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Information on EC 5.1.1.5 - lysine racemase
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5.1.1.5 lysine racemaseIUBMB Comments
The enzyme is involved in a lysine catabolic pathway.
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Word Map
- 5.1.1.5
- d-lysine
- putida
- lyr
-
enantiomers
- l-pipecolate
-
non-antibiotic
- biotechnology
- molecular biology
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota
Synonyms
lyr, lysine racemase, Racemase, lysine, 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
lyr
Racemase, lysine
-
-
-
-
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
L-lysine = D-lysine
-
-
-
-
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
racemization
racemization
-
-
-
-
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PATHWAY SOURCE
PATHWAYS
BRENDA
MetaCyc
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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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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
-
enzyme exhibits higher specific activity toward lysine in the L-lysine to D-lysine direction than in the reverse reaction
-
r
L-lysine
D-lysine
-
D-lysine is used by the transgenic plants as nitrogen source
-
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
-
-
?
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
-
-
?
additional information
?
-
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
-
-
?
additional information
?
-
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
-
-
?
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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NATURAL SUBSTRATE
NATURAL 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
-
r
L-lysine
D-lysine
-
enzyme exhibits higher specific activity toward lysine in the L-lysine to D-lysine direction than in the reverse reaction
-
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
-
-
?
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
-
-
?
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
dependent on, cofactor binding residues of the enzyme are Thr245, Gly262, Tyr78, Gly263, Arg173, and Arg260, overview
pyridoxal 5'-phosphate
-
required, addition of pyridoxal 5'-phosphate cannot further improve the specific activity of the recombinant whole-cell BL21?LYR
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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
additional information
-
the addition of metal ions including Ca2+, Co2+, Fe2+, Fe3+, K+, Ni2+, Mg2+, Mn2+, Cu2+, and Zn2+ at 1 mM has no significant effect on LYR activity
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INHIBITOR
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
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
75.5
L-arginine
pH 9.0, 50°C, recombinant His-tagged mutant T391Y/S394Y
14.9
L-arginine
pH 9.0, 50°C, recombinant His-tagged wild-type enzyme
34.3
L-lysine
pH 9.0, 50°C, recombinant His-tagged mutant T391Y/S394Y
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
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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
10.83
L-arginine
pH 9.0, 50°C, recombinant His-tagged wild-type enzyme
0.38
L-arginine
pH 9.0, 50°C, recombinant His-tagged mutant T391Y/S394Y
55.43
L-lysine
pH 9.0, 50°C, recombinant His-tagged wild-type enzyme
5.1
L-lysine
in 50 mM Tris-HCl (pH 8.0), 2 mM cobalt chloride at 30°C
2.57
L-lysine
pH 9.0, 50°C, recombinant His-tagged mutant T391Y/S394Y
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.73
L-arginine
pH 9.0, 50°C, recombinant His-tagged wild-type enzyme
0.005
L-arginine
pH 9.0, 50°C, recombinant His-tagged mutant T391Y/S394Y
2.55
L-lysine
pH 9.0, 50°C, recombinant His-tagged wild-type enzyme
0.075
L-lysine
pH 9.0, 50°C, recombinant His-tagged mutant T391Y/S394Y
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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
1043
purified recombinant His-tagged mutant S394T, substrate L-arginine, pH 8.0, 50°C
1185
purified recombinant His-tagged mutant S394Y, substrate L-arginine, pH 8.0, 50°C
1200
purified recombinant His-tagged mutant S394N, substrate L-arginine, pH 8.0, 50°C
1633
purified recombinant His-tagged mutant S394N, substrate L-lysine, pH 8.0, 50°C
2356
purified recombinant His-tagged mutant S394C, substrate L-lysine, pH 8.0, 50°C
2828
purified recombinant His-tagged enzyme, substrate L-lysine, pH 8.0, 50°C
3.61
substrate 10 mM L-lysine, in 50 mM Tris-HCl (pH 8.0), 2 mM cobalt chloride at 30°C
3127
purified recombinant His-tagged mutant S394T, substrate L-lysine, pH 8.0, 50°C
568
purified recombinant His-tagged enzyme, substrate L-arginine, pH 8.0, 50°C
887
purified recombinant His-tagged mutant S394Y, substrate L-lysine, pH 8.0, 50°C
980
purified recombinant His-tagged mutant S394C, substrate L-arginine, 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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pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
30
50
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TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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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
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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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
physiological function
-
enzyme Lyr catalyzes the conversion of D-lysine into L-lysine. Proteus mirabilis Lyr activity is independent of its putative signal peptide and can function in the eukaryotic endoplasmic reticulum
additional information
additional information
active site structure and substrate docking modeling, overview
additional information
-
unlike wild-type enzyme LyrWT, enzyme mutant LyrM37-KDEL is a truly intracellular D-lysine conversion enzyme
additional information
-
active site structure and substrate docking modeling, overview
-
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UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). LYSRA_THEMA
Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)
354
0
39717
Swiss-Prot
-
LYSR_OENOB
Oenococcus oeni (strain ATCC BAA-331 / PSU-1)
371
0
41354
Swiss-Prot
-
A0A0N7M119_9RHOB
176
0
18939
TrEMBL
-
A0A385FUY4_9ZZZZ
408
0
44571
TrEMBL
Secretory Pathway (Reliability: 1)
A0A1V5ZQM7_9BACT
92
0
10798
TrEMBL
-
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PDB
SCOP
CATH
UNIPROT
ORGANISM
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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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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
-
Lyr contains a globular catalytic core (amino acids 37-407) distinct from the putative signal peptide
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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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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
W355Y
-
site-directed mutagenesis, the mutant shows significantly decreased activity compared to the wild-type enzyme
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
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)
T391Y
site-directed mutagenesis, the mutant shows 47% reduced activity with L-lysine compared to the wild-type enzyme
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
A165K/N174L/T391Y
site-directed mutagenesis, the mutant shows no activity towards L-Ala, L-Lys, or L-Arg
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
-
S394N
-
site-directed mutagenesis, the mutant shows about 2.2fold 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
-
S394T
-
site-directed mutagenesis, the mutant shows 1.8fold increased activity with L-arginine compared to the wild-type enzyme
-
S394C
-
site-directed mutagenesis, the mutant shows 1.5fold increased activity with L-arginine 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
-
additional information
additional information
-
in an attempt to limit extracellular Lyr (while retaining the catalytic activity), amino acids 1-36 are removed from the enzyme (LyrM37) and a C-terminal KDEL ER retention motif (LyrM37-KDEL) is added
additional information
-
for D-lysine production, a two-step process for D-lysine production from L-lysine by the successive microbial racemization and asymmetric degradation with lysine racemase and decarboxylase is developed. L-lysine is rapidly racemized to give DL-lysine, and L-lysine is selectively catabolized to generate cadaverine by lysine decarboxylase. In order to obtain enantiopure D-lysine, chiral selective degradation of L-lysine from the reaction mixture of DL-lysine is necessary. Under optimal conditions, 750.7 mmol/l D-lysine is finally obtained from 1710 mmol/l L-lysine after 1 h of racemization reaction and 0.5 h of decarboxylation reaction. D-lysine yield can reach 48.8% with enantiomeric excess of 99% or more
additional information
-
for D-lysine production, a two-step process for D-lysine production from L-lysine by the successive microbial racemization and asymmetric degradation with lysine racemase and decarboxylase is developed. L-lysine is rapidly racemized to give DL-lysine, and L-lysine is selectively catabolized to generate cadaverine by lysine decarboxylase. In order to obtain enantiopure D-lysine, chiral selective degradation of L-lysine from the reaction mixture of DL-lysine is necessary. Under optimal conditions, 750.7 mmol/l D-lysine is finally obtained from 1710 mmol/l L-lysine after 1 h of racemization reaction and 0.5 h of decarboxylation reaction. D-lysine yield can reach 48.8% with enantiomeric excess of 99% or more
-
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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)
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)
gene lyr, expression of His-tagged wild-type and mutant enzymes in Escherichia coli strain BL21(DE3)
gene LYR, functional recombinant expression in Escherichia coli strain BL21(DE3), showing high lysine racemase activity. L-Lysine is rapidly racemized to give DL-lysine, and the D-lysine yield is approximately 48% after 0.5 h
-
gene OEOE0162, DNA and amino acid sequence determination and analysis, expression of the enzyme in Escherichia coli strain BL21
recombinant expression of C-terminally HA-tagged wild-type enzyme and mutant enzyme LyrM37-KDEL, codon optimized for mouse expression, in C3H10T1/2 cells or MDA-MB-231 cells. MDA-MB-231 cells are infected with pGIPZ lentivirus for GFP expression, and C3H10T1/2 cells are infected with pMSCV-pBabeMCS-IRES-RFP retrovirus for RFP expression, identification of proteotypic Lyr peptides suitable for relative isotopic quantification. Wild-type Proteus mirabilis Lyr is prolifically secreted from eukaryotic cells in contrast to mutant enzyme LyrM37-KDEL. Extracellular Lyr converts labeled D-lysine to labeled L-lysine in conditioned media and severely compromises coculture labeling efficiency. Cells stably transfected with LyrM37-KDEL achieve proliferation comparable to that with L-lysine when grown on concentrations of D-lysine greater than 1 mM
-
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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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
-
the enzyme is valuable to serve as a novel non-antibiotic selectable marker in the generation of transgenic plants
-
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
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 (Q04HB7), Oenococcus oeni
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
Wang, X.; Yang, L.; Cao, W.; Ying, H.; Chen, K.; Ouyang, P.
Efficient production of enantiopure D-lysine from L-lysine by a two-enzyme cascade system
Catalysts
6
168-178
2016
Proteus mirabilis, Proteus mirabilis BCRC10725
-
brenda
Tape, C.J.; Norrie, I.C.; Worboys, J.D.; Lim, L.; Lauffenburger, D.A.; Joergensen, C.
Cell-specific labeling enzymes for analysis of cell-cell communication in continuous co-culture
Mol. Cell. Proteomics
13
1866-1876
2014
Proteus mirabilis
brenda
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