Advertisement

D-Amino Acids pp 323-337 | Cite as

Aspartate Racemase: Function, Structure, and Reaction Mechanism

  • Masafumi Yohda
Chapter

Abstract

Aspartate racemases distribute and function to produce d-aspartate in eubacteria, archaea, invertebrates, and vertebrates. The aspartate racemases of eubacteria and hyperthermophilic archaea are pyridoxal 5′-phosphate (PLP) independent, and two conserved cysteine residues constitute the catalytic center. The crystal structure of the aspartate racemase of hyperthermophilic archaeon was determined. Based on this structure, the detailed reaction mechanism of the pyridoxal 5′-phosphate-independent aspartate racemase was studied by characterizing mutants and molecular dynamics simulations. However, it is still unclear how the catalytic cysteine residue can abstract a proton from the α-carbon. The aspartate in hyperthermophilic archaea is highly racemized, but the physiological role of aspartate racemase and d-aspartate in hyperthermophilic archaea is unknown. The aspartate racemases in invertebrates and vertebrates are PLP dependent. The aspartate racemases from invertebrates, bivalves, and Aplysia californica are homologous to serine racemases, but it has taken many years to identify the aspartate racemase responsible for the synthesis of d-Asp in mammals due to the lack of other amino acid racemases. The gene for the mammalian aspartate racemase was obtained via its homology with glutamate-oxaloacetate transaminase. Further studies on aspartate racemase will promote research on the mysterious functions of d-Asp in various organisms.

Keywords

Aspartate racemase PLP independent d-Aspartate 

References

  1. Abe K, Takahashi S, Muroki Y, Kera Y, Yamada RH (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(2):235–244. doi: 10.1093/jb/mvj028 CrossRefPubMedGoogle Scholar
  2. Johnston MM, Diven WF (1969) Studies on amino acid racemases. I. Partial purification and properties of the alanine racemase from Lactobacillus fermenti. J Biol Chem 244(19):5414–5420PubMedGoogle Scholar
  3. Kim PM, Duan X, Huang AS, Liu CY, Ming GL, Song H, Snyder SH (2010) Aspartate racemase, generating neuronal d-aspartate, regulates adult neurogenesis. Proc Natl Acad Sci U S A 107(7):3175–3179. doi: 10.1073/pnas.0914706107 CrossRefPubMedPubMedCentralGoogle Scholar
  4. Lamont HC, Staudenbauer WL, Strominger JL (1972) Partial purification and characterization of an aspartate racemase from Streptococcus faecalis. J Biol Chem 247(16):5103–5106PubMedGoogle Scholar
  5. Liu L, Iwata K, Kita A, Kawarabayasi Y, Yohda M, Miki K (2002a) Crystal structure of aspartate racemase from Pyrococcus horikoshii OT3 and its implications for molecular mechanism of PLP-independent racemization. J Mol Biol 319(2):479–489. doi: 10.1016/s0022-2836(02)00296-6 CrossRefPubMedGoogle Scholar
  6. Liu L, Iwata K, Yohda M, Miki K (2002b) Structural insight into gene duplication, gene fusion and domain swapping in the evolution of PLP-independent amino acid racemases. FEBS Lett 528(1–3):114–118CrossRefPubMedGoogle Scholar
  7. Long Z, Lee JA, Okamoto T, Sekine M, Nimura N, Imai K, Yohda M, Maruyama T, Sumi M, Kamo N, Yamagishi A, Oshima T, Homma H (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(2):317–321. doi: 10.1006/bbrc.2001.4353 CrossRefPubMedGoogle Scholar
  8. Matsumoto M, Homma H, Long Z, Imai K, Iida T, Maruyama T, Aikawa Y, Endo I, Yohda M (1999) Occurrence of free d-amino acids and aspartate racemases in hyperthermophilic archaea. J Bacteriol 181(20):6560–6563PubMedPubMedCentralGoogle Scholar
  9. Nagata Y, Fujiwara T, Kawaguchi-Nagata K, Fukumori Y, Yamanaka T (1998) Occurrence of peptidyl d-amino acids in soluble fractions of several eubacteria, archaea and eukaryotes. Biochim Biophys Acta 1379(1):76–82CrossRefPubMedGoogle Scholar
  10. Ohtaki A, Nakano Y, Iizuka R, Arakawa T, Yamada K, Odaka M, Yohda M (2008) Structure of aspartate racemase complexed with a dual substrate analogue, citric acid, and implications for the reaction mechanism. Proteins 70(4):1167–1174. doi: 10.1002/prot.21528 CrossRefPubMedGoogle Scholar
  11. Okada H, Yohda M, Giga-Hama Y, Ueno Y, Ohdo S, Kumagai H (1991) Distribution and purification of aspartate racemase in lactic acid bacteria. Biochim Biophys Acta 1078(3):377–382CrossRefPubMedGoogle Scholar
  12. Shibata K, Watanabe T, Yoshikawa H, Abe K, Takahashi S, Kera Y, Yamada R-h (2003a) Nucleotides modulate the activity of aspartate racemase of Scapharca broughtonii. Comp Biochem Physiol B Biochem Mol Biol 134(4):713–719. doi: 10.1016/s1096-4959(03)00031-9 CrossRefPubMedGoogle Scholar
  13. Shibata K, Watanabe T, Yoshikawa H, Abe K, Takahashi S, Kera Y, Yamada RH (2003b) Purification and characterization of aspartate racemase from the bivalve mollusk Scapharca broughtonii. Comp Biochem Physiol B Biochem Mol Biol 134(2):307–314CrossRefPubMedGoogle Scholar
  14. Staudenbauer W, Strominger JL (1972) Activation of d-aspartic acid for incorporation into peptidoglycan. J Biol Chem 247(16):5095–5102PubMedGoogle Scholar
  15. Wang L, Ota N, Romanova EV, Sweedler JV (2011) A novel pyridoxal 5′-phosphate-dependent amino acid racemase in the Aplysia californica central nervous system. J Biol Chem 286(15):13765–13774. doi: 10.1074/jbc.M110.178228 CrossRefPubMedPubMedCentralGoogle Scholar
  16. Yamada RH, Kera Y, Takahashi S (2006) Occurrence and functions of free d-aspartate and its metabolizing enzymes. Chem Rec 6(5):259–266. doi: 10.1002/tcr.20089 CrossRefPubMedGoogle Scholar
  17. Yamauchi T, Choi SY, Okada H, Yohda M, Kumagai H, Esaki N, Soda K (1992) Properties of aspartate racemase, a pyridoxal 5′-phosphate-independent amino acid racemase. J Biol Chem 267(26):18361–18364PubMedGoogle Scholar
  18. 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(2):234–240CrossRefPubMedGoogle Scholar
  19. Yohda M, Endo I, Abe Y, Ohta T, Iida T, Maruyama T, Kagawa Y (1996) Gene for aspartate racemase from the sulfur-dependent hyperthermophilic archaeum, Desulfurococcus strain SY. J Biol Chem 271(36):22017–22021CrossRefPubMedGoogle Scholar
  20. Yoshida T, Seko T, Okada O, Iwata K, Liu L, Miki K, Yohda M (2006) Roles of conserved basic amino acid residues and activation mechanism of the hyperthermophilic aspartate racemase at high temperature. Proteins 64(2):502–512. doi: 10.1002/prot.21010 CrossRefPubMedGoogle Scholar

Copyright information

© Springer Japan 2016

Authors and Affiliations

  1. 1.Department of Biotechnology and Life ScienceTokyo University of Agriculture and TechnologyKoganeiJapan

Personalised recommendations