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Literature summary for 5.1.1.5 extracted from

  • 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 (2012), PLoS ONE, 7, e48301.
    View publication on PubMedView publication on EuropePMC
Search for more literature for 5.1.1.5

Application

Application Comment Organism
molecular biology the enzyme is valuable to serve as a novel non-antibiotic selectable marker in the generation of transgenic plants Proteus mirabilis

Cloned(Commentary)

Cloned (Comment) Organism
expression of His6-tagged wild-type and mutant enzymes in Escherichia coli strain BL21(DE3) Proteus mirabilis

Crystallization (Commentary)

Crystallization (Comment) Organism
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 Proteus mirabilis

Protein Variants

Protein Variants Comment Organism
A165K/N174L/T391Y site-directed mutagenesis, the mutant shows no activity towards L-Ala, L-Lys, or L-Arg Proteus mirabilis
N174L site-directed mutagenesis, inactive mutant Proteus mirabilis
R173A site-directed mutagenesis, inactive mutant Proteus mirabilis
R173K site-directed mutagenesis, inactive mutant Proteus mirabilis
T391Y site-directed mutagenesis, the mutant shows 47% reduced activity with L-lysine compared to the wild-type enzyme Proteus mirabilis
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) Proteus mirabilis

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
14.9
-
 L-arginine pH 9.0, 50°C, recombinant His-tagged wild-type enzyme Proteus mirabilis
21.8
-
 L-lysine pH 9.0, 50°C, recombinant His-tagged wild-type enzyme Proteus mirabilis
34.3
-
 L-lysine pH 9.0, 50°C, recombinant His-tagged mutant T391Y/S394Y Proteus mirabilis
37.6
-
 L-lysine pH 9.0, 50°C, recombinant His-tagged mutant T391Y Proteus mirabilis
47.7
-
 L-arginine pH 9.0, 50°C, recombinant His-tagged mutant T391Y Proteus mirabilis
75.5
-
 L-arginine pH 9.0, 50°C, recombinant His-tagged mutant T391Y/S394Y Proteus mirabilis

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
L-lysine Proteus mirabilis
-
 D-lysine
-
 ?
L-lysine Proteus mirabilis BCRC10725
-
 D-lysine
-
 ?

Organism

Organism UniProt Comment Textmining
Proteus mirabilis M4GGR9 gene lyr
-
Proteus mirabilis BCRC10725 M4GGR9 gene lyr
-

Purification (Commentary)

Purification (Comment) Organism
recombinant His6-tagged wild-type and mutant enzymes from Escherichia coli strain BL21(DE3) by nickel affinity chromatography Proteus mirabilis

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
L-arginine weaker activity Proteus mirabilis D-arginine
-
 ?
L-arginine weaker activity Proteus mirabilis BCRC10725 D-arginine
-
 ?
L-lysine
-
 Proteus mirabilis D-lysine
-
 ?
L-lysine preferred substrate Proteus mirabilis D-lysine
-
 ?
L-lysine
-
 Proteus mirabilis BCRC10725 D-lysine
-
 ?
L-lysine preferred substrate Proteus mirabilis BCRC10725 D-lysine
-
 ?

Synonyms

Synonyms Comment Organism
lyr
-
 Proteus mirabilis

Temperature Optimum [°C]

Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
50
-
 assay at Proteus mirabilis

Turnover Number [1/s]

Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
0.38
-
 L-arginine pH 9.0, 50°C, recombinant His-tagged mutant T391Y/S394Y Proteus mirabilis
2.57
-
 L-lysine pH 9.0, 50°C, recombinant His-tagged mutant T391Y/S394Y Proteus mirabilis
10.17
-
 L-arginine pH 9.0, 50°C, recombinant His-tagged mutant T391Y Proteus mirabilis
10.83
-
 L-arginine pH 9.0, 50°C, recombinant His-tagged wild-type enzyme Proteus mirabilis
23.07
-
 L-lysine pH 9.0, 50°C, recombinant His-tagged mutant T391Y Proteus mirabilis
55.43
-
 L-lysine pH 9.0, 50°C, recombinant His-tagged wild-type enzyme Proteus mirabilis

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
9
-
 assay at Proteus mirabilis

Cofactor

Cofactor Comment Organism Structure
pyridoxal 5'-phosphate dependent on, cofactor binding residues of the enzyme are Thr245, Gly262, Tyr78, Gly263, Arg173, and Arg260, overview Proteus mirabilis

General Information

General Information Comment Organism
additional information active site structure and substrate docking modeling, overview Proteus mirabilis

kcat/KM [mM/s]

kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
0.005
-
 L-arginine pH 9.0, 50°C, recombinant His-tagged mutant T391Y/S394Y Proteus mirabilis
0.075
-
 L-lysine pH 9.0, 50°C, recombinant His-tagged mutant T391Y/S394Y Proteus mirabilis
0.21
-
 L-arginine pH 9.0, 50°C, recombinant His-tagged mutant T391Y Proteus mirabilis
0.61
-
 L-lysine pH 9.0, 50°C, recombinant His-tagged mutant T391Y Proteus mirabilis
0.73
-
 L-arginine pH 9.0, 50°C, recombinant His-tagged wild-type enzyme Proteus mirabilis
2.55
-
 L-lysine pH 9.0, 50°C, recombinant His-tagged wild-type enzyme Proteus mirabilis