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Enzyme Nomenclature
Information on EC 5.1.1.10 - amino-acid racemase
for references in articles please use BRENDA:EC5.1.1.10
Word Map on EC 5.1.1.10
- 5.1.1.10
-
racemization
- pyridoxal
- 5'-phosphate
-
plp-dependent
-
alpha-hydrogen
-
l-enantiomers
- d-glutamate
-
5'-phosphate-dependent
- biotechnology
- synthesis
- analysis
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The expected taxonomic range for this enzyme is: Bacteria, Eukaryota
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EC NUMBER 
COMMENTARY 
5.1.1.10
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RECOMMENDED NAME
GeneOntology No.
amino-acid racemase
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
an L-amino acid = a D-amino acid
-
-
-
-
an L-amino acid = a D-amino acid
significant internal return of the alpha-hydrogen; single base mechanism
-
an L-amino acid = a D-amino acid
enzyme abstracts a hydrogen nonstereospecifically from C-4' of the coenzyme
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an L-amino acid = a D-amino acid
the results of the mechanistic studies argue against a single base mechanism and are best rationalized in terms of a double base model where only one of the bases undergoes proton exchange with the solvent while the amino acid is enzyme-bound
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an L-amino acid = a D-amino acid
the results of the mechanistic studies argue against a single base mechanism and are best rationalized in terms of a double base model where only one of the bases undergoes proton exchange with the solvent while the amino acid is enzyme-bound
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
racemization
-
-
-
-
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
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SYSTEMATIC NAME
IUBMB Comments
amino-acid racemase
A pyridoxal-phosphate protein.
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CAS REGISTRY NUMBER
COMMENTARY
9068-61-5
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
bifunctional enzyme, racemization of serine and elimination of L-serine and L-serine-O-sulfate to form pyruvate
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bifunctional enzyme, racemization of serine and elimination of L-serine and L-serine-O-sulfate to form pyruvate
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bifunctional enzymes, racemization of serine and alpha,beta-elimination of L-serine
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isoforms A and B, bifunctional enzymes, racemization of serine and elimination of L-serine and L-serine-O-sulfate to form pyruvate
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-
-
-
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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
D-2,4-Diaminobutyrate
L-2,4-Diaminobutyrate
-
10% of the activity relative to D-Lys
-
-
D-aspartate
L-aspartate
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lower substrate affinity for D-aspartate compared to L-aspartate
-
-
?
D-homoarginine
L-homoarginine
6.2% activity, compared to D-Lys
-
-
?
L-aspartate
D-aspartate
-
higher substrate affinity for L-aspartate compared to D-aspartate
-
-
?
L-Homocysteine
D-Homocysteine
-
55% of the activity relative to L-Lys
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-
L-Selenohomocysteine
D-Selenohomocysteine
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27% of the activity relative to L-Lys
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L-serine
S-serine
-
similar substrate affinity for both L-serine and D-serine
-
-
?
L-threonine
3-hydroxy-2-butenoic acid + NH3
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alpha,beta-elimination reaction
-
-
?
D-serine
L-serine
-
similar substrate affinity for both L-serine and D-serine
-
-
?
L-2-Aminobutyrate
D-2-Aminobutyrate
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4.7% of the activity relative to D-Lys
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-
-
L-Homoarginine
L-Homoarginine
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67% of the activity relative to L-Lys
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-
L-Homoarginine
L-Homoarginine
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80% of the activity relative to L-Lys
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L-Homocitrulline
D-Homocitrulline
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34% of the activity relative to L-Lys
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-
L-Homocitrulline
D-Homocitrulline
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45% of the activity relative to L-Lys
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-
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N6-Acetyl-L-Lys
N6-Acetyl-D-Lys
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37% of the activity relative to L-Lys
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N6-Acetyl-L-Lys
N6-Acetyl-D-Lys
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80% of the activity relative to L-Lys
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-
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S-Methyl-L-Cys
S-Methyl-D-Cys
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43% of the activity relative to L-Lys
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-
additional information
?
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DAR1 has no detectable activity with 100 mM L-glutamate or 100 mM L-alanine
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-
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additional information
?
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racemization and elimination activities reside at the same active site of enzyme. Racemization activity is specific to serine, elimination activity has a broader specificity for L-amino acids with a suitable leaving group at the beta-carbon
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-
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additional information
?
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ration of elimination reaction/racemization reaction for substrate L-serine is 3.7
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-
-
additional information
?
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catalyzes nonstereospecific transamination: production of D-Glu and L-Glu from 2-oxoglutarate through transamination with L-Orn
-
-
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additional information
?
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the relative activity is 1 for Leu, 1.8 for L-2-aminobutyrate, 3.3 for L-Ala, 5.2 for norvaline, 5.9 for L-norleucine, 7.5 for D-Arg, 10.6 for L-Met, 13.2 for D-Lys, and 15.9 for L-ethionine
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-
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additional information
?
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no activity with: D-Glu, L-Ile, L-Phe, L-Thr, L-Val
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-
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
pyridoxal 5'-phosphate
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holoenzyme contains 2 mol of pyridoxal 5'-phosphate per mol of enzyme; Km: 0.2 mM
pyridoxal 5'-phosphate
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holoenzyme contains 2 mol of pyridoxal 5'-phosphate per mol of enzyme; Km: 0.0026 mM; required for maximal activity
pyridoxal 5'-phosphate
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contains 1 mol of pyridoxal 5'-phosphate per mol of subunit; holoenzyme contains 2 mol of pyridoxal 5'-phosphate per mol of enzyme
pyridoxal 5'-phosphate
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holoenzyme contains 2 mol of pyridoxal 5'-phosphate per mol of enzyme; Km: 0.0026 mM
pyridoxal 5'-phosphate
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holoenzyme contains 2 mol of pyridoxal 5'-phosphate per mol of enzyme; pyridoxal phosphate enzyme
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Ca2+
Co2+
Mg2+
Mn2+
Co2+
-
enzyme requires a divalent cation for activity. Maximal enzymatic activity with Co2+
Mg2+
-
MgCl2 alone (2 mM) has only a small effect on enzyme racemase activity, but when Mg2+ and ATP are present, the enzyme shows the largest activity for the D-Asp and D-Ser conversions
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INHIBITORS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
3-chloroalanine
-
inactivator binds to the same Lys residue which binds pyridoxyl 5'-phosphate
3-Fluoroalanine
-
inactivator binds to the same Lys residue which binds pyridoxyl 5'-phosphate
ATP
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inhibitory to L-serine O-sulfate dehydration reaction, activating for racemization reraction
O-acetylserine
-
inactivator binds to the same Lys residue which binds pyridoxyl 5'-phosphate
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
ATP
-
ATP alone (4 mM) significantly increases enzyme activity, but when the combination of ATP and Mg2+ is present, the enzyme shows the largest activity for the D-Asp and D-Ser conversions
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
30
L-Met
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crude lyophilisates, 25°C, pH 6, Vmax: 1174 micromol/min/g; crude lyophilisates, 30°C, pH 7, Vmax: 2296 micromol/min/g
15
L-serine
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in 50 mM Tris-HCl buffer, pH 8.5, for Ser reactions, at 30°C
16
L-serine
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in 50 mM Tris-HCl buffer, pH 8.5, for Ser reactions, at 30°C
additional information
additional information
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no activity with N-Succinyl-L-Pro
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additional information
additional information
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model-based calculations suggested that a methanol content of 10% and an acetonitrile content of 20% provide maximum productivity in enzyme membrane reactor (EMR) operations. However product concentrations are decreased in comparison to purely aqueous operation due to decreasing solubility of methionine with increasing organic solvent content.
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additional information
N-Succinyl-L-Arg
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low specific rotation prevented kinetic analysis
additional information
N-Succinyl-L-Asn
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low specific rotation prevented kinetic analysis
additional information
N-Succinyl-L-Asp
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low specific rotation prevented kinetic analysis
additional information
N-Succinyl-L-Cys
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low specific rotation prevented kinetic analysis
additional information
N-Succinyl-L-Gln
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low specific rotation prevented kinetic analysis
additional information
N-Succinyl-L-Glu
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low specific rotation prevented kinetic analysis
additional information
N-Succinyl-L-Lys
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low specific rotation prevented kinetic analysis
additional information
N-Succinyl-L-Thr
-
low specific rotation prevented kinetic analysis
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
additional information
-
no activity with N-Succinyl-L-Pro; N-Succinyl-L-Cys, low specific rotation prevented kinetic analysis; N-Succinyl-L-Thr, low specific rotation prevented kinetic analysis
-
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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
708.4
additional information
-
wildtype BAR, specific activity for L-Lys 100%, L-Arg 65%, L-Ala 33%, L-Ser 20%, L-Met 14%, L-Cys 14%, L-Leu 3.3%, L-His 1.6%, L-Phe 0.29%, L-Pro 0.1.3%, L-Thr 0.069%, L-Asn 0.054%, L-Asp 0.01%, L-Trp 0.006%, L-Val 0.003%
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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
37
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
-
DAR1 is localized to the medial region of the cerebral ganglion where the F- and C-clusters are situated
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LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
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PDB
SCOP
CATH
ORGANISM
UNIPROT
Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
45000
110000
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SUBUNITS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dimer
homodimer
tetramer
-
gel filtration and analytical ultracentrifugation. Tetrameric structure in the absence or presence of Co2+, 4 * 42300 Da
homodimer
-
2 * 35400, calculated from amino acid sequence; 2 * 36000, SDS-PAGE
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POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
proteolytic modification
N-terminal signal sequence is cleaved off
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Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
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pH STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
6.5 - 8.5
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the enzyme shows little racemase activity below pH 6.5 and an increasing activity between pH 7.0-8.5 in 50 mM Tris-HCl buffer
715591
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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
14 - 50
-
the enzyme activity increases between 14-45°C and starts to decrease at 50°C for both the Ser and Asp conversion
60
60
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GkNSAAR shows a gradual loss of activity at preincubation temperatures over 60°C
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GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
buffer without organic content provides excellent stability at moderate temperatures (20–35°C) while addition of 20% acetonitrile or methanol drastically reduces the half-life of the racemase
-
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STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
0-5°C, 0.01 M potassium phosphate buffer, pH 7.0, 2 mM pyridoxal 5'-phosphate, 1 month, stable
-
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli with N-terminal His-tag, purification protocol from inclusion bodies
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protein is purified by applying to a diethylaminoethyl sepharose fast flow column and a phenyl sepharose 6 fast flow column
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purified in a one-step procedure by immobilized cobalt affinity chromatography
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two enzyme lyophilisates of different purity are obtained from which the crude is sufficient for the racemization of methionine and the pure is used for asparagine
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
amino acid racemase of Pseudomonas putida DSM 3263 is overexpressed in Escherichia coli and delivered cell free extract with easily sufficient activity (20–50 U/mg total protein) for application in an enzyme membrane reactor (EMR) setting
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over-expressed in Escherichia coli
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
H152S
-
ratio of elimination reaction to racemization is 1.4 compared to 3.7 in wild-type
N154F
-
ratio of elimination reaction to racemization is 0.33 compared to 3.7 in wild-type
P153S
-
ratio of elimination reaction to racemization is 0.24 compared to 3.7 in wild-type
Q155D
-
ratio of elimination reaction to racemization is 0.25 compared to 3.7 in wild-type
I384M
-
I384M mutant BAR shows the highest activity for Trp. Using I384M mutant BAR the proportion of D-Trp reaches 43% while wildtype BAR racemizes only 6% of initial L-Trp; specific activity: 0.124 (substrate Trp), 0.0744 (substrate Phe), 0.223 (substrate Lys), 0.026 (substrate Ala)
I83L/D361V/Y396C
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specific activity: 0.0303 (substrate Trp), 0.0257 (substrate Phe), 0.473 (substrate Lys), 0.0121 (substrate Ala)
L126H/Y396C
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specific activity: 0.0524 (substrate Trp), 0.0436 (substrate Phe), 0.477 (substrate Lys), 0.0144 (substrate Ala)
Y293A/Y301S/Y396C
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specific activity: 0.0267 (substrate Trp), 0.0249 (substrate Phe), 0.458 (substrate Lys), 0.0141 (substrate Ala)
Y396C
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specific activity: 0.0487 (substrate Trp), 0.00706 (substrate Phe), 0.03215 (substrate Lys), 0.825 (substrate Ala)
additional information
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random mutagenesis on bar gene is performed to obtain mutant BAR derivates with high activity for Trp. Five positive mutant are isolated after the two-step-screening of the randomly mutated BAR; substitutions at Y396 and I384 increases the Trp specific racemization activity and the racemazation activity for overall amino acids, respectively
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
analysis
-
simple procedure for in situ analysis of stereospecificity of C-4 hydrogen transfer of NADH by an NAD-dependent dehydrogenase by combination with amino acid racemase, EC 5.1.1.10, and L-leucine dehydrogenase, EC 1.4.1.9
biotechnology
synthesis
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enzymatic production of L-Trp from DL-Ser and indole by a coupled reaction of tryptophan synthase and amino acid racemase
biotechnology
-
since commercially available D-Trp is chemically synthesized and expensive a mutant BAR protein might represent an effective method to synthesize D-Trp
biotechnology
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an enzyme lyophilisate of amino acid racemase from Pseudomonas putida is used for in situ racemization. Crystallization experiments accompanied by enzymatic racemization lead to a significant increase of crystallized L-Asn
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LINKS TO OTHER DATABASES (specific for EC-Number 5.1.1.10)
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