Lactobacillus reuteri 2'-deoxyribosyltransferase, a novel biocatalyst for tailoring of nucleosides

Applied and Environmental Microbiology

Volumn 76, Issue 5, 2010, Pages 1462-1470

  Fernández Lucas, Jesús ^a,b   Acebal, Carmen ^a   Sinisterra, José V ^b   Arroyo, Miguel ^a   De La Mata, Isabel ^a  

^a UNIVERSIDAD COMPLUTENSE DE MADRID   (Spain)

^b Industrial Biotransformations Service   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

CIRCULAR DICHROISM; HIGH ACTIVITY; LACTOBACILLUS REUTERI; MELTING TEMPERATURES; NUCLEOSIDE ANALOGUES; OPTIMAL TEMPERATURE; PH RANGE; RANDOM COIL; SECONDARY STRUCTURES; SEDIMENTATION EQUILIBRIUM ANALYSIS; TYPE II;

BIOMOLECULES; DICHROISM; ENZYMES; ESCHERICHIA COLI;

ENZYME ACTIVITY;

ARABINOSYLTRANSFERASE; BACTERIAL PROTEIN; ENZYME; GLYCOSYLTRANSFERASE; NUCLEOSIDE; NUCLEOSIDE DEOXYRIBOSYLTRANSFERASE II;

BACTERIUM; BIOTECHNOLOGY; CALORIMETRY; CATALYST; ENZYME ACTIVITY; GENE EXPRESSION; MELTING; SEDIMENTATION;

ARTICLE; CHEMISTRY; CIRCULAR DICHROISM; ENZYME STABILITY; ENZYMOLOGY; ESCHERICHIA COLI; GENE EXPRESSION; GENETICS; HEAT; KINETICS; LACTOBACILLUS REUTERI; METABOLISM; MOLECULAR CLONING; MOLECULAR WEIGHT; PH; PROTEIN MULTIMERIZATION; PROTEIN SECONDARY STRUCTURE;

BACTERIAL PROTEINS; CIRCULAR DICHROISM; CLONING, MOLECULAR; ENZYME STABILITY; ENZYMES; ESCHERICHIA COLI; GENE EXPRESSION; HOT TEMPERATURE; HYDROGEN-ION CONCENTRATION; KINETICS; LACTOBACILLUS REUTERI; MOLECULAR WEIGHT; NUCLEOSIDES; PENTOSYLTRANSFERASES; PROTEIN MULTIMERIZATION; PROTEIN STRUCTURE, SECONDARY;

ESCHERICHIA COLI; LACTOBACILLUS REUTERI;

EID: 77649228309     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.01685-09     Document Type: Article

References (56)

1. Anand, R., P. A. Kaminski, and S. E. Ealick. 2004. Structures of purine 2'-deoxyribosyltransferase, substrate complexes, and the ribosylated enzyme intermediate at 2.0 Å resolution. Biochemistry 43:2384-2393. (Pubitemid 38327833)
2. Armstrong, S. R., W. J. Cook, S. A. Short, and S. E. Ealick, 1996. Crystal structures of nucleoside 2'-deoxyribosyltransferase in native and ligand bound forms reveals architecture of the active site. Structure 4:97.
3. Becker, J., and M. Brendel. 1996. Rapid purification and characterization of two distinct N-deoxyribosyltransferases of Lactobacillus leichmannii. Biol. Chem. Hoppe-Seyler 377:357-362.
4. Bennett, E. M., C. Li, P. W. Allan, W. B. Parker, and S. E. Ealick. 2003. Structural basis for substrate specificity of Escherichia coli purine nucleoside Phosphorylase. J. Biol. Chem. 278:47110-47118.
5. Betbeder,D.,andL.K.Hutchinson.1990. Theenzymaticsynthesisofimidazoledeoxynucleosides:l-β-D-2'- deoxyribofuranosyl-5-aminoimidazole-4carboxamideandl-β-D-2'- deoxyribfuranosylbenzimidazoles.NucleosidesNucleotidesNucleicAcids9:569-577. (Pubitemid20299510)
6. Bosch, J., M. A. Roblen, C. Mehlin, E. Boni, A. Riechers, F. S. Buckner, W. C. Van Voorhis, P. J. Myler, E. A. Worthey, G. DeTitta, J. R. Luft, A. Lauricella, S. Guide, L. A. Anderson, O. Kalyuzhniy, H. M. Neely, J. Ross, T. N. Earnest, M. Soltis, L. Schoenfeld, F. Zucker, E. A. Merrit, E. Fan, C. L. M. J. Verlinde, and W. G. J. Hol. 2006. Using fragment cocktail crystallography to assist inhibitor design of Trypanosoma brucei nucleoside 2'- deoxyribosyltransferase. J. Med. Chem. 49:5939-5946.
7. Bradford, M. M. 1976. A rapid and sensitive method for the quantitation of microgram quantities utilizing the principle of protein dye binding. Anal. Biochem. 72:248-252.
8. Brown, P. H., and P. Schuck. 2006. Macromolecular size-and-shape distributions by sedimentation velocity analytical ultracentrifugation. Biophys. J. 90:4651-4661.
9. Bzowska, A., E. Kulilowska, and D. Shugar. 2000. Purine nucleoside phosphoiylases: properties, functions and clinical aspects. Pharmacol. Ther. 88: 349-425.
10. Cardinaud, R., and J. Holguin. 1979. Nucleoside deoxyribosyltransferase- II from Lactobacillus helveticus substrate specificity studied. Fyrimidine bases as acceptors. Biochim. Biophys. Acta 568:339-347.
11. Chawdhri, R., D. W. Hutchinson, and A. O. Richards. 1991. Nucleoside deoxyribosyltransferase and inosine Phosphorylase activity in lactic acid bacteria. Arch. Microbiol. 155:409-411.
12. Cheetham, P. S. J. 1998. What makes a good biocatalyst? J. Biotechnol. 66:3-12.
13. Condezo, L. A., J. Fernandez-Lucas, C. A. Garcia-Burgos, A. R. Alcántara, and J. V. Sinisterra. 2007. Enzymatic synthesis of modified nucleosides, p. 401-423. In R. N. Fatel (ed.), Biocatalysis in die pharmaceutical and biotechnology industries. CRC Press, Boca Raton, FL.
14. Cook, W., S. A. Short, and S. E. Ealick. 1990. Crystallization of preliminary X-ray investigation of recombinant Lactobacillus leichmannii 2'-deoxyribosyltransferase. J. Biol. Chem. 265:2682-2683.
15. Danzin, C., and R. Cardinaud. 1974. Deoxyribosyl transfer catalysis with trans-N-deoxyribosylase. Kinetic studies of purine-to-purine trans-N-deoxyribosylase. Eur. J. Biochem. 48:255-262.
16. Danzin, C., and R. Cardinaud. 1976. Deoxyribosyl transfer catalysis with trans-N-deoxyribosylase. Kinetic study of purine (pyrimidine) to pyrimidine (purine) trans-N-deoxyribosylase. Eur. J. Biochem. 62:365-372.
17. De Man, J. C., M. Rogosa, and M. E. Sharpe. 1960. A medium for the cultivation of lactobacilli. J. Appl. Microbiol. 23:130-135.
18. Edelhoch, H. 1967. Spectroscopic determination of tryptophan and tyrosine in proteins. Biochemistry 6:1948-1954.
19. Fukushima, M., N. Suzuki, T. Emura, S. Yano, H. Kazuno, Y. Tada, Y. Yamada, and T. Asao. 2000. Structure and activity of specific inhibitors of thymidine Phosphorylase to potentiate the function of antitumor 2'-deoxyribonucleosides. Biochem. Pharmacol. 59:1227-1236.
20. Garg, R., S. Gupta, H. Gao, M. Babu, A. Debnath, and C. Hansch. 1999. Comparative quantitative structure-activity relationship studies on anti-HIV drags. Chem. Rev. 99:3513-3560.
21. Ghiorghi, Y. K., K. I. Zeller, C. V. Dang, and P. A. Kaminski. 2007. The c-Myc target gene rcl (C6orf108) encodes a novel enzyme, deoxynucleoside 5'-mo:nophosphate N-glycosidase. J. Biol. Chem. 282:8150-8156.
22. Gill, S. C., and H. P. von Hippel. 1989. Calculation of protein extinction coefficients from amino acid sequence data. Anal. Biochem. 182:319-326.
23. Hammer-Jespersen, K. 1983. Nucleoside catabolism, p. 203-258. In A. Munch-Fetersen (ed.), Metabolism of nucleotides, and nucleobases in microorganisms. Academic Press Inc., London, United Kingdom.
24. Henley, J. P., and A. Sadana. 1985. Categorization of enzyme deactivations using a series-type mechanism. Enzyme Microb. Technol. 7:50-60.
25. Holguin, J., and R. Cardinaud. 1975. Trans-N-deoxyribosylase: purification by affinity chromatography and characterization. Eur. J. Biochem. 54:505514.
26. Huang, M. C., J. A. Montgomery, M. C. Thorpe, E. L. Stewart, J. A. Secrist, and R. L. Blakley. 1983. Formation of 3-(2'-deoxyribofuranosyl) and 9-(2'deoxyribofuranosyl) nucleosides of 8-substituted purines by nucleoside deoxyribosyltransferase. Arch. Biochim. Biophys. 222:133-144.
27. Ichikawa, E., and K. Kato. 2001. Sugar-modified nucleosides in past 10 years, a review. Curr. Med. Chem. 8:385-423.
28. Kaminski, P. A. 2002. Functional cloning, heterologous expression, and purification of two different N-deoxyribosyltransferases from Lactobacillus helveticus. J. Biol. Chem. 277:14400-14407. (Pubitemid 34952503)
29. Kaminski, P. A., P. Dächer, L. Dugué, and S. Pochet 2008. In vivo reshaping the catalytic site of nucleoside 2'-deoxyribosyltransferase for dideoxy- and didehydronucleosides via a single amino acid substitution. J. Biol. Chem. 283:20053-20059.
30. Laemmli, U. K. 1970. Cleavage of structural proteins during the assembly of die head of bacteriophage T4. Nature 227:680-685.
31. Larkin, M. A., G. Blackshields, N. P. Brown, R. Chenna, H. McGettigan, F. Valentin, I. M. Wallace, A. Wilm, R. Lopez, J. D. Thompson, T. J. Gibson, and D. G. Higgins. 2007. Clustal W and Clustal X version 2.0. Bioinformatics 23:2947-2948.
32. Laue, T. M., B. D. Shah, T. M. Ridgeway, and S. L. Pelletier. 1992. Computer aided interpretation of analytical sedimentation data for proteins, p. 90-125. In S. Harding, A. Rowe,and J. Horton (ed.), Analytical ultracentrifugation in biochemistry and polymer science. Royal Society of Chemistry, Cambridge, United Kingdom.
33. Lawrence, K. A., M. W. Jewett, P. A. Rosa, and F. C. Gherardini. 2009. Borrelia burgdorferi bb0426 encodes a 2'-deoxyribosyltransferase that plays a central role in purine salvage. Mol Microbiol. 72:1517-1529.
34. Mikhailopulo, I. A. 2007. Biotechnology of nucleic acid constituents-state of the art and perspectives. Curr. Org. Chem. 11:317-333.
35. Minton, A. P. 1997. Alternative strategies for die characterization of associations in muiticomponent solutions via measurement of sedimentation equilibrium. Prog. Colloid Polym. Sci.107:11-19.
36. Miyamoto, Y., T. Masaki, and S. Chohnan. 2007. Characterization of Ndeoxyribosyltransferase from Lactococcus lactis subsp. lactis. Biochim. Biophys. Acta 1774:1323-1330.
37. Muller, M., L. K. Hutchinson, and F. P. Guengerich. 1996. Addition of deoxyribose to guanine and modified DNA bases by Lactobacillus helveticus trans-N-deoxyribosylase. Chem. Res. Toxicol. 9:1140-1144.
38. Parker, W. B., P. W. Allan, S. E. Ealick, E. J. Sorscher, A. E. Hassan, A. V. Silamkoti, A. T. Fowler, W. R. Waud, and J. A. Secrist. 2005. Design and evaluation of 5-modified nucleoside analogs as prodrugs for an E. coli purine nucleoside Phosphorylase mutant. Nucleosides Nucleotides Nucleic Acids 24:387-392.
39. Pochet, S., L. Dugue, A. Meier, and P. Marliere. 1995. Enzymatic synthesis of l-(2-deoxy-β-D-ribofuranosyl) imidazole-4-carboxamide, a simplified DNA building block. Bioorg. Med. Chem. Lett. 5:1679-1684.
40. Porter, D. J. T., B. M. Merrill, and S. A. Short. 1995. Identification of the active site nucleophile in nucleoside 2'-deoxyribosyltransferase as glutamic acid-98. J. Biol. Chem. 270:15551-15556.
41. Porter, D. J. T., and S. A. Short. 1995. Nucleoside 2'-deoxyribosyl transferase. Fre-steady-state kinetic analysis of native enzyme and mutant enzyme with an alanyl residue replacing Glu-98. J. Biol. Chem. 270:15557-15562.
42. Prasad, A. K., S. Trikha, and V. S. Parmar. 1999. Nucleoside synthesis mediated by giycosyl transferring enzymes. Bioorg. Chem. 27:135-154.
43. Sambrook, J., E. J. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.
44. Sanger, F., S. Nicklen, and A. R. Coulson. 1977. DNA sequencing with chain terminating inhibitors. Proc. Natl. Acad. Sci U. S. A. 72:5463-5464.
45. Schnetz-Boutaud, N. C. M. C. Chapeau, and L. J. Mannet. 2001. Enzymatic synthesis of M(1)-deoxyribose, unit 1.2. In S. L. Beaucage (ed.), Current protocols in nucleic acid chemistry. John Wiley & Sons Inc., New York, NY.
46. Short, S. A., S. R. Armstrong, S. E. Ealick, and D. J. Porter. 1996. Active site amino acids that participate in the catalytic mechanism of nucleoside 2'deoxyribosyltransferase. J. Biol. Chem. 271:4978-4987.
47. Speicher, D. W. 1994. Methods and strategies for the sequence analysis of proteins on PVDF membranes. Methods 6:262-273.
48. Sreerama, N., and R. W. Woody. 2000. Estimation of protein secondary structure from CD spectra: comparison of CONTIN, SELCON and CDSSTR methods with an expanded reference set. Anal. Biochem. 282:252-260.
49. Steenkamp, D. J. 1991. The purine-2-deoxyribonuclesidase from Crithidia luciliae. Purification and trans-N-deoxyribosyltransferase activity. Eur. J. Biochem. 197:431-439.
50. Steenkamp, D. J., and T. J. Halbich. 1992. Substrate specificity of the purine 2'-deoxyribonucleosidase of Crithidia luciliae. Biochem. J. 287:125-129.
51. Taverna-Porro, M., L. A. Bouvier, C. A. Pereira, J. V. Montserrat, and A. M. Iribarren. 2008. Chemoenzymatic preparation of nucleosides from furanoses. Tetrahedron Lett. 49:2642-2645.
52. Trelles, J. A., M. Fernández, E. S. Lewkowicz, A. M. Iribarren, and J. V. Sinisterra. 2003. Purine nucleoside synchesis from uridine immobilised Enterobacter gergoviae CECT. Tetrahedron Lett. 44:2605-2609.
53. Trelles, J. A., L. Betancor, A. Schoijet, S. Porro, E. S. Lewkowicz, J. V. Sinisterra, and A. M. Iribarren. 2004. Immobilized Escherichia coli BL21 as a catalyst for the synthesis of adenine and hypoxanthine nucleosides. Chem. Biodivers. 1:280-288.
54. Utagawa, T., H. Morisawa, S. Yamanaka, A. Yamazaki, F. Yoshinaga, and Y. Hirose. 1985. Properties of nucleoside Phosphorylase from Enterobacter aerogenes. Agric Biol. Chem. 49:3239-3246.
55. Utagawa, T. 1999. Enzymatic preparation of nucleoside antibiotics. J. Mol. Catal. B Enzym. 6:215-1213
56. Vorbriiggen, H., and C. Ruth-Pohlenz. 2001. Handbook of nucleoside synthesis. John Wiley & Sons, Inc., New York, NY.