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B6db activities: 5.1.1.18

5.1.1.18
Description Serine racemase
Catalyzed reaction L-Serine = D-Serine
Cofactor Pyridoxal-phosphate.
Comments A pyridoxal-phosphate protein that is highly selective for L-serine as substrate. D-Serine is found in type-II astrocytes in mammalian brain, where it appears to be an endogenous ligand of the glycine site of N-methyl-D-aspartate (NMDA) receptors. The reaction can also occur in the reverse direction but does so more showly at physiological serine concentrations.
Validated eukaryotic enzymes (from metazoa and plants) are similar in sequence to serine ammonia-lyases (4.3.1.17), and in fact they often catalyze dehydration of serine to pyruvate in addition to serine racemization.

In bacteria, amino acid racemization is usually carried out by fold-type III enzymes (that we have grouped in the 5.1.1.1 family). In bacteria amino acid racemization is usually carried out by fold-type III enzymes (that we have grouped in the 5.1.1.1 family).
One fold-type II bacterial enzyme with some serine racemase activity (WP_013961474 from Roseobacter litoralis; see Kubota et al. 2016, Microbiology 162 53-61) is probably acting physiologically as an erythro-3-hydroxy-D-aspartate ammonia-lyase (family bhcb), as suggested by the genomic context.

An archaeal enzyme (from Pyrobaculum) that has been characterized and annotated as a Ser racemase, is in fact a promiscuous catalyst, carrying out both the deamination of L-Ser and L-Thr and, less efficiently, the racemization of the same amino acids.
For homology reasons, this sequence has been included in family 4.3.1.19 (L-Thr deaminase).

PDB 3L6R; 1V71;
Organisms -Archea -Plants -Metazoa -Human
 

Family 

5.1.1.18 (19)
 
Links Enzyme (activities) 5.1.1.18
BRENDA (activities) 5.1.1.18
KEGG (pathways) 5.1.1.18
PLPMDB (PLP mutants) 5.1.1.18
 
References
 Katane M, Saitoh Y, Uchiyama K, Nakayama K, Saitoh Y, Miyamoto T, Sekine M, Uda K, Homma H (2016) Characterization of a homologue of mammalian serine racemase from Caenorhabditis elegans: the enzyme is not critical for the metabolism of serine in vivo Genes Cells 21 966-77.

 Kubota T, Shimamura S, Kobayashi T, Nunoura T, Deguchi S (2016) Distribution of eukaryotic serine racemases in the bacterial domain and characterization of a representative protein in Roseobacter litoralis Och 149 Microbiology 162 53-61.

 Uda K, Abe K, Dehara Y, Mizobata K, Sogawa N, Akagi Y, Saigan M, Radkov AD, Moe LA. (2016) Distribution and evolution of the serine/aspartate racemase family in invertebrates Amino Acids 48 387-402.

 Ito T, Murase H, Maekawa M, Goto M, Hayashi S, Saito H, Maki M, Hemmi H, Yoshimura T. (2012) Metal ion dependency of serine racemase from Dictyostelium discoideum. Amino Acids. 43 1567-76.

 Ohnishi M, Saito M, Wakabayashi S, Ishizuka M, Nishimura K, Nagata Y, Kasai S. (2008) Purification and characterization of serine racemase from a hyperthermophilic archaeon, Pyrobaculum islandicum. J Bacteriol 190 1359-65.

 Fujitani Y; Horiuchi T; Ito K.; Sugimoto M. (2007) Serine racemases from barley, Hordeum vulgare L., and other plant species represent a distinct eukaryotic group: gene cloning and recombinant protein characterization Phytochemistry 68 1530-6.

 Fujitani, Y.; Nakajima, N.; Ishihara, K.; Oikawa, T.; Ito, K.; Sugimoto, M. (2006) Molecular and biochemical characterization of a serine racemase from Arabidopsis thaliana Phytochemistry 67 668-674.

 De Miranda, J.; Santoro, A.; Engelender, S.; Wolosker, H. (2000) Human serine racemase: moleular cloning, genomic organization and functional analysis Gene 256 183-8.

 Wolosker, H.; Blackshaw, S.; Snyder, S. H. (1999) Serine racemase: a glial enzyme synthesizing D-serine to regulate glutamate-N-methyl-D-aspartate neurotransmission Proc Natl Acad Sci U S A 96 13409-14.

Articles on 5.1.1.18
 
last changed 2019/11/20 17:12

B6db activities