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X-Ray Analysis of the Magnesium-containing Endonuclease from Serratia marcescens

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Abstract

The three-dimensional crystal structure of the DNA/RNA nonspecific endonuclease from Serratia marcescenswas refined at the resolution of 1.07 Å to Rfactor of 12.4% and R freefactor of 15.3% using the anisotropic approximation. The structure includes 3924 non-hydrogen atoms, 715 protein-bound water molecules, and a Mg2+ion in each binding site of each subunit of the nuclease homodimeric globular molecule. The 3D topological model of the enzyme was revealed, the inner symmetry of the monomers in its N-and C-termini was found, and the local environment of the magnesium cofactor in the nuclease active site was defined. Mg2+ion was found to be bound to the Asn119 residue and surrounded by five associated water molecules that form an octahedral configuration. The coordination distances for the water molecules and the Oδ1atom of Asn119 were shown to be within the range of 2.01–2.11 Å. The thermal factors for the magnesium ion in subunits are 7.08 and 4.60 Å2, and the average thermal factors for the surrounding water molecules are 11.14 and 10.30 Å2, respectively. The region of the nuclease subunit interactions was localized, and the alternative side chain conformations were defined for 51 amino acid residues of the nuclease dimer.

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REFERENCES

  1. Meiss, G., Gast, F.-U., and Pingoud, A., J. Mol. Biol., 1999, vol. 288, pp. 377-390.

    Google Scholar 

  2. Benedik, M.J. and Strych, U., FEMS Microbiol. Lett., 1998, vol. 165, pp. 1-13.

    Google Scholar 

  3. Guynn, L.J., Dai, W., and Benedik, M.J., J. Bacteriol., 1998, vol. 180, pp. 2262-2264.

    Google Scholar 

  4. Meiss, G., Gimadutdinow, O., Haberland, B., and Pingoud, A., J. Mol. Biol., 2000, vol. 297, pp. 521-534.

    Google Scholar 

  5. Nestle, M. and Roberts, W.K., J. Biol. Chem., 1969, vol. 244, pp. 5219-5225.

    Google Scholar 

  6. Filimonova, M.N., Krause, K.L., and Benedik, M.J., Biochem. Mol. Biol. Int., 1994, vol. 23, pp. 1229-1236.

    Google Scholar 

  7. Friedhoff, P., Meiss, G., Kolmes, V., Pieper, U., Gimadutdinow, O., Urbanke, C., and Pingoud A., Eur. J. Biochem., 1996, vol. 241, pp. 572-580.

    Google Scholar 

  8. Friedhoff, P., Kolmes, V., Gimadutdinow, O., Wende, W., Krause, K, and Pingoud, A., Nucleic Acids Res., 1996, vol. 24, pp. 2632-2639.

    Google Scholar 

  9. Bannikova, G.E., Blagova, E.V., Varlamov, V.P., Morgunova, E.Yu., Dement'ev, A.A., and Shlyapnikov, S.V., Bioorg. Khim., 1990, vol. 16, pp. 1678-1682.

    Google Scholar 

  10. Miller, M.D., Benedik, M.J., Sallivan, M.C., Shipley, N.S., and Krause, K.L., J. Mol. Biol., 1991, vol. 222, pp. 27-30.

    Google Scholar 

  11. Miller, M.D., Tanner, J., Alpaugh, M., Benedik, M.J., and Krause, K.L., Nature Struct. Biol., 1994, vol. 1, pp. 461-468.

    Google Scholar 

  12. Lunin, V.Yu., Levdikov, V.M., Shlyapnikov, S.V., Blagova, E.V., Lunin, V.V., Wilson, K.S., and Mikhailov, A.M., FEBS Lett., 1997, vol. 412, pp. 217-222.

    Google Scholar 

  13. Miller, M.D., Cai, J., and Krause, K.L., J. Mol. Biol., 1999, vol. 288, pp. 975-987.

    Google Scholar 

  14. Miller, M.D. and Krause, K.L., Protein Sci., 1996, vol. 5, pp. 24-33.

    Google Scholar 

  15. Franke, L. and Pingoud, A., J. Protein Chem., 1999, vol. 18, pp. 137-146.

    Google Scholar 

  16. Glusker, J.P., Adv. Protein Chem., 1991, vol. 42, pp. 1-76.

    Google Scholar 

  17. Cowan, J.A., Chem. Rev., 1998, vol. 98, pp. 1067-1087.

    Google Scholar 

  18. McPhalen, C.A., Strynadka, N.C.J., and James, M.N.G., Adv. Protein Chem., 1991, vol. 42, pp. 77-144.

    Google Scholar 

  19. Filimonova, M.N., Dement'ev, A.A., Leshchinskaya, I.B., Bakunina, G.Yu., and Shlyapnikov, S.V., Biokhimiya (Moscow), 1991, vol. 56, pp. 508-520.

    Google Scholar 

  20. Otwinowski, Z. and Minor, W., Methods Enzymol., 1997, vol. 276, pp. 307-326.

    Google Scholar 

  21. Murshudov, G., Vagin, A., and Dodson, E., Acta Cryst., 1997, vol. 53, pp. 240-255.

    Google Scholar 

  22. Jones, T.A., J. Appl. Cryst., 1978, vol. 26, pp. 268-272.

    Google Scholar 

  23. Laskowski, R.A., MacArthur, M.W., Moss, D.C., and Thornton, J.M., J. Appl. Cryst., 1993, vol. 26, pp. 283-291.

    Google Scholar 

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Shlyapnikov, S.V., Lunin, V.V., Blagova, E.V. et al. X-Ray Analysis of the Magnesium-containing Endonuclease from Serratia marcescens. Russian Journal of Bioorganic Chemistry 27, 370–377 (2001). https://doi.org/10.1023/A:1012932601549

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