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Study of Structural-Functional Organization of Nucleoside Phosphorylases of Gammaproteobacteria. Special Aspects of Functioning of Uridine Phosphorylase Phosphate-Binding Site

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Abstract

Series of mutant genes of prokaryotic uridine phosphorylases (Shewanella oneidensis MR-1, Escherichia coli) were constructed, and the resulting strains-producers of the corresponding proteins were obtained. Proteins were purified, and their physicochemical and fermentative properties were studied. On the basis of the obtained data, the role of individual amino acid residues of the polypeptide chain of uridine phosphorylases in the formation and functioning of the phosphate-binding site in these proteins was shown. The assumption of independent binding of two substrates, ion of inorganic phosphate (Pi) and uridine (Urd), by nucleoside phosphorylases, was made.

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References

  1. Leer, J.C., Hammer-Jespersen, K., and Schwartz, M., Eur. J. Biochem., 1977, vol. 75, no. 1, pp. 217–224.

    Article  CAS  PubMed  Google Scholar 

  2. Veiko, V.P., Siprashvili, Z.Z., Ratmanova, K.I., Gul’ko, L.B., Mironov, A.A., Andryukhina, R.V., and Debabov, V.G., Dokl. Ross. Akad. Nauk, 1994, vol. 339, no. 6, pp. 819–821.

    CAS  Google Scholar 

  3. Veiko, V.P., Chebotaev, D.V., Ovcharova, I.V., and Gul’ko, L.B., Bioorg. Khim., 1998, vol. 24, no. 5, pp. 381–387.

    CAS  PubMed  Google Scholar 

  4. Molchan, O.K., Dmitrieva, N.A., Romanova, D.V., Errais, Lopes L., Debabov, V.G., and Mironov, A.S., Biokhimiya, 1998, vol. 63, no. 2, pp. 235–239.

    Google Scholar 

  5. Dontsova, M.V., Savochkina, Yu.A., Gabdoulkhakov, A.G., Baidakov, S.N., Lyashenko, A.V., Zolotukhina, M., Errais, Lopes L., Garber, M.B., Morgunova, E.Yu., Nikonov, S.V, Mironov, A.S., Ealick, S.E., and Mikhailov, A.M., Acta Crystallogr. Biol. Crystallogr., 2004, vol. 60, no. 4, pp. 709–711.

    Article  Google Scholar 

  6. Krenitsky, T.A., Biochim. Biophys. Acta, 1976, vol. 429, no. 2, pp. 352–358.

    Article  CAS  PubMed  Google Scholar 

  7. Ling, F., Inoue, Y., and Kimura, A., Proc. Biochem. Soc., 1994, vol. 29, pp. 355–361.

    Article  CAS  Google Scholar 

  8. Liu, M-P., Cao, D-L., Russell, R.L., Handschumacher, R.E., and Pizzorno, G., Cancer Res., 1998, vol. 58, no. 23, pp. 5418–5424.

    CAS  PubMed  Google Scholar 

  9. Takehara, M., Ling, F., Izawa, S., Inoue, Y., and Kimura, A., Biosci. Biotechnol. Biochem., 1995, vol. 59, no. 10, pp. 1987–1990.

    Article  CAS  PubMed  Google Scholar 

  10. Mordkovich, N.N., Manuvera, V.A., Veiko, V.P., and Debabov, V.G., Biotekhnologiya, 2012, no. 1, pp. 21–30.

    Google Scholar 

  11. Luccioni, C., Beaumatin, J., and Bardot, V., Int. J. Cancer, 1994, vol. 58, no. 4, pp. 517–522.

    Article  CAS  PubMed  Google Scholar 

  12. Ashour, O.M., Naguib, F.N.M., Khalifa, M.M.A., Abdel-Raheem, M.H., Panzica, R.P., and el Kouni, M.H., Cancer Res., 1995, vol. 55, no. 5, pp. 1092–1098.

    CAS  PubMed  Google Scholar 

  13. Iigo, M., Nishikata, K., Nakajima, Y., Szinai, I., Veres, Z., Szabolcs, A., and De Clercq, E., Biochem. Pharmacol., 1990, vol. 39, no. 7, pp. 1247–1253.

    Article  CAS  PubMed  Google Scholar 

  14. Pritchard, M.D., Watson, A.J.M., Potten, C.S., Jackman, A.L., and Hickman, J.A., Proc. Natl. Acad. Sci. U. S. A., 1997, vol. 94, no. 5, pp. 1795–1799.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Renck, D., Machado, P., Souto, A.A., Rosado, L.A., Erig, T., Campos, M.M., Farias, C.B., Roesler, R., Timmers, L.F., de Souza, O.N., Santos, D.S., and Basso, L.A., J. Med. Chem., 2013, vol. 56, no. 21, pp. 8892–8902.

    Article  CAS  PubMed  Google Scholar 

  16. Jimenez, B.M., Kranz, P., Lee, C.S., Gero, A.M., and O’Sullivan, W.J., Biochem. Pharmacol., 1989, vol. 38, no. 21, pp. 3785–3789.

    Article  CAS  PubMed  Google Scholar 

  17. el Kouni, M.H., Naguib, F.N., Niedzwicki, J.G., Iltzsch, M.H., and Cha, S., J. Biol. Chem., 1988, vol. 263, no. 13, pp. 6081–6086.

    PubMed  Google Scholar 

  18. Lee, C.S., Jimenez, B.M., and O’Sullivan, W.J., Mol. Biochem. Parasitol., 1988, vol. 30, no. 3, pp. 271–277.

    Article  CAS  PubMed  Google Scholar 

  19. Konstantinova, I.D., Leont’eva, N.A., Galegov, G.A., Ryzhova, O.I., Chuvikovskii, D.V., Antonov, K.V., Esipov, R.S., Taran, S.A., Verevkina, K.N., Feofanov, S.A., and Miroshnikov, A.I., Bioorg. Khim., 2004, vol. 30, no. 6, pp. 613–620.

    CAS  PubMed  Google Scholar 

  20. Utagawa, T., J. Mol. Cat. B: Enzymatic, 1999, vol. 6, pp. 215–222.

    Article  CAS  Google Scholar 

  21. Komatsu, H. and Araki, T., Nucleosides, Nucleotides Nucleic Acids, 2005, vol. 24, nos. 5–7, pp. 1127–1130.

    Article  CAS  PubMed  Google Scholar 

  22. Roivainen, J., Elizarova, T., Lapinjoki, S., Mikhailopulo, I.A., Esipov, R.S., and Miroshnikov, A.I., Nucleosides, Nucleotides Nucleic Acids, 2007, vol. 26, nos. 8–9, pp. 905–909.

    Article  CAS  PubMed  Google Scholar 

  23. Mikhailopulo, I.A. and Miroshnikov, A.I., Acta Naturae, 2010, vol. 2, no. 2, pp. 38–61.

    Google Scholar 

  24. Visser, D.F., Hennessy, F., Rashamuse, J., Pletschke, B., and Brady, D., J. Mol. Cat. B: Enzymatic, 2011, vol. 68, pp. 279–285.

    Article  CAS  Google Scholar 

  25. Sambrook, J., Fritsch, E.F., and Maniatis, T., Molecular Cloning: a Laboratory Manual, New York: Cold Spring Harbor Laboratory Press, 1989.

    Google Scholar 

  26. Ho, S.N., Hunt, H.D., Horton, R.M., Pullen, J.K., and Pease, L.R., Gene, 1989, vol. 77, no. 1, pp. 51–59.

    Article  CAS  PubMed  Google Scholar 

  27. Veiko, V.P., Ratmanova, K.I., Osipov, A.S., Bulenkov, M.T., and Pugachev, V.V., Bioorg. Khim., 1991, vol. 17, no. 5, pp. 685–689.

    CAS  PubMed  Google Scholar 

  28. Bradford, M.M., Anal. Biochem., 1976, vol. 2, pp. 248–254.

    Article  Google Scholar 

  29. Laemmli, U.K., Nature, 1970, vol. 227, no. 5259, pp. 680–685.

    Article  CAS  PubMed  Google Scholar 

  30. Veiko, V.P., Siprashvili, Z.Z., Ratmanova, K.I., Gul’ko, L.B., Andryukhina, R.V., and Debabov, V.G., Biotekhnologiya, 1994, no. 4, pp. 2–4.

    Google Scholar 

  31. Veiko, V.P., Siprashvili, Z.Z., Ratmanova, K.I., and Gul’ko, L.B., Bioorg. Khim., 1995, vol. 21, no. 11, pp. 834–837.

    CAS  PubMed  Google Scholar 

  32. Veiko, V.P., Siprashvili, Z.Z., Ratmanova, K.I., Gul’ko, L.B., and Mironov, A.A., Mol. Bio. (Moscow), 1996, vol. 30, no. 1, pp. 170–176.

    CAS  Google Scholar 

  33. Chebotaev, D.V., Gul’ko, L.B., Veiko, V.P., and Debabov, V.G., Biotekhnol., 1999, no. 6, pp. 3–10.

    Google Scholar 

  34. Chebotaev, D.V., Gul’ko, L.B., and Veiko, V.P., Bioorg. Khim., 2001, vol. 27, no. 3, pp. 184–190.

    Google Scholar 

  35. Caradoc-Davies, T.T., Cutfield, S.M., Lamont, I.L., and Cutfield, J.F., J. Mol. Biol., 2004, vol. 337, no. 2, pp. 337–354.

    Article  CAS  PubMed  Google Scholar 

  36. Lashkov, A.A., Zhukhlistova, N.E., Gabdulkhakov, A.G., and Mikhailov, A.M., Kristallografiya, 2009, vol. 54, no. 2, pp. 291–302.

    Google Scholar 

  37. Bu, W., Settembre, E.C., el Kouni, M.H., and Ealick, S.E., Acta Crystallogr. D. Biol. Crystallogr., 2005, vol. 61, no. 7, pp. 863–872.

    Article  PubMed  Google Scholar 

  38. Lashkov, A.A., Gabdulkhakov, A.G., Prokofev, I.I., Seregina, T.A., Sotnichenko, S.E., Lyashenko, A.V., Shtil, A.A., Mironov, A.S., Betzeld, C., and Mikhailov, A.M., Acta Cryst. Struct. Biol. Cryst. Commun., 2012, vol. 68, no. 11, pp. 1394–1397.

    Article  CAS  Google Scholar 

  39. Prokofev, I.I., Lashkov, A.A., Gabdoulkhakov, A.G., Dontsova, M.V., Seregina, T.A., Mironov, A.S., Betzel, C., and Mikhailov, A.M., Acta Crystallog. Sect. F, 2014, vol. 70, no. 1, pp. 60–63.

    Article  CAS  Google Scholar 

  40. Mordkovich, N.N., Safonova, T.N., Manuvera, V.A., Veiko, V.P., Polyakov, K.M., Alekseev, K.S., Mikhailov, S.N., and Popov, V.O., Dokl. Ross. Akad. Nauk, 2013, vol. 451, no. 2, pp. 225–227.

    Google Scholar 

  41. Safonova, T.N., Mordkovich, N.N., Polyakov, K.M., Manuvera, V.A., Veiko, V.P., and Popov, V.O., Acta Crystallogr. Sect. F. Struct. Biol. Cryst. Commun, 2012, vol. 68, no. 11, pp. 1387–1389.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Safonova, T.N., Mikhailov, S.N., Veiko, V.P., Mordkovich, N.N., Manuvera, V.A., Alekseev, C.S., Kovalchuk, M.V., Popov, V.O., and Polyakov, K.M., Acta Crystallogr. D. Biol. Crystallogr, 2014, vol. 70, no. 12, pp. 3310–3319.

    Article  CAS  PubMed  Google Scholar 

  43. Dayhoff, M.O., Atlas of protein sequence and structure: national biomedical research foundation. Ed. M.O. Dayhoff, Washington, DC: Silver Spring, 1972.

  44. Safonova, T.N., Mordkovich, N.N., Veiko, V.P., Okorokova, N.A., Manuvera, V.A., Dorovatovskii, P.V., Popov, V.O., and Polyakov, K.M., Acta Crystallogr. D Struct Biol, 2016, vol. 72, no. 2, pp. 203–210.

    Article  CAS  PubMed  Google Scholar 

  45. Lashkov, A.A., Zhukhlistova, N.E., Gabdoulkhakov, A.H., Shtil, A.A., Efremov, R.G., Betzel, C., and Mikhailov, A.M., Acta Crystallogr. D. Biol. Crystallogr., 2010, vol. 66, no. 1, pp. 51–60.

    Article  CAS  PubMed  Google Scholar 

  46. Lashkov, A.A., Zhukhlistova, N.E., Gabdulkhakov, A.G., and Mikhailov, A.M., Kristallografiya, 2009, vol. 54, no. 2, pp. 291–302.

    Google Scholar 

  47. Oliva, I., Zuffi, G., Barile, D., Orsini, G., Tonon, G., De Giola, L., and Ghisotti, D., J. Biochem., 2004, vol. 135, no. 4, pp. 495–499.

    Article  CAS  PubMed  Google Scholar 

  48. Burling, F.T., Kniewel, R., Buglino, J.A., Chadha, T., Beckwith, A., and Lima, C.D., Acta Crystallogr., 2003, vol. 59, pp. 73–76.

    Google Scholar 

  49. Cook, W.J., Koszalka, G.W., Hall, W.W., Narayana, S.V.L., and Ealick, S.E., J. Biol. Chem., 1987, vol. 262, no. 6, pp. 2852–2853.

    CAS  PubMed  Google Scholar 

  50. Nihira, T., Saito, Y., Chiku, K., Kitaoka, M., Ohtsubo, K., and Nakai, H., FEBS Lett., 2013, vol. 587, no. 21, pp. 3382–3386.

    Article  CAS  PubMed  Google Scholar 

  51. Konrad, A., Piskur, J., and Liberles, D.A., Gene, 2012, vol. 510, no. 2, pp. 154–161.

    Article  CAS  PubMed  Google Scholar 

  52. Giuseppe, P.O., Martins, N.H., Meza, A.N., Santos, C.R., Pereira, H.D., and Murakami, M.T., PLoS One, 2012, vol. 7, no. 9, pp. 1–11.

    Article  Google Scholar 

  53. Dessanti, P., Zhang, Y., Allegrini, S., Tozzi, M.G., Sgarrella, F., and Ealick, S.E., Acta Crystallogr. D. Biol. Crystallogr., 2012, vol. 68, no. 3, pp. 239–248.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Kochetkov, N.K., Budovskii, E.I., Sverdlov, E.D., Simukova, N.A., Turchinskii, M.F., and Shibaev, V.N., in Organicheskaya khimiya nukleinovykh kislot (TRANSLATION), Moscow: Khimiya, 1970, pp. 134–140.

    Google Scholar 

  55. Miyahara, T., Nakatsuji, H., and Wada, T., J. Phys. Chem. A, 2014, vol. 118, no. 16, pp. P. 2931–2941.

    Article  CAS  PubMed  Google Scholar 

  56. Pugmire, M.J. and Ealick, S.E., Biochem. J., 2002, vol. 361, no. 1, pp. 1–25.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Schwartz, M., Eur. J. Biochem., 1971, vol. 21, no. 2, pp. 191–198.

    Article  CAS  PubMed  Google Scholar 

  58. Kim, B.K., Cha, S., and Parks, R.E., J. Biol. Chem., 1968, vol. 243, no. 8, pp. 1771–1776.

    CAS  PubMed  Google Scholar 

  59. Kraut, A. and Yamada, E.W., J. Biol. Chem., 1971, vol. 246, no. 1, pp. 2021–2030.

    CAS  PubMed  Google Scholar 

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Authors and Affiliations

  1. Fundamentals of Biotechnology Federal Research Center, Bach Institute of Biochemistry, Russian Academy of Sciences, Moscow, 119071, Russia

    N. N. Mordkovich, T. N. Safonova, A. N. Antipov, N. A. Okorokova & V. P. Veiko

  2. Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, 119992, Russia

    V. A. Manuvera

  3. Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia

    K. M. Polyakov

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  1. N. N. Mordkovich
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  2. T. N. Safonova
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  3. A. N. Antipov
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  4. V. A. Manuvera
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Correspondence to V. P. Veiko.

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Original Russian Text © N.N. Mordkovich, T.N. Safonova, A.N. Antipov, V.A. Manuvera, K.M. Polyakov, N.A. Okorokova, V.P. Veiko, 2018, published in Prikladnaya Biokhimiya i Mikrobiologiya, 2018, Vol. 54, No. 1, pp. 16–25.

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Mordkovich, N.N., Safonova, T.N., Antipov, A.N. et al. Study of Structural-Functional Organization of Nucleoside Phosphorylases of Gammaproteobacteria. Special Aspects of Functioning of Uridine Phosphorylase Phosphate-Binding Site. Appl Biochem Microbiol 54, 12–20 (2018). https://doi.org/10.1134/S0003683818010064

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