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Information on EC 5.1.1.5 - lysine racemase and Organism(s) Proteus mirabilis and UniProt Accession M4GGR9
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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
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enantiomers
- l-pipecolate
-
non-antibiotic
- molecular biology
- biotechnology
The taxonomic range for the selected organisms is: Proteus mirabilis
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota
Synonyms
lysine racemase, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
Racemase, lysine
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
racemization
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PATHWAY SOURCE
PATHWAYS
BRENDA
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SYSTEMATIC NAME
IUBMB Comments
lysine racemase
The enzyme is involved in a lysine catabolic pathway.
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
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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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
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
pyridoxal 5'-phosphate
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required, addition of pyridoxal 5'-phosphate cannot further improve the specific activity of the recombinant whole-cell BL21?LYR
pyridoxal 5'-phosphate
dependent on, cofactor binding residues of the enzyme are Thr245, Gly262, Tyr78, Gly263, Arg173, and Arg260, overview
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
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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
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
hydroxylamine
completely inhibition of the enzyme's L-Lys racemization at 5 mM, partially restored by the addition of pyridoxal 5'-phosphate
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
14.9
L-arginine
pH 9.0, 50°C, recombinant His-tagged wild-type enzyme
75.5
L-arginine
pH 9.0, 50°C, recombinant His-tagged mutant T391Y/S394Y
34.3
L-lysine
pH 9.0, 50°C, recombinant His-tagged mutant T391Y/S394Y
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.38
L-arginine
pH 9.0, 50°C, recombinant His-tagged mutant T391Y/S394Y
10.83
L-arginine
pH 9.0, 50°C, recombinant His-tagged wild-type enzyme
2.57
L-lysine
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
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.005
L-arginine
pH 9.0, 50°C, recombinant His-tagged mutant T391Y/S394Y
0.73
L-arginine
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
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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
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
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
50
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
physiological function
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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
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unlike wild-type enzyme LyrWT, enzyme mutant LyrM37-KDEL is a truly intracellular D-lysine conversion enzyme
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). PDB
SCOP
CATH
UNIPROT
ORGANISM
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
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Lyr contains a globular catalytic core (amino acids 37-407) distinct from the putative signal peptide
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
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
A165K/N174L/T391Y
site-directed mutagenesis, the mutant shows no activity towards L-Ala, L-Lys, or L-Arg
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)
additional information
additional information
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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
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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
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
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
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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
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
molecular biology
the enzyme is valuable to serve as a novel non-antibiotic selectable marker in the generation of transgenic plants
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
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
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)
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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
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Release 2023.1 (January 2023)
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