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X-ray structures of uridine phosphorylase from Vibrio cholerae in complexes with uridine, thymidine, uracil, thymine, and phosphate anion: Substrate specificity of bacterial uridine phosphorylases

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Abstract

In many types of human tumor cells and infectious agents, the demand for pyrimidine nitrogen bases increases during the development of the disease, thus increasing the role of the enzyme uridine phosphorylase in metabolic processes. The rational use of uridine phosphorylase and its ligands in pharmaceutical and biotechnology industries requires knowledge of the structural basis for the substrate specificity of the target enzyme. This paper summarizes the results of the systematic study of the three-dimensional structure of uridine phosphorylase from the pathogenic bacterium Vibrio cholerae in complexes with substrates of enzymatic reactions—uridine, phosphate anion, thymidine, uracil, and thymine. These data, supplemented with the results of molecular modeling, were used to consider in detail the structural basis for the substrate specificity of uridine phosphorylases. It was shown for the first time that the formation of a hydrogen-bond network between the 2′-hydroxy group of uridine and atoms of the active-site residues of uridine phosphorylase leads to conformational changes of the ribose moiety of uridine, resulting in an increase in the reactivity of uridine compared to thymidine. Since the binding of thymidine to residues of uridine phosphorylase causes a smaller local strain of the β-N1-glycosidic bond in this the substrate compared to the uridine molecule, the β-N1-glycosidic bond in thymidine is more stable and less reactive than that in uridine. It was shown for the first time that the phosphate anion, which is the second substrate bound at the active site, interacts simultaneously with the residues of the β5-strand and the β1-strand through hydrogen bonding, thus securing the gate loop in a conformation

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Authors and Affiliations

  1. Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics”, Russian Academy of Sciences, Moscow, 119333, Russia

    I. I. Prokofev, A. A. Lashkov, A. G. Gabdulkhakov, V. V. Balaev, T. A. Seregina & A. M. Mikhailov

  2. State Research Institute of Genetics and Selection of Industrial Microorganisms, Moscow, 117545, Russia

    A. S. Mironov

  3. University of Hamburg, Mittelweg 177, Hamburg, 20148, Germany

    C. Betzel

Authors
  1. I. I. Prokofev
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  2. A. A. Lashkov
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  3. A. G. Gabdulkhakov
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  4. V. V. Balaev
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  5. T. A. Seregina
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  6. A. S. Mironov
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  7. C. Betzel
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  8. A. M. Mikhailov
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Corresponding author

Correspondence to A. A. Lashkov.

Additional information

Original Russian Text © I.I. Prokofev, A.A. Lashkov, A.G. Gabdulkhakov, V.V. Balaev, T.A. Seregina, A.S. Mironov, C. Betzel, A.M. Mikhailov, 2016, published in Kristallografiya, 2016, Vol. 61, No. 6, pp. 919–939.

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Prokofev, I.I., Lashkov, A.A., Gabdulkhakov, A.G. et al. X-ray structures of uridine phosphorylase from Vibrio cholerae in complexes with uridine, thymidine, uracil, thymine, and phosphate anion: Substrate specificity of bacterial uridine phosphorylases. Crystallogr. Rep. 61, 954–973 (2016). https://doi.org/10.1134/S1063774516060134

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