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Literature summary for 5.1.1.10 extracted from

  • Miyamoto, T.; Katane, M.; Saitoh, Y.; Sekine, M.; Homma, H.
    Identification and characterization of novel broad-spectrum amino acid racemases from Escherichia coli and Bacillus subtilis (2017), Amino Acids, 49, 1885-1894 .
    View publication on PubMed

Cloned(Commentary)

Cloned (Comment) Organism
gene racX, recombinant expression of C-terminally His-tagged enzyme in Escherichia coli strain BL21(DE3) pLysS Bacillus subtilis
gene ygeA, recombinant expression of C-terminally His-tagged enzyme in Escherichia coli strain BL21(DE3) pLysS Escherichia coli

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
additional information
-
additional information kinetics, Hanes-Woolf plots Escherichia coli
additional information
-
additional information kinetics, Hanes-Woolf plots Bacillus subtilis
25.1
-
D-homoserine pH 8.5, 37°C, recombinant enzyme Escherichia coli
27.9
-
L-lysine pH 8.5, 37°C, recombinant enzyme Bacillus subtilis
69.3
-
D-Lysine pH 8.5, 37°C, recombinant enzyme Bacillus subtilis
171
-
L-homoserine pH 8.5, 37°C, recombinant enzyme Escherichia coli

Organism

Organism UniProt Comment Textmining
Bacillus subtilis P32960
-
-
Bacillus subtilis 168 P32960
-
-
Escherichia coli P03813
-
-
Escherichia coli K-12 / MG1655 P03813
-
-

Purification (Commentary)

Purification (Comment) Organism
recombinant C-terminally His-tagged enzyme from Escherichia coli strain BL21(DE3) pLysS by nickel affinity chromatography Escherichia coli
recombinant C-terminally His-tagged enzyme from Escherichia coli strain BL21(DE3) pLysS by nickel affinity chromatography Bacillus subtilis

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
D-arginine 78.1% activity compared to LL-diaminopimelate Bacillus subtilis L-arginine
-
r
D-homoserine high activity with 75% of the activity in the other direction Escherichia coli L-homoserine
-
r
D-lysine 93.5% activity compared to LL-diaminopimelate Bacillus subtilis L-lysine
-
r
D-methionine 4.8% activity compared to L-homoserine Escherichia coli L-methionine
-
r
D-ornithine 46.7% activity compared to LL-diaLinopimelate Bacillus subtilis L-ornithine
-
r
L-alanine 0.9% activity compared to L-homoserine Escherichia coli D-alanine
-
r
L-alanine 25.9% activity compared to LL-diaminopimelate Bacillus subtilis D-alanine
-
r
L-aminobutyrate 4.0% activity compared to LL-diaminopimelate Bacillus subtilis D-aminobutyrate
-
r
L-aminobutyrate 4.6% activity compared to L-homoserine Escherichia coli D-aminobutyrate
-
r
L-arginine 90.5% activity compared to LL-diaminopimelate Bacillus subtilis D-arginine
-
r
L-asparagine 10.3% activity compared to LL-diaminopimelate Bacillus subtilis D-asparagine
-
r
L-asparagine 4.9% activity compared to L-homoserine Escherichia coli D-asparagine
-
r
L-glutamine 0.7% activity compared to L-homoserine Escherichia coli D-glutamine
-
r
L-glutamine 14.4% activity compared to LL-diaminopimelate Bacillus subtilis D-glutamine
-
r
L-histidine 32.1% activity compared to LL-diaminopimelate Bacillus subtilis D-histidine
-
r
L-histidine 7.9% activity compared to L-homoserine Escherichia coli D-histidine
-
r
L-homoserine best substrate Escherichia coli D-homoserine
-
r
L-homoserine 9.3% activity compared to LL-diaminopimelate Bacillus subtilis D-homoserine
-
r
L-homoserine 9.3% activity compared to LL-diaminopimelate Bacillus subtilis 168 D-homoserine
-
r
L-homoserine best substrate Escherichia coli K-12 / MG1655 D-homoserine
-
r
L-isoleucine 3.9% activity compared to L-homoserine Escherichia coli D-isoleucine
-
r
L-leucine 6.6% activity compared to L-homoserine Escherichia coli D-leucine
-
r
L-lysine 81.2% activity compared to LL-diaminopimelate Bacillus subtilis D-lysine
-
r
L-Methionine 13.1% activity compared to LL-diaminopimelate Bacillus subtilis D-Methionine
-
r
L-Methionine 6.0% activity compared to L-homoserine Escherichia coli D-Methionine
-
r
L-Methionine 7.9% activity compared to L-homoserine Escherichia coli D-Methionine
-
r
L-Methionine 6.0% activity compared to L-homoserine Escherichia coli K-12 / MG1655 D-Methionine
-
r
L-Norleucine 1.2% activity compared to L-homoserine Escherichia coli D-Norleucine
-
r
L-Norleucine 5.6% activity compared to LL-diaminopimelate Bacillus subtilis D-Norleucine
-
r
L-Norleucine 5.6% activity compared to LL-diaminopimelate Bacillus subtilis 168 D-Norleucine
-
r
L-Norleucine 1.2% activity compared to L-homoserine Escherichia coli K-12 / MG1655 D-Norleucine
-
r
L-Norvaline 3.6% activity compared to LL-diaminopimelate Bacillus subtilis D-Norvaline
-
r
L-Norvaline 5.8% activity compared to L-homoserine Escherichia coli D-Norvaline
-
r
L-Norvaline 3.6% activity compared to LL-diaminopimelate Bacillus subtilis 168 D-Norvaline
-
r
L-Norvaline 5.8% activity compared to L-homoserine Escherichia coli K-12 / MG1655 D-Norvaline
-
r
L-Ornithine 86.2% activity compared to LL-diaminopimelate Bacillus subtilis D-Ornithine
-
r
L-Ornithine 86.2% activity compared to LL-diaminopimelate Bacillus subtilis 168 D-Ornithine
-
r
L-phenylalanine 0.6% activity compared to L-homoserine Escherichia coli D-phenylalanine
-
r
L-phenylalanine 21.9% activity compared to LL-diaminopimelate Bacillus subtilis D-phenylalanine
-
r
L-serine 1.5% activity compared to L-homoserine Escherichia coli D-serine
-
r
L-serine 19.1% activity compared to LL-diaminopimelate Bacillus subtilis D-serine
-
r
L-tyrosine 22.8% activity compared to LL-diaminopimelate Bacillus subtilis D-tyrosine
-
r
L-valine 6.2% activity compared to L-homoserine Escherichia coli D-valine
-
r
LL-diaminopimelate best substrate Bacillus subtilis meso-diaminopimelate
-
r
LL-diaminopimelate 0.7% activity compared to L-homoserine Escherichia coli meso-diaminopimelate
-
r
additional information enzyme RacX displays broad substrate specificity but low catalytic activity. RacX preferentially racemizes arginine, lysine, and ornithine. Histochemic product analysis and quantification by HPLC and spectroscopy Bacillus subtilis ?
-
?
additional information enzyme YgeA displays broad substrate specificity but low catalytic activity. YgeA preferentially catalyzes the racemization of homoserine. Histochemic product analysis and quantification by HPLC and spectroscopy Escherichia coli ?
-
?
additional information enzyme RacX displays broad substrate specificity but low catalytic activity. RacX preferentially racemizes arginine, lysine, and ornithine. Histochemic product analysis and quantification by HPLC and spectroscopy Bacillus subtilis 168 ?
-
?
additional information enzyme YgeA displays broad substrate specificity but low catalytic activity. YgeA preferentially catalyzes the racemization of homoserine. Histochemic product analysis and quantification by HPLC and spectroscopy Escherichia coli K-12 / MG1655 ?
-
?

Subunits

Subunits Comment Organism
More quaternary structure analysis of the enzyme using BN-PAGE, overview Escherichia coli
More quaternary structure analysis of the enzyme using BN-PAGE, overview Bacillus subtilis

Synonyms

Synonyms Comment Organism
broad-spectrum amino acid racemase
-
Escherichia coli
broad-spectrum amino acid racemase
-
Bacillus subtilis
PLP-independent amino acid racemase
-
Escherichia coli
PLP-independent amino acid racemase
-
Bacillus subtilis
RacX
-
Bacillus subtilis
YgeA
-
Escherichia coli

Temperature Optimum [°C]

Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
37
-
-
Escherichia coli
37
-
-
Bacillus subtilis

Temperature Range [°C]

Temperature Minimum [°C] Temperature Maximum [°C] Comment Organism
25 45 activity range, RacX shows less than half of the activity at 37°C, almost inactive at 50°C, profile overview Bacillus subtilis
25 50 activity range, activity increases from 25°C to 37°C and is highest at 37°C. Activity decreases from 40°C to 50°C, and is almost absent at 55°C, profile overview Escherichia coli

Turnover Number [1/s]

Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
0.0013
-
L-lysine pH 8.5, 37°C, recombinant enzyme Bacillus subtilis
0.0037
-
D-Lysine pH 8.5, 37°C, recombinant enzyme Bacillus subtilis

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
8.5
-
-
Escherichia coli
8.5
-
assay at Bacillus subtilis

pH Range

pH Minimum pH Maximum Comment Organism
7 10 activity range, over 50% of maximal activity at pH 8.0-9.5, profile overview Escherichia coli
7.5 9.5 activity range, profile overview Bacillus subtilis

Cofactor

Cofactor Comment Organism Structure
additional information pyridoxal 5'-phosphate is not required by the enzyme Escherichia coli
additional information pyridoxal 5'-phosphate is not required by the enzyme Bacillus subtilis

General Information

General Information Comment Organism
additional information conformational structure modeling of RacX based on the structure of Asp racemase from Pyrococcus horikoshi, PDB ID 1JFL Bacillus subtilis

kcat/KM [mM/s]

kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
0.000047
-
L-lysine pH 8.5, 37°C, recombinant enzyme Bacillus subtilis
0.000054
-
D-Lysine pH 8.5, 37°C, recombinant enzyme Bacillus subtilis