Email this article Modeling of Phosphoribosylpyrophosphate Synthetase from Thermus Thermophilus in Complex with ATP and Ribose 5-Phosphate
- Authors: Podshivalov D.D.1,2,3, Sidorov-Biryukov D.D.1,2, Timofeev V.I.1,2,3, Litunov A.A.1, Kostromina M.A.1, Sinitsyna K.V.1, Muravieva T.I.1, Kuranova I.P.1,2,3, Esipov R.S.1
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Affiliations:
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Moscow
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” Russian Academy of Sciences
- National Research Centre “Kurchatov Institute,”
- Issue: Vol 64, No 1 (2019)
- Pages: 94-97
- Section: Structure of Macromolecular Compounds
- URL: https://journal-vniispk.ru/1063-7745/article/view/193621
- DOI: https://doi.org/10.1134/S1063774519010206
- ID: 193621
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Abstract
The positions of the substrates (ATP and ribose 5 phosphate) of phosphoribosylpyrophosphate synthetase from Thermus thermophilus were determined by molecular dynamics simulations. The simulation brought the system to an equilibrium state, with the binding poses of the ligands in the active site being stable. Based on the results of simulation of the complex, the environment of the substrates was analyzed and the amino-acid residues of the enzyme that form polar interactions with the substrates were identified. Candidate sites for mutagenesis, which can be mutated in order to broaden the substrate specificity toward ribose 5-phosphate, are proposed.
About the authors
D. D. Podshivalov
Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Moscow; Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics”Russian Academy of Sciences; National Research Centre “Kurchatov Institute,”
Email: tostars@mail.ru
Russian Federation, Moscow, 117997; Moscow, 119333; Moscow, 123098
D. D. Sidorov-Biryukov
Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Moscow; Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics”Russian Academy of Sciences
Email: tostars@mail.ru
Russian Federation, Moscow, 117997; Moscow, 119333
V. I. Timofeev
Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Moscow; Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics”Russian Academy of Sciences; National Research Centre “Kurchatov Institute,”
Author for correspondence.
Email: tostars@mail.ru
Russian Federation, Moscow, 117997; Moscow, 119333; Moscow, 123098
A. A. Litunov
Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Moscow
Email: tostars@mail.ru
Russian Federation, Moscow, 117997
M. A. Kostromina
Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Moscow
Email: tostars@mail.ru
Russian Federation, Moscow, 117997
K. V. Sinitsyna
Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Moscow
Email: tostars@mail.ru
Russian Federation, Moscow, 117997
T. I. Muravieva
Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Moscow
Email: tostars@mail.ru
Russian Federation, Moscow, 117997
I. P. Kuranova
Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Moscow; Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics”Russian Academy of Sciences; National Research Centre “Kurchatov Institute,”
Email: tostars@mail.ru
Russian Federation, Moscow, 117997; Moscow, 119333; Moscow, 123098
R. S. Esipov
Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Moscow
Email: tostars@mail.ru
Russian Federation, Moscow, 117997
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