Information on EC 5.1.1.13 - aspartate racemase

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The expected taxonomic range for this enzyme is: Eukaryota, Bacteria, Archaea

EC NUMBER
COMMENTARY hide
5.1.1.13
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RECOMMENDED NAME
GeneOntology No.
aspartate racemase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
L-aspartate = D-aspartate
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
racemization
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
alanine metabolism
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Alanine, aspartate and glutamate metabolism
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SYSTEMATIC NAME
IUBMB Comments
aspartate racemase
Also acts, at half the rate, on L-alanine.
CAS REGISTRY NUMBER
COMMENTARY hide
37237-56-2
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ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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-
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Manually annotated by BRENDA team
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-
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Manually annotated by BRENDA team
NBRC 14252
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Manually annotated by BRENDA team
strain SY
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-
Manually annotated by BRENDA team
strain SY
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-
Manually annotated by BRENDA team
strain ATCC 9790, strain IAM 10065, no activity in strain IAM 10067
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-
Manually annotated by BRENDA team
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Manually annotated by BRENDA team
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-
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Manually annotated by BRENDA team
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-
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Manually annotated by BRENDA team
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-
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Manually annotated by BRENDA team
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-
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Manually annotated by BRENDA team
no activity in Bifidobacterium bifidum
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-
-
Manually annotated by BRENDA team
no activity in Leuconostoc mesenteroides
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-
-
Manually annotated by BRENDA team
no activity in Pediococcus pentosaceus
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-
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Manually annotated by BRENDA team
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-
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Manually annotated by BRENDA team
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-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
malfunction
physiological function
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aspartate racemase regulates adult neurogenesis
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
D-aspartate
L-aspartate
show the reaction diagram
L-Ala
D-Ala
show the reaction diagram
L-Asp
D-Asp
show the reaction diagram
L-aspartate
D-aspartate
show the reaction diagram
L-Cysteate
D-Cysteate
show the reaction diagram
L-Cysteine sulfinate
D-Cysteine sulfinate
show the reaction diagram
additional information
?
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NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
L-Asp
D-Asp
show the reaction diagram
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the enzyme regulates synthesis of the endogenous D-Asp
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-
?
L-aspartate
D-aspartate
show the reaction diagram
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
pyridoxal 5'-phosphate
additional information
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
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enzyme contains no significant amount of metal
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2-Nitro-5-thiocyanobenzoate
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5,5'-dithiobis(2-nitrobenzoate)
alpha-methyl-DL-aspartic acid
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10 mM, 12% inhibition
Amino-oxyacetate
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complete inhibition
amino-oxyacetic acid
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Citric acid
competitive
D-cycloserine
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D-penicillamine
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GTP
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non-competitive inhibition
HgCl2
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0.1 M, complete inhibition, pH 7.0, 30°C, 30 min
hydroxylamine
iodoacetamide
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L-Cycloserine
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L-Penicillamine
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N-ethylmaleimide
p-chloromercuribenzoate
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PCMB
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0.1 M, complete inhibition, pH 7.0, 30°C, 30 min
phenylhydrazine
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sodium borhydride
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thiol reagents
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-
additional information
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
ADP
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10 mM ADP increases the activity to 320% of the control
pyridoxal phosphate
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racemase contains bound pyridoxal phosphate
SH-protecting reagents
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e.g., 2-mercaptoethanol and dithiothreitol increase activity 2fold
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additional information
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.94 - 8.7
D-Asp
17.2 - 164
D-Aspartate
13.4 - 35
L-Asp
0.7 - 159
L-aspartate
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
6.4 - 42.9
D-Aspartate
2.6 - 14.9
L-aspartate
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1.48 - 1.98
ATP
7.4
Citric acid
pH 8.0, 70°C
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.39
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for L-aspartate
22.6
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for D-aspartate
460
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Vmax of recombinant enzyme, activity is assayed in 500 nl of pyrydoxal 5'-phosphate (100 nM), 0.49 ml of recombinant enzyme (0.5 mg/ml), and 0.01 mL of 1 mM L-aspartate at 37°C for 1 h in 10 mM Tris (pH 7.5)
1160
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70°C, pH not specified in the publication
additional information
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the pituitary gland is the tissue which contains the highest enzymatic activity, with 20.0 EU/mg protein, followed by: testis; brain, liver, kidney and serum, 1 enzyme unit (EU) is defined as the amount of the enzyme capable of generating 1 nmol of D-Asp in 60 min of incubation at 37°C and in the assay conditions (0.1 M Tris-HCl,10 mM EDTA, 0.1 M sodium L-aspartate)
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6.5 - 8.5
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pH 6.5: 59% of maximal activity, pH 8.5: 74% of maximal activity
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
90
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activity increases with temperature from 37°C
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
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enzyme is purified from foot muscle of Scapharca broughtonii
Manually annotated by BRENDA team
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no significant seasonal differences in racemase concentration
Manually annotated by BRENDA team
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concentration of the enzyme in optic lobe is 6fold higher than in the retina
Manually annotated by BRENDA team
additional information
PDB
SCOP
CATH
ORGANISM
UNIPROT
Escherichia coli (strain B / BL21-DE3)
Escherichia coli (strain B / BL21-DE3)
Picrophilus torridus (strain ATCC 700027 / DSM 9790 / JCM 10055 / NBRC 100828)
Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
27000
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gel filtration
27945
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x * 27945, calculation from nucleotide sequence
30000
-
1 * 30000, SDS-PAGE
37100
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predicted from cDNA
39000
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39000, SDS-PAGE
51000 - 63000
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gel filtration
60000
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gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
homodimer
monomer
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
catalytically inactive mutant C82A in complex with citric acid, 2.0 A resolution. Citric acid binds to the catalytic site, which induces a conformational change to close the active site. Residue R48 is responsible for recognizing carboxyl groups of the substrates L-/D-aspartates and stabilizing a reaction intermediate, and L164 is responsible for stabilizing a closed state structure
sitting drop vapour diffusion method at 293 K, space group P21 with a: 65.5 A, b: 58.7 A, c: 67 A and beta 109.6°
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sitting drop vapour diffusion method at 293 K, space groups: P21 with a: 65.5 A, b: 58.7 A, c: 67.0 A, and beta: 109.6°, P212121 with a: 68.1 A, b: 135 A and c: 151.5 A, and P3121 with a and b: 80.6 A and c: 70.3 A
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pH STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5.5 - 7.5
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stable
2077
6 - 7
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30°C, 30 min, stable
661647
6 - 9
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thermal stability shows a bimodal dependence on pH, with minimum stability at pH 7.5, and remarkably stability at pH 6 and pH 8-9. 10 min, pH 8, 66% loss of activity
2075
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
30
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30 min, stable up to 30°C in 0.1 M Tes buffer, pH 6.5 containing 4 mM dithiothreitol and 1 mM EDTA
50
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1 h, about 60% loss of activity, pH 7.2
60
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30 min, stable up to 60°C in presence of 40 mM D-Asp
100
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thermal stability shows a bimodal dependence on pH, with minimum stability at pH 7.5, and remarkably stability at pH 6 and pH 8-9. 10 min, pH 8, 66% loss of activity
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
aspartate racemase is purified from the Scapharca broughtonii foot muscle by a procedure that includes sodium sulfate fractionation and blue sepharose column chromatography. The purified enzyme (225 mg) is digested at 25°C for 12 h with 80 mg of lysyl endopeptidase in a reaction mixture comprising 50 mM Tris-HCl, pH 8.0, containing 2 M guanidine hydrochloride, and the resulting peptides is resolved by reverse phase high performance liquid chromatography on a capcell Pac C-8 column (0.2 mm x 15 cm) using an acetonitrile gradient in 0.06% trifluoroacetic acid
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His-tagged aspartate racemase is purified on Talon metal affinity resin
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
cloned in Escherichia coli
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enzyme is cloned into pET vector, which is transformed into BL21 Escherichia coli
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expression in Escherichia coli
expression in Synechocystes PCC 6803 with a His6-tag
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overexpression in Escherichia coli
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
K136W
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the importance of lysine-136, the presumed proton donor, is highlighted by its mutation to tryptophan, which virtually abolishes racemase activity
additional information
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the cDNA included an open reading frame of 1017 bp encoding a protein of 338 amino acids, and the deduced amino acid sequence contains a pyridoxal 5'-phosphate-binding motif
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
analysis
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estimation of age from dentin by using the racemization reaction of Asp
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