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
Meiss, G., Gast, F.-U., and Pingoud, A., J. Mol. Biol., 1999, vol. 288, pp. 377-390.
Benedik, M.J. and Strych, U., FEMS Microbiol. Lett., 1998, vol. 165, pp. 1-13.
Guynn, L.J., Dai, W., and Benedik, M.J., J. Bacteriol., 1998, vol. 180, pp. 2262-2264.
Meiss, G., Gimadutdinow, O., Haberland, B., and Pingoud, A., J. Mol. Biol., 2000, vol. 297, pp. 521-534.
Nestle, M. and Roberts, W.K., J. Biol. Chem., 1969, vol. 244, pp. 5219-5225.
Filimonova, M.N., Krause, K.L., and Benedik, M.J., Biochem. Mol. Biol. Int., 1994, vol. 23, pp. 1229-1236.
Friedhoff, P., Meiss, G., Kolmes, V., Pieper, U., Gimadutdinow, O., Urbanke, C., and Pingoud A., Eur. J. Biochem., 1996, vol. 241, pp. 572-580.
Friedhoff, P., Kolmes, V., Gimadutdinow, O., Wende, W., Krause, K, and Pingoud, A., Nucleic Acids Res., 1996, vol. 24, pp. 2632-2639.
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.
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.
Miller, M.D., Tanner, J., Alpaugh, M., Benedik, M.J., and Krause, K.L., Nature Struct. Biol., 1994, vol. 1, pp. 461-468.
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.
Miller, M.D., Cai, J., and Krause, K.L., J. Mol. Biol., 1999, vol. 288, pp. 975-987.
Miller, M.D. and Krause, K.L., Protein Sci., 1996, vol. 5, pp. 24-33.
Franke, L. and Pingoud, A., J. Protein Chem., 1999, vol. 18, pp. 137-146.
Glusker, J.P., Adv. Protein Chem., 1991, vol. 42, pp. 1-76.
Cowan, J.A., Chem. Rev., 1998, vol. 98, pp. 1067-1087.
McPhalen, C.A., Strynadka, N.C.J., and James, M.N.G., Adv. Protein Chem., 1991, vol. 42, pp. 77-144.
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.
Otwinowski, Z. and Minor, W., Methods Enzymol., 1997, vol. 276, pp. 307-326.
Murshudov, G., Vagin, A., and Dodson, E., Acta Cryst., 1997, vol. 53, pp. 240-255.
Jones, T.A., J. Appl. Cryst., 1978, vol. 26, pp. 268-272.
Laskowski, R.A., MacArthur, M.W., Moss, D.C., and Thornton, J.M., J. Appl. Cryst., 1993, vol. 26, pp. 283-291.
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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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DOI: https://doi.org/10.1023/A:1012932601549