Sequence analysis of enzymes with asparaginase activity.

• Authors: Dominika Borek , Mariusz Jaskólski
• Languages of publication: EN

Abstracts

EN

Asparaginases catalyze the hydrolysis of asparagine to aspartic acid and ammonia. Enzymes with asparaginase activity play an important role both in the metabolism of all living organisms as well as in pharmacology. The main goal of this paper is to attempt a classification of all known enzymes with asparaginase activity, based on their amino acid sequences. Some possible phylogenetic consequences are also discussed using dendrograms and structural information derived from crystallographic studies.

Keywords

EN

N-terminal nucleophile hydrolase; lysophospholipase; tRNA amidotransferase; aspartylglucosaminidase; asparaginase; L-asparagine

• Publisher: Polish Biochemical Society
• Journal: Acta Biochimica Polonica
• Year: 2001
• Volume: 48
• Issue: 4
• Pages: 893-902

Dates

published

2001

received

2001-10-16

accepted

2001-11-17

Contributors

author

Dominika Borek

• Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznań, Poland

author

Mariusz Jaskólski

• Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland

References

• 1. Atkins, C.A., Pate, S.J. & Sharkey, P.J. (1975) Asparaginase metabolism - key to the nitrogen nutrition of developing legume seeds. Plant Physiol. 56, 807-812.
• 2. Gomes, M.A.F. & Sodek, L. (1984) Allantoinase and asparaginase activities in maturing fruits of nodulated and non-nodulated soybeans. Physiol. Plant 62, 105-109.
• 3. Sieciechowicz, K.A., Joy, K.W. & Ireland, R.J. (1988) The metabolism of asparagine in plants. Phytochemistry 27, 663-671.
• 4. Broome, J. (1961) Evidence that the L-asparaginase activity of guinea pig serum is responsible for its antilymphoma effects. Nature 191, 1114-1115.
• 5. Mashburn, L. & Wriston, J. (1963) Tumor inhibitory effect of L-asparaginase. Biochem. Biophys. Res. Commun. 12, 50-55.
• 6. Mashburn, L. & Wriston, J. (1964) Tumor inhibitory effect of L-asparaginase from Escherichia coli. Arch. Biochem. Biophys. 105, 450-452.
• 7. Campbell, H.A., Mashburn, L.T., Boyse, A.E. & Old, L.J. (1967) Two L-asparaginases from Escherichia coli B. Their separation, purification, and antitumor activity. Biochemistry 6, 721-730.
• 8. Campbell, H.A. & Mashburn, L.T. (1969) L-Asparaginase EC-2 from Escherichia coli. Some substrate specificity characteristics. Biochemistry 8, 3768-3775.
• 9. Roberts, J., Prager, M.D. & Bachynsky, N. (1966) The antitumor activity of Escherichia coli L-asparaginase. Cancer Res. 26, 2213- 2217.
• 10. Boyse, E., Old, L., Campbell, H. & Mashburn, L. (1967) Suppression of murine leukemias by L-asparaginase, incidence of sensitivity among leukemias of various types: Comparative inhibitory activities of guinea pig serum L-asparaginase and Escherichia coli L-asparaginase. J. Exp. Med. 125, 17-31.
• 11. Lay, H., Ekert, H. & Colebatch, J. (1975) Combination chemotherapy for children with acute lymphocytic leukemia who fail to respond to standard remission-induction therapy. Cancer 36, 1220-1222.
• 12. Bodey, G., Hewlett, J., Coltman, C., Rodriquez, V. & Freireich, E. (1974) Therapy of adult acute leukemia with daunorubicin and L-asparaginase. Cancer 33, 626-630.
• 13. Swain, A.L., Jaskólski, M., Housset, D., Rao, J.K.M. & Wlodawer, A. (1993) Crystal structure of Escherichia coli L-asparaginase, an enzyme used in cancer therapy. Proc. Natl. Acad. Sci. U.S.A. 90, 1474-1478.
• 14. Lubkowski, J., Palm, G.J., Gilliland, G.L., Derst, C. & Rohm, K.H. (1996) Crystal structure and amino acid sequence of Wolinella succinogenes L-asparaginase. Eur. J. Biochem. 241, 201-207.
• 15. Bonthron, D.T. & Jaskólski, M. (1997) Why a benign mutation kills enzyme activity. Structure-based analysis of the A176V mutant of Saccharomyces cerevisiae L-asparaginase I. Acta Biochim. Polon. 44, 491-504.
• 16. Lubkowski, J., Wlodawer, A., Ammon, H.L., Copeland, T.D. & Swain, A.L. (1994) Structural characterization of Pseudomonas 7A glutaminase-asparaginase. Biochemistry 33, 10257-10265.
• 17. Lubkowski, J., Wlodawer, A., Housset, D., Weber, I.T., Ammon, H.L., Murphy, K.C. & Swain, A.L. (1994) Refined crystal structure of Acinetobacter glutaminasificans glutaminase-asparaginase. Acta Crystallogr.D 50, 826-832.
• 18. Jerlstrom, P.G., Bezjak, D.A., Jennings, M.P. & Beacham, I.R. (1989) Structure and expression in Escherichia coli K-12 of the L-asparaginase I-encoding ansA gene and its flanking regions. Gene 78, 37-46.
• 19. Sugimoto, H., Odani, S. & Yamashita, S. (1998) Cloning and expression of cDNA encoding rat liver 60-kDa lysophospholipase containing an asparaginase-like region and ankyrin repeat. J. Biol. Chem. 273, 12536- 12542.
• 20. Curnow, A.W., Ibba, M. & Söll, D. (1996) tRNA-dependent asparagine formation. Nature 382, 589-590.
• 21. Tumbula, D.L., Becker, H.D., Chang, W. & Söll, D. (2000) Domain-specific recruitment of amide amino acids for protein synthesis. Nature 407, 106-110.
• 22. Becker, H.D. & Kern, D. (1998) Thermus thermophilus: A link in evolution of the tRNA-dependent amino acid amidation pathways. Proc. Natl. Acad. Sci. U.S.A. 95, 12832- 12837.
• 23. Wong, J.T.F. (1975) A co-evolution theory of the genetic code. Proc. Natl. Acad. Sci. U.S.A. 72, 1909-1912.
• 24. Wong, J.T.F. (1976) The evolution of a universal genetic code. Proc. Natl. Acad. Sci. U.S.A. 73, 2336-2340.
• 25. Lea, P.J., Farnden, L. & Miflin, B.J. (1978) The purification and properties of asparaginase from Lupinus species. Phytochemistry 17, 217-222.
• 26. Lea, P.J. & Miflin, B.J. (1980) The Biochemistry of Plants; vol. 5, pp. 290-293, Academic Press, New York.
• 27. Lea, P.J., Festenstein, G., Hughes, J.S. & Miflin, B.J. (1984) An immunological and enzymological survey of asparaginase in seeds of Lupinus. Phytochemistry 3, 511-514.
• 28. Dickson, J.M.J.J., Vincze, E., Grant, M.R., Smith, L.A., Rodber, K.A., Farnden, K.J.F. & Reynolds, P.H.S. (1992) Molecular cloning of the gene encoding developing seed L-asparaginase from Lupinus angustifolius. Plant Mol. Biol. 20, 333-336.
• 29. Lough, T.J., Chang, K.S., Carne, A., Monk, B.C., Reynolds, P.H. & Farnden, K.J. (1992) L-Asparaginase from developing seeds of Lupinus arboreus. Phytochemistry 31, 1519- 1527.
• 30. Lough, T.J., Reddington, B.D., Grant, M.R., Hill, D.F., Reynolds, P.H. & Farnden, K.J. (1992) The isolation and characterisation of a cDNA clone encoding L-asparaginase from developing seeds of lupin ( Lupinus arboreus). Plant Mol. Biol. 19, 391-399.
• 31. Borek, D., Podkowinski, J., Kisiel, A. & Jaskolski, M. (1999) Isolation and characterization of cDNA encoding L-asparaginase from Lupinus luteus (Accession No. AF112444). (PGR99-050) Plant Physiol. 119, 1568.
• 32. Mononen, I., Fisher, K.J., Kaartinen, V. & Aronson, N.N., Jr. (1993) Aspartylglycosaminuria: Protein chemistry and molecular biology of the most common lysosomal storage disorder of glycoprotein degradation. FASEB J. 7, 1247-1256.
• 33. Larsen, R.A., Knox, T.M. & Miller, C.G. (2001) Aspartic peptide hydrolases in Salmonella enterica serovar Typhimurium. J. Bacteriol. 183, 3089-3097.
• 34. Brannigan, J.A., Dodson, G., Duggleby, H.J., Moody, P.C., Smith, J.L., Tomchick, D.R. & Murzin, A.G. (1995) A protein catalytic framework with an N-terminal nucleophile is capable of self-activation.Nature 378, 416-419.
• 35. Duggleby, H.J., Tolley, S.P., Hill, C.P., Dodson, E.J., Dodson, G. & Moody, P.C. (1995) Penicillin acylase has a single-amino- acid catalytic centre. Nature 373, 264-268.
• 36. Lowe, J., Stock, D., Jap, B., Zwickl, P., Baumeister, W. & Huber, R. (1995) Crystal structure of the 20S proteasome from the archaeon T. acidophilum at 3.4 Å resolution. Science 268, 533-539.
• 37. Bewley, J.D. & Black, M. (1994) Seeds. Physiology of Development and Germination; 2nd edn., pp. 334-335, Plenum Press, New York.
• 38. Tarentino, A.L. & Maley, F. (1969) The purification and properties of a beta-aspartyl N-acetylglucosylamine amidohydrolase from hen oviduct. Arch. Biochem. Biophys. 130, 295-303.
• 39. Noronkoski, T., Stoineva, I.B., Petkov, D.D. & Mononen, I. (1997) Recombinant human glycosylasparaginase catalyzes hydrolysis of L-asparagine. FEBS Lett. 412, 149-152.
• 40. Liu, Y., Guan, C. & Aronson, N.N. (1998) Site-directed mutagenesis of essential residues involved in the mechanism of bacterial glycosylasparaginase. J. Biol. Chem. 273, 9688-9694.
• 41. Oinonen, C., Tikkanen, R., Rouvinen, J. & Peltonen, L. (1995) Three-dimensional structure of human lysosomal aspartylglucosaminidase. Nat. Struct. Biol. 2, 1102-1108.
• 42. Xuan, J., Tarentino, A.L., Grimwood, B.G., Plummer, T.H., Jr., Cui, T., Guan, C. & Van Roey, P. (1998) Crystal structure of glycosylasparaginase from Flavobacterium meningosepticum. Protein Sci. 7, 774-781.
• 43. Guo, H.C., Xu, Q., Buckley, D. & Guan, C. (1998) Crystal structures of Flavobacterium glycosylasparaginase. An N-terminal nucleophile hydrolase activated by intramolecular proteolysis. J. Biol. Chem. 273, 20205-20212.
• 44. Xu, Q., Buckley, D., Guan, C. & Guo, H.C. (1999) Structural insights into the mechanism of intramolecular proteolysis. Cell 98, 651-661.
• 45. Blattner, F.R., Plunkett, G., 3rd, Bloch, C.A., Perna, N.T., Burland, V., Riley, M., Collado- Vides, J., Glasner, J.D., Rode, C.K., Mayhew, G.F., Gregor, J., Davis, N.W., Kirkpatrick, H.A., Goeden, M.A., Rose, D.J., Mau, B. & Shao, Y. (1997) The complete genome sequence of Escherichia coli K-12. Science 277, 1453-1474.
• 46. Borek, D. & Jaskolski, M. (2000) Crystallization and preliminary crystallographic studies of a new L-asparaginase encoded by the Escherichia coli genome. Acta Crystallogr.D 56, 1505-1507.
• 47. Ortuño-Olea, L. & Durán-Vargas, S. (2000) The L-asparagine operon of Rhizobium etli contains a gene encoding an atypical asparaginase. FEMS Microbiol. Lett. 189, 177-182.
• 48. Benson, D.A., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J., Rapp, B.A. & Wheeler, D.L. (2000) GenBank. Nucleic Acids Res. 28, 15-18.
• 49. Karlin, S. & Altschul, S.F. (1990) Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc. Natl. Acad. Sci. U.S.A. 87, 2264-2268.
• 50. Karlin, S. & Altschul, S.F. (1993) Applications and statistics for multiple high-scoring segments in molecular sequences. Proc. Natl. Acad. Sci. U.S.A. 90, 5873-5877.
• 51. Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F. & Higgins, D.G. (1997) The CLUSTALX windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25, 4876-4882.
• 52. Saitou, N. & Nei, M. (1987) The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406-425.
• 53. Page, R.D.M. (1996) TreeView: An application to display phylogenetic trees on personal computers. Comput. Appl. Biosci. 12, 357-358.
• 54. Woese, C. (2000) Interpreting the universal phylogenetic tree. Proc. Natl. Acad. Sci. U.S.A. 97, 8392-8396.
• 55. Borek, D. (2001) Ph.D. Thesis. A. Mickiewicz University, Poznań, Poland.
• 56. Hofmann, K., Bucher, P., Falquet, L. & Bairoch, A. (1999) The PROSITE database, its status in 1999. Nucleic Acids Res. 27, 215- 219.