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Literature summary for 5.1.1.18 extracted from

  • Ito, T.; Hayashida, M.; Kobayashi, S.; Muto, N.; Hayashi, A.; Yoshimura, T.; Mori, H.
    Serine racemase is involved in D-aspartate biosynthesis (2016), J. Biochem., 160, 345-353 .
    View publication on PubMed
Search for more literature for 5.1.1.18

Activating Compound

Activating Compound Comment Organism Structure
ATP activates Mus musculus
ATP activates Rattus norvegicus
hydroxylamine activates Ser racemase activity, but inhibits Asp racemase activity Mus musculus
additional information no effect on Ser racemase activity by EDTA, KCl, and NaCl. Asp racemization is activated by divalent cations and nucleotide complexes Mus musculus

Cloned(Commentary)

Cloned (Comment) Organism
gene Srr, DNA and amino acid sequence determination and analysis, the single guide (sg) RNA target sequence in the exon 4 of Srr are annealed and subcloned into the BsbI site of pX362 to yield the pXSrre4T1, the circular pXSrre4T1 plasmid is transfected into PC-12 cells, recombinant expression of His-tagged wild-type enzyme in Escherichia coli strain BL21(DE3) Rattus norvegicus
gene Srr, recombinant expression of wild-type and mutant enzymes in Rattus norvegicus PC-12 cells, recombinant expression of N-terminally His-tagged wild-type and mutant enzymes in Escherichia coli strain BL21(DE3). SRR-overexpressing PC-12 cells produce endogenous D-Asp and D-Ser Mus musculus

Protein Variants

Protein Variants Comment Organism
additional information induction of mutation by CRISPR/Cas9 genome editing in Srr loci in PC-12 cells. Generation of SRR-KO PC-12 cells. Two independent SRR-KO PC12 cell clones, Nos. 16 and 21, are identified/selected as SRR-KO samples. Clone No. 16 contains a 1-bp insertion in exon 4 of both alleles, resulting in a frame-shift and premature termination of SRR translation to yield a severely truncated protein (69 amino acid residues). The No. 21 clone possesses an 8-bp and 1-bp deletion in each locus of SRR exon 4, and results in a frame-shift and truncation of the enzyme of the protein size by 66 amino acid residues. Both truncated proteins are predicted to lose the enzyme activity. No significant decreases in the intracellular D-Asp levels are observed in the SRR-KO cells Rattus norvegicus
S84A site-directed mutagenesis, SRR mutant S84A shows Ser dehydratase activity, but no Ser racemase activity, the S84A mutation completely abolishes racemization activity for both Ser and Asp. Mutation S84A results in the loss of the enzyme's D-Ser dehydrase activity without changing L-Ser dehydrase activity Mus musculus

Inhibitors

Inhibitors Comment Organism Structure
additional information Asp racemization is inhibited by EDTA and hydroxylamine Mus musculus

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
additional information
-
 additional information kinetic parameters of Ser dehydratase activity and Asp racemase activity of wild-type and mutant enzymes Mus musculus
3.8
-
 L-serine pH 8.0, 37°C, recombinant wild-type enzyme Mus musculus

Metals/Ions

Metals/Ions Comment Organism Structure
Ca2+ activates Mus musculus
Mg2+ activates Mus musculus
Mg2+ activates Rattus norvegicus

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
L-aspartate Mus musculus
-
 D-aspartate
-
 r
L-serine Mus musculus
-
 D-serine
-
 r
L-serine Rattus norvegicus
-
 D-serine
-
 r
additional information Mus musculus enzyme SRR recognizes L-Asp as an in vivo substrate in addition to L- and D-Ser ?
-
 ?

Organism

Organism UniProt Comment Textmining
Mus musculus Q9QZX7
-
-
Rattus norvegicus Q76EQ0
-
-

Purification (Commentary)

Purification (Comment) Organism
recombinant His-tagged wild-type and mutant enzymes from Escherichia coli strain BL21(DE3) by nickel affinity chromatography and dialysis Mus musculus
recombinant His-tagged wild-type enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography and dialysis Rattus norvegicus

Reaction

Reaction Comment Organism Reaction ID
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 Mus musculus
a

Source Tissue

Source Tissue Comment Organism Textmining
brain
-
 Mus musculus
-
frontal cortex
-
 Mus musculus
-
hippocampus
-
 Mus musculus
-
PC-12 cell
-
 Rattus norvegicus
-

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
L-aspartate
-
 Mus musculus D-aspartate
-
 r
L-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 Mus musculus D-aspartate
-
 r
L-serine
-
 Mus musculus D-serine
-
 r
L-serine
-
 Rattus norvegicus D-serine
-
 r
L-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 Mus musculus D-serine
-
 r
additional information enzyme SRR recognizes L-Asp as an in vivo substrate in addition to L- and D-Ser Mus musculus ?
-
 ?
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 Mus musculus ?
-
 ?

Synonyms

Synonyms Comment Organism
More cf. EC 5.1.1.13 Mus musculus
More cf. EC 5.1.1.13 Rattus norvegicus
SRR
-
 Mus musculus
SRR
-
 Rattus norvegicus

Temperature Optimum [°C]

Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
37
-
 assay at Mus musculus
37
-
 assay at Rattus norvegicus

Turnover Number [1/s]

Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
0.77
-
 L-serine pH 8.0, 37°C, recombinant wild-type enzyme Mus musculus

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
8
-
 assay at Mus musculus
8
-
 assay at Rattus norvegicus

Cofactor

Cofactor Comment Organism Structure
pyridoxal 5'-phosphate
-
 Mus musculus

General Information

General Information Comment Organism
malfunction D-Asp levels are significantly lower in the hippocampi and frontal cortices of SRR-knockout mice, approximately half the levels recorded from wild-type mice. These results are consistent with those from a previous study. In contrast, D-Asp abundance is not altered in the cerebellums or testes of SRR-knockout mice Mus musculus
malfunction no significant decreases in the intracellular D-Asp levels are observed in the SRR-KO cells, the intracellular concentration of D-Ser in the SRR-KO PC12 cells is visibly lower than that in the controls Rattus norvegicus
physiological function rat PC-12 cells rely on a non-SRR-based mechanism to produce the majority of its D-Asp Rattus norvegicus
physiological function serine racemase, SRR, is involved in D-aspartate biosynthesis, SRR is responsible for D-Asp production in certain organs and/or tissues Mus musculus

kcat/KM [mM/s]

kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
0.202
-
 L-serine pH 8.0, 37°C, recombinant wild-type enzyme Mus musculus