Advertisement

D-Amino Acids pp 257-268 | Cite as

d-Amino Acid-Metabolizing Enzyme

  • Tohru YoshimuraEmail author
Chapter

Abstract

To understand the roles of d-amino acids, information about their metabolizing enzymes is indispensable. This section provides an overview of important enzymes related to the synthesis and degradation of d-amino acids.

Keywords

d-Amino acid oxidase d-Amino acid aminotransferase d-Asparate oxidase Serine racemase d-Serine dehydratase 

References

  1. Abe K, Takahashi S, Muroki Y et al (2006) Cloning and expression of the pyridoxal 5'-phosphate-dependent aspartate racemase gene from the bivalve mollusk Scapharca broughtonii and characterization of the recombinant enzyme. J Biochem 139:235–244CrossRefPubMedGoogle Scholar
  2. Adams E, Frank L (1980) Metabolism of proline and the hydroxyprolines. Annu Rev Biochem 49:1005–1061CrossRefPubMedGoogle Scholar
  3. Arias CA, Martín-Martinez M, Blundell TL et al (1999) Characterization and modelling of VanT: a novel, membrane-bound, serine racemase from vancomycin-resistant Enterococcus gallinarum BM4174. Mol Microbiol 31:1653–1664CrossRefPubMedGoogle Scholar
  4. Cook SP, Galve-Roperh I, Martínez del Pozo A et al (2002) Direct calcium binding results in activation of brain serine racemase. J Biol Chem 277:27782–27792CrossRefPubMedGoogle Scholar
  5. De Miranda J, Santoro A, Engelender S et al (2000) Human serine racemase: moleular cloning, genomic organization and functional analysis. Gene 256:183–188CrossRefPubMedGoogle Scholar
  6. De Miranda J, Panizzutti R, Foltyn VN et al (2002) Cofactors of serine racemase that physiologically stimulate the synthesis of the N-methyl-d-aspartate (NMDA) receptor coagonist d-serine. Proc Natl Acad Sci U S A 99:14542–14547CrossRefPubMedPubMedCentralGoogle Scholar
  7. Dowhan W Jr, Snell EE (1970) d-Serine dehydratase from Escherichia coli. II. Analytical studies and subunit structure. J Biol Chem 245:4618–4628PubMedGoogle Scholar
  8. Foltyn VN, Bendikov I, De Miranda J et al (2005) Serine racemase modulates intracellular d-serine levels through an α, β-elimination activity. J Biol Chem 280:1754–1763CrossRefPubMedGoogle Scholar
  9. Fujitani Y, Nakajima N, Ishihara K et al (2006) Molecular and biochemical characterization of a serine racemase from Arabidopsis thaliana. Phytochemistry 67:668–674CrossRefPubMedGoogle Scholar
  10. Fujitani Y, Horiuchi T, Ito K et al (2007) Serine racemases from barley, Hordeum vulgare L., and other plant species represent a distinct eukaryotic group: gene cloning and recombinant protein characterization. Phytochemistry 68:1530–1536CrossRefPubMedGoogle Scholar
  11. Funakoshi M, Sekine M, Katane M et al (2008) Cloning and functional characterization of Arabidopsis thaliana d-amino acid aminotransferase - d-aspartate behavior during germination. FEBS J 275:1188–1200CrossRefPubMedGoogle Scholar
  12. Gallo KA, Knowles JR (1993) Purification, cloning, and cofactor independence of glutamate racemase from Lactobacillus. Biochemistry 32:3981–3990CrossRefPubMedGoogle Scholar
  13. Goto M, Yamauchi T, Kamiya N et al (2009) Crystal structure of a homolog of mammalian serine racemase from Schizosaccharomyces pombe. J Biol Chem 284:25944–25952CrossRefPubMedPubMedCentralGoogle Scholar
  14. Ito T, Takahashi K, Naka T et al (2007) Enzymatic assay of d-serine using d-serine dehydratase from Saccharomyces cerevisiae. Anal Biochem 37:167–172CrossRefGoogle Scholar
  15. Ito T, Hemmi H, Kataoka K et al (2008) A novel zinc-dependent d-serine dehydratase from Saccharomyces cerevisiae. Biochem J 409:399–406CrossRefPubMedGoogle Scholar
  16. Ito T, Murase H, Maekawa M et al (2012) Metal ion dependency of serine racemase from Dictyostelium discoideum. Amino Acids 43:1567–1576CrossRefPubMedGoogle Scholar
  17. Ito T, Maekawa M, Hayashi S et al (2013) Catalytic mechanism of serine racemase from Dictyostelium discoideum. Amino Acids 44:1073–1084CrossRefPubMedGoogle Scholar
  18. Karakawa S, Miyoshi Y, Konno R et al (2013) Two-dimensional high-performance liquid chromatographic determination of day-night variation of d-alanine in mammals and factors controlling the circadian changes. Anal Bioanal Chem 405:8083–8091CrossRefPubMedGoogle Scholar
  19. Katane M, Homma H (2010) d-Aspartate oxidase: the sole catabolic enzyme acting on free d-aspartate in mammals. Chem Biodivers 7:1435–1449CrossRefPubMedGoogle Scholar
  20. Kim PM, Duan X, Huang AS et al (2010) Aspartate racemase, generating neuronal d-aspartate, regulates adult neurogenesis. Proc Natl Acad Sci U S A 107:3175–3179CrossRefPubMedPubMedCentralGoogle Scholar
  21. Long Z, Lee JA, Okamoto T et al (2001) Occurrence of d-amino acids and a pyridoxal 5'-phosphate-dependent aspartate racemase in the acidothermophilic archaeon, Thermoplasma acidophilum. Biochem Biophys Res Commun 281:317–321CrossRefPubMedGoogle Scholar
  22. Matsuda S, Katane M, Maeda K et al (2015) Biosynthesis of d-aspartate in mammals: the rat and human homologs of mouse aspartate racemase are not responsible for the biosynthesis of d-aspartate. Amino Acids 47:975–985CrossRefPubMedGoogle Scholar
  23. Ohnishi M, Saito M, Wakabayashi S et al (2008) Purification and characterization of serine racemase from a hyperthermophilic archaeon, Pyrobaculum islandicum. J Bacteriol 190:1359–1365CrossRefPubMedGoogle Scholar
  24. Rudnick G, Abeles RH (1975) Reaction mechanism and structure of the active site of proline racemase. Biochemistry 14:4515–4522CrossRefPubMedGoogle Scholar
  25. Shibata K, Watanabe T, Yoshikawa H et al (2003) Purification and characterization of aspartate racemase from the bivalve mollusk Scapharca broughtonii. Comp Biochem Physiol B Biochem Mol Biol 134:307–314CrossRefPubMedGoogle Scholar
  26. Smith MA, Mack V, Ebneth A et al (2010) The structure of mammalian serine racemase: evidence for conformational changes upon inhibitor binding. J Biol Chem 285:12873–12881CrossRefPubMedPubMedCentralGoogle Scholar
  27. Strísovský K, Jirásková J, Mikulová A et al (2005) Dual substrate and reaction specificity in mouse serine racemase: identification of high-affinity dicarboxylate substrate and inhibitors and analysis of the β-eliminase activity. Biochemistry 44:13091–13100CrossRefPubMedGoogle Scholar
  28. Sun S, Toney MD (1999) Evidence for a two-base mechanism involving tyrosine-265 from arginine-219 mutants of alanine racemase. Biochemistry 38:4058–4065CrossRefPubMedGoogle Scholar
  29. Tanaka H, Yamamoto A, Ishida T et al (2008) d-Serine dehydratase from chicken kidney: a vertebral homologue of the cryptic enzyme from Burkholderia cepacia. J Biochem 143:49–57CrossRefPubMedGoogle Scholar
  30. Tanaka-Hayashi A, Hayashi S, Inoue R et al (2015) Is d-aspartate produced by glutamic-oxaloacetic transaminase-1 like 1 (Got1l1): a putative aspartate racemase? Amino Acids 47:79–86CrossRefPubMedGoogle Scholar
  31. Tanizawa K, Masu Y, Asano S et al (1989a) Thermostable d-amino acid aminotransferase from a thermophilic Bacillus species. Purification, characterization, and active site sequence determination. J Biol Chem 264:2445–2449PubMedGoogle Scholar
  32. Tanizawa K, Asano S, Masu Y et al (1989b) The primary structure of thermostable d-amino acid aminotransferase from a thermophilic Bacillus species and its correlation with l-amino acid aminotransferases. J Biol Chem 264:2450–2454PubMedGoogle Scholar
  33. Tokuyama S, Hatano K (1996) Overexpression of the gene for N-acylamino acid racemase from Amycolatopsis sp. TS-1-60 in Escherichia coli and continuous produciton of optically active methionine by a bioreactor. Appl Microbiol Biotechnol 44:774–777PubMedGoogle Scholar
  34. Toney MD (2011) Controlling reaction specificity in pyridoxal phosphate enzymes. Biochim Biophys Acta 1814:1407–1418CrossRefPubMedPubMedCentralGoogle Scholar
  35. Urusova DV, Isupov MN, Antonyuk S et al (2012) Crystal structure of d-serine dehydratase from Escherichia coli. Biochim Biophys Acta 1824:422–432CrossRefPubMedGoogle Scholar
  36. Wang L, Ota N, Romanova EV et al (2011) A novel pyridoxal 5'-phosphate-dependent amino acid racemase in the Aplysia californica central nervous system. J Biol Chem 286:13765–13774CrossRefPubMedPubMedCentralGoogle Scholar
  37. Watanabe A, Yoshimura T, Mikami B et al (2002) Reaction mechanism of alanine racemase from Bacillus stearothermophilus: x-ray crystallographic studies of the enzyme bound with N-(5'-phosphopyridoxyl)alanine. J Biol Chem 277:19166–19172CrossRefPubMedGoogle Scholar
  38. Wolosker H, Mori H (2012) Serine racemase: an unconventional enzyme for an unconventional transmitter. Amino Acids 43:1895–1904CrossRefPubMedGoogle Scholar
  39. Wolosker H, Sheth KN, Takahashi M et al (1999a) Purification of serine racemase: biosynthesis of the neuromodulator d-serine. Proc Natl Acad Sci U S A 96:721–725CrossRefPubMedPubMedCentralGoogle Scholar
  40. Wolosker H, Blackshaw S, Snyder SH (1999b) Serine racemase: a glial enzyme synthesizing d-serine to regulate glutamate-N-methyl-d-aspartate neurotransmission. Proc Natl Acad Sci U S A 96:13409–13414CrossRefPubMedPubMedCentralGoogle Scholar
  41. Yamada T, Komoto J, Takata Y et al (2003) Crystal structure of serine dehydratase from rat liver. Biochemistry 42:12854–12865CrossRefPubMedGoogle Scholar
  42. Yamauchi T, Goto M, Wu HY et al (2009) Serine racemase with catalytically active lysinoalanyl residue. J Biochem 145:421–424CrossRefPubMedGoogle Scholar
  43. Yohda M, Okada H, Kumagai H (1991) Molecular cloning and nucleotide sequencing of the aspartate racemase gene from lactic acid bacteria Streptococcus thermophilus. Biochim Biophys Acta 1089:234–240CrossRefPubMedGoogle Scholar
  44. Yoshimura T, Goto M (2008) d-Amino acids in the brain: structure and function of pyridoxal phosphate-dependent amino acid racemases. FEBS J 275:3527–3537CrossRefPubMedGoogle Scholar

Copyright information

© Springer Japan 2016

Authors and Affiliations

  1. 1.Department of Applied Molecular Biosciences, Graduate School of Bioagricultural SciencesNagoya UniversityChikusa-Ku, NagoyaJapan

Personalised recommendations