMBER
COMMENTARY
9024-10-6
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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
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
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
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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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
L-lysine
D-lysine
-
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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-
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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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-
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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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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
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
?
-
-
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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-
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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
?
-
-
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
-
-
-
additional information
?
-
-
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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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
pyridoxal 5'-phosphate
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dependent on, cofactor binding residues of the enzyme are Thr245, Gly262, Tyr78, Gly263, Arg173, and Arg260, overview
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
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
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INHIBITORS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
23.48
D-Lysine
in 50 mM Tris-HCl (pH 8.0), 2 mM cobalt chloride at 30°C
2 - 6
L-lysine
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pH 8.0, 50°C, recombinant mutant S394C; pH 8.0, 50°C, recombinant mutant S394N
16.21
L-lysine
in 50 mM Tris-HCl (pH 8.0), 2 mM cobalt chloride at 30°C
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
2.16
D-Lysine
in 50 mM Tris-HCl (pH 8.0), 2 mM cobalt chloride at 30°C
5.1
L-lysine
in 50 mM Tris-HCl (pH 8.0), 2 mM cobalt chloride at 30°C
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
30
50
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PDB
SCOP
CATH
ORGANISM
UNIPROT
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
42700
protein composed of 393 amino acids with the calculated molecular mass, confirmed by SDS-PAGE
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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, 20°C, X-ray diffraction structure determination and analysis at 1.74 A resolution
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pH STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
5 - 9
about 15% of maximal activity is observed at pHs of below 5 and above 9
701800
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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
50
the enzyme shows considerable stability at 50°C, with a half-life of about 3 days
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
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 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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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
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY
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
-
site-directed mutagenesis, the mutant shows no activity towards L-Ala, L-Lys, or L-Arg
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
-
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
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site-directed mutagenesis, the mutant shows no activity towards L-Ala, L-Lys, or L-Arg
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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
-
site-directed mutagenesis, the mutant shows 1.8fold increased activity with L-arginine compared to the wild-type enzyme
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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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APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
biotechnology
enzyme is a novel non-antibiotic selectable marker for plant transformation
molecular biology
molecular biology
-
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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LINKS TO OTHER DATABASES (specific for EC-Number 5.1.1.5)
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