Substrate specificity of pyrimidine nucleoside phosphorylases of NP-II family probed by X-ray crystallography and molecular modeling
- Authors: Balaev V.V.1, Lashkov A.A.1, Prokofev I.I.1, Gabdulkhakov A.G.1, Seregina T.A.2, Mironov A.S.2, Betzel C.3, Mikhailov A.M.1
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Affiliations:
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics”
- State Research Institute of Genetics and Selection of Industrial Microorganisms
- University of Hamburg
- Issue: Vol 61, No 5 (2016)
- Pages: 830-841
- Section: Structure of Macromolecular Compounds
- URL: https://journals.rcsi.science/1063-7745/article/view/190316
- DOI: https://doi.org/10.1134/S1063774516050023
- ID: 190316
Cite item
Abstract
Pyrimidine nucleoside phosphorylases, which are widely used in the biotechnological production of nucleosides, have different substrate specificity for pyrimidine nucleosides. An interesting feature of these enzymes is that the three-dimensional structure of thymidine-specific nucleoside phosphorylase is similar to the structure of nonspecific pyrimidine nucleoside phosphorylase. The three-dimensional structures of thymidine phosphorylase from Salmonella typhimurium and nonspecific pyrimidine nucleoside phosphorylase from Bacillus subtilis in complexes with a sulfate anion were determined for the first time by X-ray crystallography. An analysis of the structural differences between these enzymes demonstrated that Lys108, which is involved in the phosphate binding in pyrimidine nucleoside phosphorylase, corresponds to Met111 in thymidine phosphorylases. This difference results in a decrease in the charge on one of the hydroxyl oxygens of the phosphate anion in thymidine phosphorylase and facilitates the catalysis through SN2 nucleophilic substitution. Based on the results of X-ray crystallography, the virtual screening was performed for identifying a potent inhibitor (anticancer agent) of nonspecific pyrimidine nucleoside phosphorylase, which does not bind to thymidine phosphorylase. The molecular dynamics simulation revealed the stable binding of the discovered compound—2-pyrimidin-2-yl-1H-imidazole-4-carboxylic acid—to the active site of pyrimidine nucleoside phosphorylase.
About the authors
V. V. Balaev
Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics”
Email: alashkov83@gmail.com
Russian Federation, Leninskii pr. 59, Moscow, 119333
A. A. Lashkov
Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics”
Author for correspondence.
Email: alashkov83@gmail.com
Russian Federation, Leninskii pr. 59, Moscow, 119333
I. I. Prokofev
Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics”
Email: alashkov83@gmail.com
Russian Federation, Leninskii pr. 59, Moscow, 119333
A. G. Gabdulkhakov
Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics”
Email: alashkov83@gmail.com
Russian Federation, Leninskii pr. 59, Moscow, 119333
T. A. Seregina
State Research Institute of Genetics and Selection of Industrial Microorganisms
Email: alashkov83@gmail.com
Russian Federation, Pervyi Dorozhnyi proezd 1, Moscow, 117545
A. S. Mironov
State Research Institute of Genetics and Selection of Industrial Microorganisms
Email: alashkov83@gmail.com
Russian Federation, Pervyi Dorozhnyi proezd 1, Moscow, 117545
C. Betzel
University of Hamburg
Email: alashkov83@gmail.com
Germany, Mittelweg 177, Hamburg, 20148
A. M. Mikhailov
Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics”
Email: alashkov83@gmail.com
Russian Federation, Leninskii pr. 59, Moscow, 119333