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L-serine = D-serine

-
-
-
-
L-serine = D-serine
reaction mechanism, overview
L-serine = D-serine
racemase and dehydratase reaction mechanism of serine racemase, overview
-
L-serine = D-serine
racemase and dehydratase reaction mechanism of serine racemase, overview
L-serine = D-serine
substrate recognition mechanism and catalytic mechanisms of both reactions, the racemization and the dehydration of serine, residues Lys57 and Ser82 located on the protein and solvent sides, respectively, with respect to the cofactor plane, are acid-base catalysts that shuttle protons to the substrate. Racemization mechanism via carbanion intermediate, alpha-aminoacrylate intermediate, and pyridoxal 5'-phosphate-lysine-D-alanine Schiff base
L-serine = D-serine
L-serine forms Schiff base with the cofactor pyridoxal 5'-phosphate, the free (non-pyridoxal 5'-phosphate cofactor binding) amino group of K56 is in the vicinity of the hydrogen on the Calpha atom, allowing the side chain of K56 to extract the proton away from the Ca atom and form a planar intermediate. the hydroxyl group of S84, on the re-face of this planar intermediate, donates its hydrogen to the Calpha atom of the intermediate resulting in the formation of D-serine. The subsequent attack of K56 on the cofactor forms the Schiff base and releases D-serine as the product. If the starting substrate is D-serine, S84 is likely to be protonated, favoring the extraction of hydrogen from the Calpha atom of pyridoxal 5'-phosphate-D-serine. The resulting planar intermediate allows K56 amino group to provide a proton from the si-face, restoring the L-serine intermediate. As a result, K56 reacts with pyridoxal 5'-phosphate to form the Schiff base and releases the L-serine as the final product. Catalytic mechanism, overview
L-serine = D-serine
the abstraction and addition of alpha-hydrogen to L- and D-serine are conducted by residues K56 and S81 at the si- and re-sides, respectively, of pyridoxal 5'-phosphate, K56 functions as a residue that abstracts the alpha-hydrogen from the Schiff base intermediate, two-base catalytic mechanism, overview
-
L-serine = D-serine
two-base racemization mechanism, overview. The enzyme utilizes a two-base mechanism wherein one enantiospecific Broensted base abstracts the proton from the L-Ser-pyridoxal 5'-phosphate aldimine and the conjugate acid of a second enantiospecific Bronsted base protonates the intermediate to form the D-Ser-pyridoxal 5'-phosphate aldimine, and vice versa
-
L-serine = D-serine
analysis of the catalytic reaction mechanism and intermediate stabilization in mammalian serine racemase using multiscale quantum-classical simulations, hybrid quantum mechanics/molecular mechanics molecular dynamics simulations in conjunction with umbrella sampling are performed, overview. The unprotonated pyridoxal 5'-phosphate-substrate intermediate is stabilized mostly due to solvation effects contributed by water molecules and active-site residues, as well as long-range electrostatic interactions with the enzyme environment
L-serine = D-serine
analysis of the catalytic reaction mechanism and intermediate stabilization in mammalian serine racemase using multiscale quantum-classical simulations, hybrid quantum mechanics/molecular mechanics molecular dynamics simulations in conjunction with umbrella sampling are performed, overview. The unprotonated pyridoxal 5'-phosphate-substrate intermediate is stabilized mostly due to solvation effects contributed by water molecules and active-site residues, as well as long-range electrostatic interactions with the enzyme environment
L-serine = D-serine
reaction mechanism, the enzyme catalyzes the racemization of serine, but also the alpha,beta-elimination of serine forming pyruvate. Mechanicistically, the racemization and alpha,beta-elimination reactions share the same intermediate, represented by a resonance-stabilized carbanion. The intermediate forms a partition between the two pathways. L-Serine binds to pyridoxal 5'-phosphate, yielding an external aldimine intermediate, followed by the abstraction of the alpha-proton by Lys56 and formation of a planar resonance-stabilized carbanion. At this point, protonation in the opposite side of the carbanion intermediate (mediated by the Ser84-OH group) generates D-serine. Since the proton abstraction and the reprotonation steps are performed by different residues (Lys56 and Ser84) that work as acid/base catalysts, serine racemase racemization is consistent with a two-base mechanism
L-serine = D-serine
reaction mechanism, the enzyme catalyzes the racemization of serine, but also the alpha,beta-elimination of serine forming pyruvate. Mechanicistically, the racemization and alpha,beta-elimination reactions share the same intermediate, represented by a resonance-stabilized carbanion. The intermediate forms a partition between the two pathways. L-Serine binds to pyridoxal 5'-phosphate, yielding an external aldimine intermediate, followed by the abstraction of the alpha-proton by Lys56 and formation of a planar resonance-stabilized carbanion. At this point, protonation in the opposite side of the carbanion intermediate (mediated by the Ser84-OH group) generates D-serine. Since the proton abstraction and the reprotonation steps are performed by different residues (Lys56 and Ser84) that work as acid/base catalysts, serine racemase racemization is consistent with a two-base mechanism
L-serine = D-serine
reversible racemization and irreversible dehydration reactions are catalyzed by eukaryotic serine racemase, overview
L-serine = D-serine
SRR catalyses Ser racemization via a two-base mechanism in which two catalytic residues, Lys56 and Ser84 play vital roles in the abstraction and donation of alpha-proton of L-Ser and D-Ser, respectively
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beta-chloro-L-alanine
pyruvate + NH3 + ?
-
the artificial serine racemase substrate is degraded via alpha,beta-elimination
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?
D-alanine
L-alanine
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r
D-serine
S-serine
-
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-
-
?
D-threonine
L-threonine
13% of the activity with L-serine
-
-
r
L-arginine
D-arginine
7% of the activity with L-serine
-
-
?
L-glutamine
D-glutamine
4.5% of the activity with L-serine
-
-
?
L-serine O-sulfate
O-sulfopyruvate + NH3
L-serine O-sulfate
pyruvate + NH3 + ?
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the artificial serine racemase substrate is degraded via alpha,beta-elimination
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-
?
L-serine-O-sulfate
O-sulfopyruvate + NH3
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elimination reaction
-
-
?
L-threo-3-hydroxyaspartate
D-threo-3-hydroxyaspartate
L-threo-3-hydroxyaspartate
pyruvate + NH3 + ?
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the artificial serine racemase substrate is degraded via alpha,beta-elimination
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-
?
L-threonine
2-oxobutanoate + NH3
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alpha,beta-elimination reaction
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-
?
rac-threo-3-hydroxyaspartate
D-threo-3-hydroxyaspartate
additional information
?
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D-serine

L-serine
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r
D-serine
L-serine
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r
D-serine
L-serine
-
-
-
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r
D-serine
L-serine
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racemization reaction
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-
r
D-serine
L-serine
-
racemization reaction
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r
D-serine
L-serine
38% of the activity with L-serine
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r
D-serine
L-serine
-
-
-
-
?
D-serine
L-serine
-
-
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r
D-serine

pyruvate + NH3
-
-
-
?
D-serine
pyruvate + NH3
-
-
-
-
?
D-serine
pyruvate + NH3
-
alpha,beta-elimination reaction
-
-
?
L-alanine

D-alanine
13% of the activity with L-serine
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-
?
L-alanine
D-alanine
very low activity
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r
L-alanine
D-alanine
very low activity
-
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r
L-alanine
D-alanine
very low activity
-
-
r
L-alanine
D-alanine
-
-
-
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r
L-aspartate

D-aspartate
low activity
-
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r
L-aspartate
D-aspartate
low activity
-
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r
L-aspartate
D-aspartate
low activity
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r
L-aspartate
D-aspartate
-
-
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r
L-aspartate
D-aspartate
enzyme SRR catalyses Asp racemization by a mechanism similar to Ser racemization. Lys56 performs the alpha-proton abstraction/donation of L-Asp and Ser84 is responsible for alpha-proton transferring for D-Asp
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r
L-serine

D-serine
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r
L-serine
D-serine
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?
L-serine
D-serine
highly specific for
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?
L-serine
D-serine
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r
L-serine
D-serine
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r
L-serine
D-serine
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-
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r
L-serine
D-serine
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alanine racemase 2, Alr2, converts L-serine to an approximately equal amount of D-serine. When tested with D-serine, Alr2 does not convert as much, and nearly 75% of the D-serine remains in the D-form
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r
L-serine
D-serine
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-
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r
L-serine
D-serine
-
alanine racemase 2, Alr2, converts L-serine to an approximately equal amount of D-serine. When tested with D-serine, Alr2 does not convert as much, and nearly 75% of the D-serine remains in the D-form
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r
L-serine
D-serine
-
-
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r
L-serine
D-serine
-
-
-
-
?
L-serine
D-serine
-
-
-
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r
L-serine
D-serine
-
-
-
-
?
L-serine
D-serine
-
-
-
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r
L-serine
D-serine
-
-
-
?
L-serine
D-serine
-
-
-
-
?
L-serine
D-serine
-
-
-
?
L-serine
D-serine
-
-
-
-
?
L-serine
D-serine
-
-
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r
L-serine
D-serine
-
-
-
-
r
L-serine
D-serine
-
-
-
r
L-serine
D-serine
-
-
-
-
r
L-serine
D-serine
-
-
-
r
L-serine
D-serine
-
-
-
-
r
L-serine
D-serine
-
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r
L-serine
D-serine
-
-
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r
L-serine
D-serine
-
-
D-serine is an important modulator of the N-methyl-D-aspartate receptor function
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?
L-serine
D-serine
-
racemization reaction
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r
L-serine
D-serine
-
D-serine is an N-methyl-d-aspartate receptor co-agonist, synthesized by serine racemase and degraded by d-amino acid oxidase
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?
L-serine
D-serine
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the astrocytic enzyme synthesizes the N-methyl-D-aspartate receptor coagonist D-serine, and is involved in development of schizophrenia and glutamatergic dysfunction, astrocytes may play a direct role in N-methyl-D-aspartate receptor dysfunction in schizophrenia, overview
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?
L-serine
D-serine
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enzyme residues S84 and P111 are crucial for enzyme activity
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?
L-serine
D-serine
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r
L-serine
D-serine
-
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662116, 679781, 681530, 703957, 705049, 705289, 706532, 714348, 716344, 726664, 727279, 728034 -
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?
L-serine
D-serine
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-
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r
L-serine
D-serine
-
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?
L-serine
D-serine
-
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r
L-serine
D-serine
-
-
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r
L-serine
D-serine
-
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r
L-serine
D-serine
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specific for synthesis of D-serine
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?
L-serine
D-serine
-
-
D-serine is an important modulator of the N-methyl-D-aspartate receptor function
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?
L-serine
D-serine
-
racemization reaction
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r
L-serine
D-serine
D-serine is a coagonist with glutamate at NMDA receptors, postsynaptic stimulation of nitric-oxide formation feeds back to presynaptic cells to S-nitrosylate SR and decrease D-serine availability to postsynaptic NMDA receptors, enzyme regulation, mechanism, overview
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?
L-serine
D-serine
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developmental regulation of enzyme expression in neuronal ganglion cells of the retina, overview, D-serine is the endogenous ligand for the glycine modulatory binding site of the NMDA receptor
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?
L-serine
D-serine
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D-serine is stored primarily within astrocytes ensheathing neuronal synapses containing NMDA receptors, model of D-serine signalling in the brain, overview
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?
L-serine
D-serine
enzyme SRR catalyses Ser racemization via a two-base mechanism in which two catalytic residues, Lys and Ser play vital roles in the abstraction and donation of alpha-proton of L-Ser and D-Ser, respectively
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r
L-serine
D-serine
-
-
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?
L-serine
D-serine
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developmental regulation of enzyme expression in neuronal ganglion cells of the retina, overview, D-serine is the endogenous ligand for the glycine modulatory binding site of the NMDA receptor
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?
L-serine
D-serine
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?
L-serine
D-serine
-
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D-serine is an important modulator of the N-methyl-D-aspartate receptor function
-
?
L-serine
D-serine
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r
L-serine
D-serine
-
racemization reaction
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r
L-serine
D-serine
SerR is highly specific for serine
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r
L-serine
D-serine
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r
L-serine
D-serine
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r
L-serine
D-serine
the forward reaction is preferred, serine is preferred to threonine
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r
L-serine
D-serine
-
-
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?
L-serine
D-serine
-
-
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r
L-serine
D-serine
-
-
-
?
L-serine
D-serine
-
-
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r
L-serine
D-serine
-
-
highly selctive toward L-serine
-
?
L-serine
D-serine
-
D-serine is an endogenous N-methyl-D-aspartate, NMDA, receptor coagonist
-
?
L-serine
D-serine
D-serine, an endogenous co-agonist of N-methyl-D-aspartate receptors in vertebrate retina, modulates glutamate sensitivity of retinal neurons, overview
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?
L-serine
D-serine
-
mechanisms regulating D-serine production by the enzyme serine racemase via translocation from cytosol to membranes, overview
D-serine is a physiological coagonist of N-methyl D-aspartate receptors, NMDARs, that plays a major role in several NMDAR-dependent events
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?
L-serine
D-serine
-
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r
L-serine
D-serine
Roseobacter litoralis ATCC 49566 / DSM 6996 / JCM 21268 / NBRC 15278 / OCh 149
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r
L-serine
D-serine
-
-
-
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?
L-serine
D-serine
-
-
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?
L-serine
D-serine
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r
L-serine
D-serine
on binding of the substrate, the small domain rotates toward the large domain to close the active site, substrate binding structure, Lys57 is the catalytic residue of the wild-type enzyme, overview
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r
L-serine
D-serine
-
-
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r
L-serine
D-serine
-
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-
r
L-serine

pyruvate + NH3
-
elimination reaction
-
-
?
L-serine
pyruvate + NH3
-
-
-
-
?
L-serine
pyruvate + NH3
-
-
-
?
L-serine
pyruvate + NH3
-
-
-
-
?
L-serine
pyruvate + NH3
-
alpha,beta-elimination reaction
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-
?
L-serine O-sulfate

O-sulfopyruvate + NH3
-
-
-
-
?
L-serine O-sulfate
O-sulfopyruvate + NH3
-
-
-
?
L-threo-3-hydroxyaspartate

D-threo-3-hydroxyaspartate
i.e. L-THA, Ser racemase shows activity toward D,L-THA and L-THA, D-THA cannot act as a substrate and/or inhibitor for the enzyme. The highest level of activity is detected with L-THA
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-
r
L-threo-3-hydroxyaspartate
D-threo-3-hydroxyaspartate
i.e. L-THA, Ser racemase shows activity toward D,L-THA and L-THA. D-THA cannot act as a substrate and/or inhibitor for the enzyme. The highest level of activity is detected with L-THA
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r
L-threonine

D-threonine
-
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r
L-threonine
D-threonine
the forward reaction is preferred, serine is preferred to threonine
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r
L-threonine
D-threonine
40% of the activity with L-serine
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r
rac-threo-3-hydroxyaspartate

D-threo-3-hydroxyaspartate
i.e. L-THA, Ser racemase shows activity toward D,L-THA and L-THA, D-THA cannot act as a substrate and/or inhibitor for the enzyme. The highest level of activity is detected with L-THA
-
-
?
rac-threo-3-hydroxyaspartate
D-threo-3-hydroxyaspartate
i.e. L-THA, Ser racemase shows activity toward D,L-THA and L-THA. D-THA cannot act as a substrate and/or inhibitor for the enzyme. The highest level of activity is detected with L-THA
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-
?
additional information

?
-
-
enzyme product may serve as a ligand for setting the sensitivity of N-methyl-D-aspartate receptors under physiological conditions
-
-
?
additional information
?
-
the bifunctional enzyme catalyzes not only serine racemization but also dehydration of serine to pyruvate
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-
?
additional information
?
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-
the bifunctional enzyme catalyzes not only serine racemization but also dehydration of serine to pyruvate
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?
additional information
?
-
the enzyme does not appear to metabolize D- and L-Ser in vivo
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-
?
additional information
?
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the enzyme does not appear to metabolize D- and L-Ser in vivo
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?
additional information
?
-
the recombinant enzyme T01H8.2 expressed in Escherichia coli exhibits Ser racemase activity in addition to low, but detectable, Asp and Ala racemase activities in vitro. T01H8.2 shows dehydratase activity toward several hydroxyamino acids in addition to racemase activity. The enzyme does not appear to metabolize D- and L-Ser in vivo. Substrate specificity, overview. No activity on L-Glu
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?
additional information
?
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-
the recombinant enzyme T01H8.2 expressed in Escherichia coli exhibits Ser racemase activity in addition to low, but detectable, Asp and Ala racemase activities in vitro. T01H8.2 shows dehydratase activity toward several hydroxyamino acids in addition to racemase activity. The enzyme does not appear to metabolize D- and L-Ser in vivo. Substrate specificity, overview. No activity on L-Glu
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?
additional information
?
-
the enzyme does not appear to metabolize D- and L-Ser in vivo
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?
additional information
?
-
the recombinant enzyme T01H8.2 expressed in Escherichia coli exhibits Ser racemase activity in addition to low, but detectable, Asp and Ala racemase activities in vitro. T01H8.2 shows dehydratase activity toward several hydroxyamino acids in addition to racemase activity. The enzyme does not appear to metabolize D- and L-Ser in vivo. Substrate specificity, overview. No activity on L-Glu
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?
additional information
?
-
-
the enzyme catalyzes racemization and dehydration of both isomers of serine
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?
additional information
?
-
specific for L-serine
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?
additional information
?
-
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specific for L-serine
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-
?
additional information
?
-
-
enzyme additionally catalyzes elimination reaction of D-/L-serine and of L-serine-O-sulfate
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?
additional information
?
-
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the enzyme also performs an elimination reaction
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?
additional information
?
-
-
serine racemase is the pyridoxal 5'-phosphate-dependent enzyme that catalyzes L-serine racemisation to D-serine, and L- and D-serine beta-elimination in mammalian brain
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?
additional information
?
-
-
the enzyme binds to the glutamate receptor interacting protein, to protein interacting with C kinase 1, and Golgi-localized protein Golga 3
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?
additional information
?
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analysis of enzyme-substrate-cofactor interactions in the active site, overview
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-
?
additional information
?
-
-
analysis of enzyme-substrate-cofactor interactions in the active site, overview
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-
?
additional information
?
-
reactions catalyzed by serine racemase are racemization and alpha,beta-elimination, mechanisms, overview
-
-
?
additional information
?
-
the recombinant enzyme expressed in Escherichia coli exhibits Ser racemase activity in addition to low, but detectable, Asp and Ala racemase activities in vitro. T01H8.2 shows dehydratase activity toward several hydroxyamino acids in addition to racemase activity. Substrate specificity, overview. No activity on L-Glu
-
-
?
additional information
?
-
-
the recombinant enzyme expressed in Escherichia coli exhibits Ser racemase activity in addition to low, but detectable, Asp and Ala racemase activities in vitro. T01H8.2 shows dehydratase activity toward several hydroxyamino acids in addition to racemase activity. Substrate specificity, overview. No activity on L-Glu
-
-
?
additional information
?
-
the bifunctional enzyme catalyzes not only serine racemization but also dehydration of serine to pyruvate
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-
?
additional information
?
-
-
the bifunctional enzyme catalyzes not only serine racemization but also dehydration of serine to pyruvate
-
-
?
additional information
?
-
-
enzyme modulates physiologic regulation of cerebellar granule cell migration
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-
?
additional information
?
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enzyme product may serve as a ligand for setting the sensitivity of N-methyl-D-aspartate receptors under physiological conditions
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-
?
additional information
?
-
-
main enzyme to synthesize D-serine
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-
?
additional information
?
-
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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-
?
additional information
?
-
-
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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-
?
additional information
?
-
-
ratio of elimination reaction/racemization reaction for substrate L-serine is 3.7
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-
?
additional information
?
-
-
ratio of synthesized pyruvate/D-serine is about 3
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?
additional information
?
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serine racemase is the major enzyme for D-serine production in the brain, D-serine is the predominant endogenous coagonist of the NMDA receptor in the forebrain, and D-serine may be involved in controlling the extent of NMDA receptor-mediated neurotoxic insults observed in disorders including Alzheimerâs disease.
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-
?
additional information
?
-
-
enzyme additionally catalyzes eleimination reaction of D-/L-serine and of L-serine-O-sulfate
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-
?
additional information
?
-
-
the enzyme binds to the glutamate receptor interacting protein, to protein interacting with C kinase 1, and Golgi-localized protein Golga 3. The carboxy terminus of both the mouse and human enzyme contains an amino acid domain that binds to PSD-95/DlgA/zo-1 (PDZ)-containing proteins, such as GRIP and PICK1, which subsequently activates the racemase. The PDZ domain is an important protein-protein interaction motif
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-
?
additional information
?
-
enzyme SRR recognizes L-Asp as an in vivo substrate in addition to L- and D-Ser
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-
?
additional information
?
-
reactions catalyzed by serine racemase are racemization and alpha,beta-elimination, mechanisms, overview
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-
?
additional information
?
-
the enzyme has two enzymatic activities, namely, racemization and alpha,beta-elimination
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-
?
additional information
?
-
wild-type enzyme SRR and SRR mutant S84A show Ser dehydratase activity. SRR-catalysed Asp racemization is less efficient and 550fold lower than that of Ser racemization
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?
additional information
?
-
in addition to a serine racemase reaction, SerR catalyzes D- and L-serine dehydratase reactions, where the two compounds are converted to pyruvate, overview
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-
?
additional information
?
-
-
in addition to a serine racemase reaction, SerR catalyzes D- and L-serine dehydratase reactions, where the two compounds are converted to pyruvate, overview
-
-
?
additional information
?
-
-
serine racemase is a bifunctional enzyme with racemase and dehydratase activities towards D- and L-serine
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-
?
additional information
?
-
-
substrate specificity, the bifunctional enzyme shows high L-serine/L-threonine dehydratase activity, overview
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substrate specificity, the bifunctional enzyme shows high L-serine/L-threonine dehydratase activity, overview
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enzyme product may serve as a ligand for setting the sensitivity of N-methyl-D-aspartate receptors under physiological conditions
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role for D-serine in peripheral nerve transduction
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serine racemase may negatively regulate cellular differentiation through the inhibition of sry-typeHMGbox 9, i.e.Sox9 transcriptional activity in chondrocytes
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regulation of the D-serine content in the forebrain and in C6 glioma cells, that lack the main degerative enzyme D-amino acid oxidase, might act via mechanisms including SRR operating in alpha,beta-eliminase mode, converting D-serine to pyruvate, and regulation by serine transport, in which the alanine-serine-cysteine transporter ASCT2 is implicated, overview. D-serine transport mediated by ASCT2 contributes prominently to D-serine homeostasis when DAO activity is absent
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the enzyme binds to the Golgi-localized protein Golga 3. The N-terminal of serine racemase contains residues that bind to Golga 3, which results in inhibition of ubiqitin-proteosomal serine racemase degradation
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analysis of enzyme-substrate-cofactor interactions in the active site, overview
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the recombinant enzyme RiSR exhibits both racemization and dehydration activities exclusively towards serine. The catalytic efficiency for L-serine racemization of RiSR is 34fold higher than that of L-serine dehydration. RiSR primarily catalyses serine racemization rather than dehydration. The kcat/Km ratios of D-/L-serine and the racemization/dehydration ratio for RiSR are 0.95/1.01 and 34.4/38.3, respectively
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Roseobacter litoralis ATCC 49566 / DSM 6996 / JCM 21268 / NBRC 15278 / OCh 149
the recombinant enzyme RiSR exhibits both racemization and dehydration activities exclusively towards serine. The catalytic efficiency for L-serine racemization of RiSR is 34fold higher than that of L-serine dehydration. RiSR primarily catalyses serine racemization rather than dehydration. The kcat/Km ratios of D-/L-serine and the racemization/dehydration ratio for RiSR are 0.95/1.01 and 34.4/38.3, respectively
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the enzyme also catalyzes the dehydration of D- and L-serine resulting in pyruvate
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the enzyme also catalyzes the dehydration of D- and L-serine resulting in pyruvate
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the enzyme catalyzes both the racemization and alpha,beta-elimination reaction of L- and D-serine to yield pyruvate and ammonia
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