Abstract
Phosphoribosyl pyrophosphate synthetase from Escherichia coli was cloned, purified, and crystallized. Single crystals of the enzyme were grown under microgravity. The X-ray diffraction data set was collected at the Spring-8 synchrotron facility and used to determine the three-dimensional structure of the enzyme by the molecular-replacement method at 2.71 Å resolution. The active and regulatory sites in the molecule of E. coli phosphoribosyl pyrophosphate synthetase were revealed by comparison with the homologous protein from Bacillus subtilis, the structure of which was determined in a complex with functional ligands. The conformations of polypeptide-chain fragments surrounding and composing the active and regulatory sites were shown to be identical in both proteins.
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H. G. Khorana, J. F. Fernandes, and A. Kornberg, J. Biol. Chem. 230, 941 (1958).
R. L. Switzer, J. Biol. Chem. 244, 2854 (1969).
M. A. Becker, K. O. Raivio, B. Bakay, et al., J. Clin. Invest. 65, 109 (1980).
B. Hove-Jensen and P. Nygaard, Eur. J. Biochem. 65, 109 (1982).
B. Hove-Jensen, Mol. Microbiol. 3, 1487 (1983).
B. Hove-Jensen, J. Bacteriol. 170, 1148 (1988).
K. F. Jensen, Metabolism of 5-Phosphoribosyl 1-Pyrophosphate (PRPP) in Escherichia Coli and Salmonella Typhimurium. Metabolism of Nucletides Nucleosides and Nucleobases in Microorganism, Ed. by A. Munch-Petersen (Academic, London, 1983), p. 1–25.
R. L. Switzer, J. Biol. Chem. 244, 2854 (1969).
I. H. Fox and N. K. Kelley, J. Biol. Chem. 247, 2126 (1972).
D. G. Roth, E. Shelton, and T. F. Deuel, J. Biol. Chem. 249, 291 (1974).
K. Arnvig, B. Hove-Jensen, and R. L. Switzer, Eur. J. Biochem. 192, 195 (1990).
M. Willemoes, D. Nilsson, and B. Hove-Jensen, Biochemistry 35, 8181 (1996).
R. L. Switzer and D. C. Sogin, J. Biol. Chem. 249, 5304 (1973).
M. A. Becker, P. J. Kostel, and L. J. Meyer, J. Biol. Chem. 250, 379 (1975).
K. J. Gibson, K. R. Schubert, and R. L. Switzer, J. Biol. Chem. 257, 2391 (1982).
E. R. Zoref, A. de Viries, and O. Sperling, J. Clin. Invest. 56, 1093 (1975).
B. J. Roessler, J. M. Nosal, P. R. Smith, et al., J. Biol. Chem. 268, 26476 (1993).
B. N. Krath and B. Hove-Jensen, Protein Sci. 10, 2317 (2001).
S. Li, Y. Lu, B. Peng, and J. Ding, Biochem. J. 401, 39 (2007).
M. A. Becker, P. Y. Kostel, L. U. Meyer, et al., Proc. Natl. Acad. Sci. USA. 70, 2749 (1973).
A. Kadziola, C. H. Jepsen, E. Johansson, et al., J. Mol. Biol. 354, 815 (2005).
M. M. Cherney, L. T. Cherney, C. R. Garen, et al., J. Mol. Biol. 413, 844 (2011).
M. Willemoës and B. Hove-Jensen, Biochemistry 36, 5078 (1997).
M. Willemoës, B. Hove-Jensen, and S. Larsen, J. Biol. Chem. 275, 35408 (275.).
K. H. Harlow and R. L. Switzer, J. Biol. Chem. 265, 5487 (1990).
I. Hilden, B. Hove-Jensen, and K. W. Harlow, J. Biol. Chem. 270, 20730 (1995).
B. Hove-Jensen, W. Kenneth, K. W. Harlow, et al., J. Biol. Chem. 261, 6765 (1986).
B. Hove-Jensen, A-K. Bentsen, and K. W. Harlow, FEBS J. 272, 3631 (2005).
T. A. Eriksen, A. Kadziola, A.-K. Bentsen, et al., Nature Struct. Biol. 7, 303 (2000).
T. A. Eriksen, A. Kadziola, and S. Larsen, Protein Sci. 11, 271 (2002).
B. N. Krath and B. Hove-Jensen, Plant. Physiol. 119, 497 (1999).
B. N. Krath, T. A. Eriksen, T. S. Poulsen, et al., Biochim. Biophys. Acta 1430, 403 (1999).
E. V. Klyachko, R. S. Shakulov, and Yu. I. Koslov, Patent RF 200412050/13/ 07 (07.20,).
A. I. Mikhailopulo and A. I. Miroshnikov, Acta Nat. 36 (2010).
I. P. Kuranova, E. A. Smirnova, Y. A. Abramchik, et al., Crystallogr. Rep. 56, 884 (2011).
H. Tanaka, K. Inaka, S. Sugiyama, et al., J. Synchrotron Radiat. 11, 45 (2004).
V. I. Timofeev, Yu. A. Abramchik, N. E. Zhukhlistova, et al., Crystallogr. Rep. 60 (5), 685 (2015).
Z. Otwinowski and W. Minor, Methods Enzymol. 276, 307 (1997).
A. J. McCoy, R. W. Grosse-Kunstleve, L. C. Storoni, et al., Acta Crystallogr. D 61, 458 (2005).
G. N. Murshudov, A. A. Vagin, and E. J. Dodson, Acta Crystallogr. D 53, 240 (1997).
P. Emsley and K. Cowtan, Acta Crystallogr. D 60, 2126 (2004).
B. W. Matthews, J. Mol. Biol. 33, 491 (1968).
J. M. Krahn, J. H. Kim, M. R. Burns, et al., Biochemistry 36, 11061 (1997).
G. Scapin, D. H. Ozturk, C. Grubmeyer, et al., Biochemistry 34, 10744 (1995).
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Original Russian Text © V.I. Timofeev, Yu.A. Abramchik, N.E. Zhukhlistova, T.I. Muravieva, R.S. Esipov, I.P. Kuranova, 2016, published in Kristallografiya, 2016, Vol. 61, No. 1, pp. 51–61.
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Timofeev, V.I., Abramchik, Y.A., Zhukhlistova, N.E. et al. Three-dimensional structure of phosphoribosyl pyrophosphate synthetase from E. coli at 2.71 Å resolution. Crystallogr. Rep. 61, 44–54 (2016). https://doi.org/10.1134/S1063774516010247
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DOI: https://doi.org/10.1134/S1063774516010247