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X-Ray Structure and Molecular Dynamics Study of Uridine Phosphorylase from Vibrio cholerae in Complex with 2,2'-Anhydrouridine

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Abstract

The high-resolution three-dimensional structure of uridine phosphorylase from the pathogenic bacterium Vibrio cholerae in complex with the competitive inhibitor 2,2'-anhydrouridine was determined by X-ray diffraction (RCSBPDB ID: 6RCA). The three-dimensional structure of this complex is compared with the previously determined structures of V. cholerae uridine phosphorylase in complex with the substrate (uridine) and S. typhimurium uridine phosphorylase in complex with 2,2'-anhydrouridine. The protein–inhibitor and protein–substrate binding free energies were calculated by the free-energy perturbation method. The number of stable hydrogen bonds between the 2,2'-anhydrouridine molecule and the active site of the enzyme is smaller and these bonds are longer compared to the natural substrate of the enzyme (uridine). However, calculations taking into account solvation energy of the molecule and the entropy effects showed that the binding of the inhibitor (2,2'-anhydrouridine) at the active site of the protein is energetically more favorable than the binding of the native substrate (uridine). These results may be useful in the design of new inhibitors with a higher selectivity for the binding sites of uridine phosphorylases.

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ACKNOWLEDGMENTS

The calculations were performed by Hybrid high-performance computing cluster of FRC CS RAS [48].

Funding

This work was supported by the Ministry of Science and Higher Education within the State assignment FSRC “Crystallography and Photonics” RAS.

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Authors and Affiliations

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

    P. A. Eistrikh-Heller, S. V. Rubinsky, I. I. Prokofev, A. G. Gabdulkhakov & A. A. Lashkov

  2. State Research Institute of Genetics and Selection of Industrial Microorganisms of the National Research Center “Kurchatov Institute”, 117545, Moscow, Russia

    A. S. Mironov

Authors
  1. P. A. Eistrikh-Heller
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  2. S. V. Rubinsky
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  3. I. I. Prokofev
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  4. A. G. Gabdulkhakov
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  5. A. S. Mironov
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  6. A. A. Lashkov
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Correspondence to A. A. Lashkov.

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Translated by T. Safonova

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Eistrikh-Heller, P.A., Rubinsky, S.V., Prokofev, I.I. et al. X-Ray Structure and Molecular Dynamics Study of Uridine Phosphorylase from Vibrio cholerae in Complex with 2,2'-Anhydrouridine. Crystallogr. Rep. 65, 269–277 (2020). https://doi.org/10.1134/S1063774520020066

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  • DOI: https://doi.org/10.1134/S1063774520020066

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